WO2024129974A1 - Bactéries recombinantes destinées à être utilisées pour le traitement de troubles dans lesquels l'oxalate est préjudiciable - Google Patents

Bactéries recombinantes destinées à être utilisées pour le traitement de troubles dans lesquels l'oxalate est préjudiciable Download PDF

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WO2024129974A1
WO2024129974A1 PCT/US2023/084033 US2023084033W WO2024129974A1 WO 2024129974 A1 WO2024129974 A1 WO 2024129974A1 US 2023084033 W US2023084033 W US 2023084033W WO 2024129974 A1 WO2024129974 A1 WO 2024129974A1
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oxalate
gene
seq
day
subject
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PCT/US2023/084033
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Caroline Kurtz
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Synlogic Operating Company, Inc.
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/14—Prodigestives, e.g. acids, enzymes, appetite stimulants, antidyspeptics, tonics, antiflatulents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/18—Drugs for disorders of the alimentary tract or the digestive system for pancreatic disorders, e.g. pancreatic enzymes

Definitions

  • Oxalate the ionic form of oxalic acid, arises in the human body from dietary intake or from endogenous synthesis. Oxalate is ubiquitous in plants and plant-derived foods, and as such, is inevitably part of the human diet. Endogenously-synthesized oxalate is primarily derived from glyoxylate in the liver where excess glyoxylate is converted to oxalate by glycolate oxidase or lactate dehydrogenase (Robijn et al., Kidney Int. 80: 1146-58 (2011)). Healthy individuals normally excrete urinary oxalate in ranges between 20-40 mg of oxalate per 24 hours.
  • urinary oxalate excretion at concentrations exceeding 40-45 mg per 24 hours is clinically considered hyperoxaluria (Robijn et al. (2011)).
  • Hyperoxaluria is characterized by increased urinary excretion of and elevated systemic levels of oxalate, and urinary oxalate levels are typically about 90-500 mg per 24 hours in primary hyperoxaluria and about 45-130 mg per 24 hours in enteric hyperoxaluria. If left untreated, hyperoxaluria can cause significant morbidity and mortality, including the development of renal stones (kidney stones), nephrocalcinosis (increased calcium in the kidney), crystallopathy and most significantly, End Stage Renal Disease (Tasian et al., J. Am. Soc. Nephrol., 2018; 29(6): 1731-1740 and Siener et al., Kidney International, 2013:83: 1144-1149).
  • Hyperoxalurias can generally be divided into two clinical categories: primary and secondary hyperoxalurias.
  • Primary hyperoxalurias are autosomal-recessive inherited diseases resulting from mutations in one of several genes involved in oxalate metabolism (Hoppe et al. , Nephr. Dial. Transplant. 26: 3609-15 (2011)).
  • the primary hyperoxalurias are characterized by elevated urinary oxalate excretion which ultimately may result in recurrent urolithiasis, crystallopathy, progressive nephrocalcinosis and early end-stage renal disease.
  • systemic deposition of calcium oxalate may occur in various organ systems which can lead to bone disease, erythropoietin refractory anemia, skin ulcers, digital gangrene, cardiac arrhythmias, and cardiomyopathy (Hoppe et al. (2011)).
  • PHI Primary hyperoxaluria type I
  • AGT alanine glyoxalate aminotransferase
  • PHII Primary hyperoxaluria type II
  • GSHPR glyoxylate/hydroxypyruvate reductase
  • GR glyoxylate/hydroxypyruvate reductase
  • HPR hydroxypyruvate reductase
  • DGDH D-glycerate dehydrogenase
  • Secondary hyperoxaluria typically results from conditions underlying increased absorption of oxalate, including increased dietary intake of oxalate, increased intestinal absorption of oxalate, excessive intake of oxalate precursors, gut microflora imbalances, and genetic variations of intestinal oxalate transporters (Bhasin et al., 2015; Robijn et al. (2011)).
  • enteric hyperoxaluria Increased oxalate absorption with consequent hyperoxaluria, often referred to as enteric hyperoxaluria, is observed in patients with a variety of intestinal disorders, including the syndrome of bacterial overgrowth, Crohn’s disease, inflammatory bowel disease, as well as other malabsorptive states, such as, after jejunoileal bypass for obesity, after gastric ulcer surgery, and chronic mesenteric ischemia (Pardi et al. , Am. J.
  • the present disclosure provides engineered bacterial cells, pharmaceutical compositions thereof, and methods of modulating and treating disorders in which oxalate is detrimental.
  • the engineered bacteria disclosed herein have been constructed to comprise genetic circuits composed of, for example, one or more oxalate catabolism genes to treat the disease, as well as other optional circuitry designed to ensure the safety and non-colonization of a subject that is administered the engineered bacteria, such as, for example, auxotrophies.
  • engineered bacteria are safe and well tolerated and augment the innate activities of the subject’s microbiome to achieve a therapeutic effect.
  • a method for reducing the levels of oxalate in a subject comprising administering to the subject a pharmaceutical composition comprising a recombinant bacterium comprising one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked to a directly or indirectly first promoter that is not associated with the oxalate catabolism enzyme gene in nature, thereby reducing the levels of oxalate in the subject.
  • the one or more gene sequences is operably linked directly to the first promoter.
  • the one or more gene sequences is operably linked indirectly to the first promoter.
  • the first promoter is an inducible promoter.
  • the first promoter is a constitutive promoter.
  • the recombinant bacterium has an oxalate consumption activity of Ipmol/lxlO 9 cell. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 50-600 mg/day, about 100-550 mg/day, about 100-500 mg/day, about 100-400 mg/day, about 100-300 mg/day. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 150-300 mg/day.
  • the recombinant bacterium has an oxalate consumption activity of about 50 mg/day, about 100 mg/day, about 150 mg/day, about 200 mg/day, about 210 mg/day, about 211 mg/day, about 225 mg/day, about 250 mg/day, about 275 mg/day, about 300 mg/day, about 325 mg/day, about 350 mg/day, about 350 mg/day, about 375 mg/day, about 400 mg/day, about 425 mg/day, about 450 mg/day, about 475 mg/day, about 500 mg/day, about 525 mg/day, about 550 mg/day, about 575 mg/day, or about 600 mg/day.
  • the recombinant bacterium has an oxalate consumption activity of about 50 mg/day, about 100 mg/day, about 150 mg/day, about 200 mg/day, about 211 mg/day, about 225 mg/day, about 250 mg/day, about 275 mg/day, about 300 mg/day, about 325 mg/day, about 350 mg/day, about 350 mg/day, about 375 mg/day, about 400 mg/day, about 425 mg/day, about 450 mg/day, about 475 mg/day, about 500 mg/day, about 525 mg/day, about 550 mg/day, about 575 mg/day, or about 600 mg/day under anaerobic conditions.
  • the recombinant bacterium has an oxalate consumption activity of about 50 mg/day, about 100 mg/day, about 150 mg/day, about 200 mg/day, about 211 mg/day, about 225 mg/day, about 250 mg/day, about 275 mg/day, about 300 mg/day, about 325 mg/day, about 350 mg/day, about 350 mg/day, about 375 mg/day, about 400 mg/day, about 425 mg/day, about 450 mg/day, about 475 mg/day, about 500 mg/day, about 525 mg/day, about 550 mg/day, about 575 mg/day, or about 600 mg/day under anaerobic conditions when administered to the subject three times per day.
  • the anaerobic conditions are conditions in the intestine and/or colon of the subject.
  • the recombinant bacterium has an oxalate consumption activity of about 0.2 pmole/hr, about 0.5 pmole/hr, about 0.8 pmole/hr, about 1.0 pmole/hr, about 1.2 pmole/hr, about 1.5 pmole/hr, or about 1.6 pmole/hr under anaerobic conditions.
  • the recombinant bacterium has an oxalate consumption activity of at least 0.2 pmole/hr, at least 0.5 pmole/hr, at least 0.8 pmole/hr, at least 1.0 pmole/hr, at least 1.2 pmole/hr, at least 1.5 pmole/hr, or at least 1.6 pmole/hr under anaerobic conditions.
  • the recombinant bacterium has an oxalate consumption activity of about 0.2 pmole/hr to about 1.6 pmole/hr, about 0.5 pmole/hr to about 1.5 pmole/hr, or about 1.0 pmole/hr to about 1.5 pmole/hr under anaerobic conditions. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 0.5 pmole/hr to about 1.5 pmole/hr under anaerobic conditions. In one embodiment, the anaerobic conditions are conditions in the intestine and/or colon of the subject.
  • the method reduces acute levels of oxalate in the subject by about two fold. In one embodiment, the method reduces acute levels of oxalate in the subject by about three fold. In one embodiment, the method reduces chronic levels of oxalate in the subject by about two fold. In one embodiment, the method reduces chronic levels of oxalate in the subject by about three fold.
  • the method reduces acute levels of oxalate in the subject to about 25 mg/day, about 30 mg/day, about 40 mg/day, about 50 mg/day, about 60 mg/day, about 70 mg/day, about 80 mg/day, about 90 mg/day, or about 100 mg/day. In one embodiment, the method reduces chronic levels of oxalate in the subject to about 25 mg/day, about 30 mg/day, about 40 mg/day, about 50 mg/day, about 60 mg/day, about 70 mg/day, about 80 mg/day, about 90 mg/day, or about 100 mg/day.
  • UOx in the subject is reduced by at least about 14%, at least about 15%, at least about 20%, at least about 21%, at least about 22%, at least about 23%, at least about 24%, at least about 25%, at least about 26%, at least about 27%, at least about 28%, at least about 29%, at least about 30%, at least about 31%, at least about 32%, at least about 33%, at least about 34%, at least about 35%, at least about 36%, at least about 37%, at least about 38%, at least about 39%, at least about 40%, at least about 45%, or at least about 50% in the subject after administration as compared to a control level of UOx.
  • UOx in the subject is reduced by at least about 14% to about 50%, at least about 14% to about 45%, at least about 15% to about 50%, at least about 15% to about 45%, at least about 15% to about 40%, at least about 20% to about 50%, at least about 25% to about 50%, at least about 30% to about 50%, at least about 20% to about 40%, at least about 20% to about 45%, at least about 25% to about 45, or at least about 25% to about 40% in the subject after administration as compared to a control level of UOx.
  • the control level of UOx is a level of UOx in the subject prior to administration.
  • control level of UOx is a level of UOx in a subject, or in a population of subjects, having an oxalate disease or disorder who did not receive treatment, wherein the disease or disorder is hyperoxaluria, primary hyperoxaluria, dietary hyperoxaluria, enteric hyperoxaluria, short bowel syndrome, chronic pancreatitis, inflammatory bowel disease (IBD), cystic fibrosis, kidney disease, and/or Roux-en-Y gastric bypass.
  • the disease or disorder is short bowel syndrome or Roux-en-Y gastric bypass.
  • UOx:creatinine ratio in the subject is reduced by at least about 14%, at least about 15%, at least about 20%, at least about 21%, at least about 22%, at least about 23%, at least about 24%, at least about 25%, at least about 26%, at least about 27%, at least about 28%, at least about 29%, at least about 30%, at least about 31%, at least about 32%, at least about 33%, at least about 34%, at least about 35%, at least about 36%, at least about 37%, at least about 38%, at least about 39%, at least about 40%, at least about 45%, or at least about 50% in the subject after administration as compared to a control UOx:creatinine ratio.
  • UOx:creatinine ratio in the subject is reduced by at least about 14% to about 50%, at least about 14% to about 45%, at least about 15% to about 50%, at least about 15% to about 45%, at least about 15% to about 40%, at least about 20% to about 50%, at least about 25% to about 50%, at least about 30% to about 50%, at least about 20% to about 40%, at least about 20% to about 45%, at least about 25% to about 45, or at least about 25% to about 40% in the subject after administration as compared to a control
  • control UOx:creatinine ratio is a level of UOx in the subject prior to administration.
  • control UOx:creatinine ratio is a UOx:creatinine ratio in a subject, or in a population of subjects, having an oxalate disease or disorder who did not receive treatment, wherein the disease or disorder is hyperoxaluria, primary hyperoxaluria, dietary hyperoxaluria, enteric hyperoxaluria, short bowel syndrome, chronic pancreatitis, inflammatory bowel disease (IBD), cystic fibrosis, kidney disease, and/or Roux-en-Y gastric bypass.
  • IBD inflammatory bowel disease
  • the disease or disorder is short bowel syndrome or Roux-en-Y gastric bypass.
  • the method reduces acute levels of oxalate in the subject by at least about 40% by day 5 after administration. In one embodiment, the method reduces acute levels of oxalate in the subject by at least about 50% by day 5 after administration. In one embodiment, the method reduces acute levels of oxalate in the subject by at least about 60% by day 5 after administration. In one embodiment, the method reduces acute levels of oxalate in the subject by at least about 70% by day 5 after administration. In one embodiment, the method reduces acute levels of oxalate in the subject by at least about 80% by day 5 after administration.
  • the method reduces acute levels of oxalate in the subject by at least about 10% by about 24 hours after administration. In one embodiment, the method reduces acute levels of oxalate in the subject by at least about 15% by about 24 hours after administration. In one embodiment, the method reduces acute levels of oxalate in the subject by at least about 20% by about 24 hours after administration.
  • the level of oxalate, or the acute level of oxalate, or the chronic level of oxalate is a level of urinary oxalate (UOx).
  • UOx urinary oxalate
  • the level of UOx in the subject is less than 44 mg/24h after administration.
  • the mean 24-hour urinary oxalate level in the subject after administration is less than 44 mg, less than 43 mg, less than 42 mg, less than 41 mg, less than 40 mg, less than 39 mg, less than 38 mg, about 45 mg to about 35 mg, about 44 mg to about 36 mg, about 43 mg to about 37 mg, about 42 mg to about 38 mg, about 41 mg to about 39 mg, or about 40 mg.
  • the recombinant bacterium is of the genus Escherichia. In one embodiment, the recombinant bacterium is of the species Escherichia coli strain Nissle.
  • the pharmaceutical composition is administered orally.
  • the subject is fed a meal within one hour of administering the pharmaceutical composition.
  • the subject is fed a meal concurrently with administering the pharmaceutical composition.
  • the subject is a human subject.
  • a recombinant bacterium comprising one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked directly or indirectly to a first promoter that is not associated with the oxalate catabolism enzyme gene in nature.
  • the one or more gene sequences is operably linked directly to the first promoter.
  • the one or more gene sequences is operably linked indirectly to the first promoter.
  • the first promoter is an inducible promoter.
  • the first promoter is a constitutive promoter.
  • the recombinant bacterium has an oxalate consumption activity of 1 pmol/lxlO 9 cell. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 150-300 mg/day under anaerobic conditions. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 200 mg/day under anaerobic conditions. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 200 mg/day under anaerobic conditions when administered to the subject three times per day. In one embodiment, the anaerobic conditions are conditions in the intestine and/or colon of the subject.
  • the one or more gene sequences comprise a scaciE3 gene, an frc gene, and an oxdC gene.
  • the scaaE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 502.
  • the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 500.
  • the oxdC gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 501.
  • the scaciE3 gene comprises SEQ ID NO: 502.
  • the frc gene comprises SEQ ID NO: 500.
  • the oxdC gene comprises SEQ ID NO: 501.
  • the recombinant bacterium further comprises a gene encoding an oxalate importer.
  • the gene encoding the oxalate importer is an oxlT gene.
  • the oxlT gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 510.
  • the oxlT gene comprises SEQ ID NO: 510.
  • the recombinant bacterium further comprises an auxotrophy.
  • the auxotrophy is a thyA auxotrophy.
  • thyA has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 391.
  • the recombinant bacterium further comprises a deletion in an endogenous phage.
  • the endogenous phage comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 292.
  • the endogenous phase comprises a sequence of SEQ ID NO: 292.
  • the recombinant bacterium does not comprise a gene encoding for antibiotic resistance.
  • the first promoter is an inducible promoter.
  • the inducible promoter is induced by low oxygen or anaerobic conditions, temperature, or the hypoxic environment of a tumor.
  • the inducible promoter is an FNR promoter.
  • the FNR promoter is a promoter selected from the group consisting of any one of SEQ ID NOs: 1-12.
  • the recombinant bacterium comprises an oxlT gene under the control of an inducible promoter, optionally an FNR promoter; an scaciE3 gene, an oxcd gene, and an frc gene under the control of an inducible promoter, optionally an FNR promoter, a thyA deletion (or auxotrophy) and a deletion of endogenous phage 3.
  • the recombinant bacterium comprises HA910::FNR_ox/7 1 , WA 2.. Y ⁇ A ⁇ _scaaE3-oxcd-frc, AthyA, Aphage 3.
  • the recombinant bacterial cell further comprises a modified endogenous colibactin island.
  • the modified endogenous colibactin island comprises one or more modified clb sequences selected from the group consisting of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c»J(SEQ ID c/ (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO:
  • the recombinant bacterium is SYN5752, SYN7169, or SYNB8802. In one embodiment, the recombinant bacterium is SYNB8802.
  • the subject has hyperoxaluria.
  • the hyperoxaluria is primary hyperoxaluria, dietary hyperoxaluria, or enteric hyperoxaluria.
  • the subject has short bowel syndrome, chronic pancreatitis, inflammatory bowel disease (IBD), cystic fibrosis, kidney disease, and/or Roux-en-Y gastric bypass.
  • IBD inflammatory bowel disease
  • the subject has urinary oxalate (Uox) levels of at least 70 mg/day prior to the administering. In one embodiment, the subject exhibits a decrease in Uox levels of at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or 80% after the administering. In one embodiment, the subject has eGFR ⁇ 30 mL/min/1.73 m 2 , requires hemodialysis, or has systemic oxalosis prior to the administering.
  • the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria, about 2xlO n live recombinant bacteria, about 3xl0 n live recombinant bacteria, about 4xlO n live recombinant bacteria, about 4.5x 10" live recombinant bacteria, about 5xl0 n live recombinant bacteria, about 6xlO n live recombinant bacteria, about IxlO 12 live recombinant bacteria, or about 2xl0 12 live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about 6xlO n live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about 3x10 11 live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria. In one embodiment, the administering is about 4.5x 10" live recombinant bacteria. In one embodiment, the administering is about 5x10 11 live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about IxlO 12 live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about 2xl0 12 live recombinant bacteria.
  • the administering are about 5xlO n live recombinant bacteria with meals three times per day.
  • the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria to about 2xl0 12 live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about IxlO 12 live recombinant bacteria to about 2xI0 12 live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about 5xlO n live recombinant bacteria to about 2xI0 12 live recombinant bacteria.
  • the administering is once per day. In another embodiment, the administering is twice per day. In another embodiment, the administering is oral, with meals, once per day. In another embodiment, the administering is oral, with meals, twice per day. In another embodiment, the administering is oral, with meals, three times per day.
  • a proton pump inhibitor is administered to the subject.
  • the PPI is esomeprazole.
  • esomeprazole is administered at 20 mg once daily.
  • esomeprazole is administered at 40 mg once daily.
  • the administering of the PPI is once a day.
  • galactose is administered to the subject in combination with, e.g., at the same time as, or in the same composition or formulation as, the recombinant bacteria described herein.
  • the administering of galactose is once a day, twice per day, three times per day, or with meals.
  • the galactose is administered to the subject in the same composition or formulation as the recombinant bacteria described herein.
  • the galactose is D- galactose.
  • a proton pump inhibitor (PPI) and galactose are administered to the subject in combination with the recombinant bacteria described herein.
  • the PPI is esomeprazole.
  • esomeprazole is administered at 20 mg once daily.
  • esomeprazole is administered at 40 mg once daily.
  • the administering of the PPI and galactose is once a day, twice per day, three times per day, or with meals.
  • galactose is administered at about 0.1 g to about 3 g, about 0.1 g to about 2.5 g, about 0. 1 g to about 2.0 g, about 0.1 g to about 1.5 g, about 0. 1 g to about 1.0 g, about 0.1 g to about 0.5 g, about 0.5 g to about 3 g, about 0.5 g to about 2.5 g, about 0.5 g to about 2.0 g, about 0.5 g to about 1.5 g, about 0.5 g to about 1.0 g, about 1.0 g to about 3 g, about 1.0 g to about 2.5 g, about 1.0 g to about 2.0 g, about 1.0 g to about 1.5 g, about 1.5 g to about 3 g, about 1.5 g to about 2.5 g, about 1.5 g to about 2.0 g, about 2.0 g to about 3 g, about 2.0 g to about 2.5 g, or about 2.5 g to about 3 g.
  • galactose is administered at about 1.0 g. In some embodiments, galactose is administered at about 0.5 g. In some embodiments, galactose is administered at about 2.0 g.
  • the disclosure provides a bacterial cell that has been genetically engineered to comprise one or more genes, gene cassettes, and/or synthetic circuits encoding one or more oxalate catabolism enzyme(s) or oxalate catabolism pathway, and is capable of metabolizing oxalate and/or other metabolites, such as oxalyl-CoA.
  • the genetically engineered bacterial cells and pharmaceutical compositions comprising the bacterial cells may be used to treat and/or prevent diseases associated with disorders in which oxalate is detrimental, such as primary hyperoxalurias and secondary hyperoxalurias.
  • the disclosure provides a bacterial cell that has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s). In some embodiments, the disclosure provides a bacterial cell has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and is capable of reducing the level of oxalate and/or other metabolites, for example, oxalyl-CoA. In some embodiments, the bacterial cell has been engineered to comprise gene sequence(s) encoding one or more transporter(s) (importer(s)) of oxalate.
  • the bacterial cell has been engineered to comprise gene sequence(s) encoding one or more exporter(s) of formate.
  • the engineered bacteria comprise gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)).
  • the engineered bacteria comprise gene sequence(s) encoding one or more of the following: (i) one or more transporter(s) of oxalate; (ii) one or more exporter(s) of formate; (iii) one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)); and (iv) any combination thereof.
  • the bacterial cell has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and one or more transporter(s) (importer(s)) of oxalate.
  • the bacterial cell of the disclosure has been genetically engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and one or more exporter(s) of formate.
  • genetically engineered bacteria comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and one or more polypeptide(s), which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)).
  • the bacterial cell has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and gene sequence(s) encoding one or more of the following: (i) one or more transporter(s) of oxalate; (ii) one or more exporter(s) of formate; (iii) one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)); and (iv) any combination thereof.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) is operably linked to an inducible promoter.
  • the gene sequence(s) encoding one or more oxalate transporter(s) (importer(s)) is operably linked to an inducible promoter.
  • the gene sequence(s) encoding one or more exporter(s) of formate is operably linked to an inducible promoter.
  • the gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate is operably linked to an inducible promoter.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more oxalate transporter(s) (importer(s)) are operably linked to an inducible promoter.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more exporter(s) of formate are operably linked to an inducible promoter.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate are operably linked to an inducible promoter.
  • any one or more of the following gene sequences are operably linked to an inducible promoter: (i) gene sequence(s) encoding one or more oxalate catabolism enzyme(s); (ii) gene sequence(s) encoding one or more oxalate transporter(s); (iii) gene sequence(s) encoding one or more exporter(s) of formate; and (iv) gene sequence(s) encoding one or more polypeptide (s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)).
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions, e.g., such as those conditions found in the mammalian gut.
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more oxalate transporter(s) (importer(s)) operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions, e.g., such as those conditions found in the mammalian gut.
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more exporter(s) of formate operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions, e.g., such as those conditions found in the mammalian gut.
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)) operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions, e.g., such as those conditions found in the mammalian gut.
  • formate e.g., oxalate: formate antiporter(s)
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more oxalate transporter(s) (importer(s)) are operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more exporter(s) of formate are operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate are operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions.
  • any one or more of the following gene sequences are operably linked to an inducible promoter that is induced under low oxygen and/or anaerobic conditions: (i) gene sequence(s) encoding one or more oxalate catabolism enzyme(s); (ii) gene sequence(s) encoding one or more oxalate transporter(s); (iii) gene sequence(s) encoding one or more exporter(s) of formate; and (iv) gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)).
  • the inducible promoter is a lacl promoter which can be induced with IPTG.
  • one or more of the above gene sequences are operably linked to an IPTG inducible promoter, e.g., the Ptac promoter, having lacl operator.
  • the lac repressor gene, lacl is placed upstream of the gene Ptac- construct in reverse orientation to allow for divergent transcription.
  • the inducible promoter is a IPTG inducible promoter.
  • the IPTG inducible promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 17.
  • the recombinant bacterium further comprises a gene sequence encoding a repressor of the Lac promoter.
  • the gene sequence encoding a repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 15.
  • the repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 16.
  • the inducible promoter is a pBAD promoter which can be induced with arabinose.
  • one or more of the above gene sequences are operably linked to an temperature inducible promoter, having a operators for cI38 or cI857 repressor binding.
  • the cI38 or cI857 repressor gene is placed upstream of the gene operably linked to the temperature sensitive promoter in reverse orientation to allow for divergent transcription.
  • the disclosure provides a bacterial cell that has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) that is operably linked to an inducible promoter that is induced by environmental signals and/or conditions found in the mammalian gut (e.g., induced by metabolites (e.g., oxalate metabolites) or other biomolecules found in the mammalian gut, and/or induced by inflammatory conditions (e.g., reactive nitrogen species and/or reactive oxygen species)).
  • an inducible promoter that is induced by environmental signals and/or conditions found in the mammalian gut (e.g., induced by metabolites (e.g., oxalate metabolites) or other biomolecules found in the mammalian gut, and/or induced by inflammatory conditions (e.g., reactive nitrogen species and/or reactive oxygen species)).
  • the environmental signals and/or conditions found in the mammalian gut may be signals and conditions found in a healthy mammalian gut or signals and conditions found in a diseased mammalian gut, such as the gut of a subject having hyperoxaluria or other condition in which the level of oxalate and/or an oxalate metabolite is elevated, and/or the gut of a subject having an inflammatory condition, such as irritable bowel disease, an autoimmune disease, and any other condition that results in inflammation in the gut.
  • a diseased mammalian gut such as the gut of a subject having hyperoxaluria or other condition in which the level of oxalate and/or an oxalate metabolite is elevated
  • an inflammatory condition such as irritable bowel disease, an autoimmune disease, and any other condition that results in inflammation in the gut.
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) operably linked to an inducible promoter that is induced under inflammatory conditions, e.g. , such as inflammatory conditions found in a mammalian gut.
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more oxalate transporter(s) (importer(s)) operably linked to an inducible promoter that is induced under inflammatory conditions, e.g., such as inflammatory conditions found in a mammalian gut.
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more exporter(s) of formate operably linked to an inducible promoter that is induced under inflammatory conditions, e.g., such as inflammatory conditions found in a mammalian gut.
  • the disclosure provides a bacterial cell which has been engineered to comprise gene sequence(s) encoding one or more polypeptide (s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)) operably linked to an inducible promoter that is induced under inflammatory conditions, e.g., such as inflammatory conditions found in a mammalian gut.
  • formate e.g., oxalate: formate antiporter(s)
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more oxalate transporter(s) (importer(s)) are operably linked to an inducible promoter that is induced under inflammatory conditions.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more exporter(s) of formate are operably linked to an inducible promoter that is induced under inflammatory conditions.
  • the gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and the gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate are operably linked to an inducible promoter that is induced under inflammatory conditions.
  • any one or more of the following gene sequences are operably linked to an inducible promoter that is induced under inflammatory conditions: (i) gene sequence(s) encoding one or more oxalate catabolism enzyme(s); (ii) gene sequence(s) encoding one or more oxalate transporter(s); (iii) gene sequence(s) encoding one or more exporter(s) of formate; and (iv) gene sequence(s) encoding one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)).
  • an inducible promoter that is induced under inflammatory conditions: (i) gene sequence(s) encoding one or more oxalate catabolism enzyme(s); (ii) gene sequence(s) encoding one or more oxalate transporter(s); (iii) gene sequence(s) encoding one
  • the disclosure provides a bacterial cell that has been engineered to comprise gene sequence(s) encoding one or more polypeptide(s) capable of reducing the level of oxalate and/or other metabolites, for example, oxalyl-CoA, in low-oxygen environments, e.g., the gut.
  • the bacterial cell has been genetically engineered to comprise one or more circuits encoding one or more oxalate catabolism enzyme(s) and is capable of processing and reducing levels of oxalate, and/or oxalyl -CoA e.g., in low-oxygen environments, e.g., the gut.
  • the genetically engineered bacterial cells and pharmaceutical compositions comprising the bacterial cells of the disclosure may be used to import excess oxalate and/or oxalyl-CoA into the bacterial cell in order to treat and/or prevent conditions associated with disorders in which oxalate is detrimental, such as primary hyperoxalurias and secondary hyperoxalurias.
  • the genetically engineered bacterial cells and pharmaceutical compositions comprising the bacterial cells of the disclosure may be used to convert excess oxalate and/or oxalyl-CoA into non-toxic molecules in order to treat and/or prevent conditions associated with disorders in which oxalate is detrimental, such as primary hyperoxalurias and secondary hyperoxalurias.
  • the one or more gene sequences comprise a scaciE3 gene, an frc gene, and an oxdC gene.
  • the scaaE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 502.
  • the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 500.
  • the oxdC gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 501.
  • the recombinant bacterium further comprises a gene encoding an oxalate importer.
  • the gene encoding the oxalate importer is an oxlT gene.
  • the oxlT gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 510.
  • the recombinant bacterium further comprises an auxotrophy.
  • the auxotrophy is a thyA auxotrophy.
  • the recombinant bacterium further comprises a deletion in an endogenous phage.
  • the endogenous phage comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 292.
  • the recombinant bacterial cell further comprises a modified endogenous colibactin island.
  • the modified endogenous colibactin island comprises one or more modified clb sequences selected from the group consisting of clbA (SEQ ID NO: 294, clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c//>J(SEQ ID NO: 303), clbK (SEQ ID NO: 304), clbL (SEQ ID NO: 305), clbM (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO: 294, cl
  • the modified endogenous colibactin island comprises a deletion of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c//G (SEQ ID NO: 303), c//>7 (SEQ ID NO: 304), clbL (SEQ ID NO: 305), c/ (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO: 309), clbQ (SEQ ID NO: 294), c
  • the recombinant bacterium does not comprise a gene encoding for antibiotic resistance.
  • the first promoter is an inducible promoter, optionally when the inducible promoter is a FNR promoter, optionally wherein the FNR promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 1-12.
  • the inducible promoter is a Pr/Pl promoter.
  • the Pr/Pl promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 19, 22, and 25.
  • the recombinant bacterium further comprises a gene sequence encoding a mutant repressor of the Pr/Pl promoter.
  • the gene sequence encoding a mutant repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 20 and 23.
  • the inducible promoter is a IPTG inducible promoter.
  • the IPTG inducible promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 17.
  • the recombinant bacterium further comprises a gene sequence encoding a repressor of the Lac promoter.
  • the gene sequence encoding a repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 16.
  • the repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 16.
  • the present disclosure provides recombinant bacterial cells, pharmaceutical compositions thereof, and methods of modulating and treating disorders in which oxalate is detrimental.
  • the genetically engineered bacterial cells and pharmaceutical compositions comprising the bacterial cells of the disclosure may be used to convert excess oxalate and/or oxalic acid into non-toxic molecules in order to treat and/or prevent conditions associated with disorders in which oxalate is detrimental, such as primary hyperoxalurias and secondary hyperoxalurias.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding at least one oxalate catabolism enzyme and is capable of processing and reducing levels of oxalate, in low-oxygen environments, e.g., the gut.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding an importer of oxalate and is capable of reducing levels of oxalate, in low-oxygen environments, e.g., the gut.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding an exporter of formate and is capable of reducing levels of oxalate, in low-oxygen environments, e.g., the gut.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding an oxalate: formate antiporter and is capable of reducing levels of oxalate, in low-oxygen environments, e.g., the gut.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding at least one oxalate catabolism enzyme and is capable of processing and reducing levels of oxalate, in inflammatory environments, such as may be present in the gut.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding an importer of oxalate and is capable of reducing levels of oxalate, in inflammatory environments, e.g., such as may be present in the gut.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding an exporter of formate and is capable of reducing levels of oxalate, in inflammatory environments, e.g., such as may be present in the gut.
  • a bacterial cell has been engineered to comprise at least one heterologous gene encoding an oxalate: formate antiporter and is capable of reducing levels of oxalate, in inflammatory environments, e.g., such as may be present in the gut.
  • the at least one oxalate catabolism enzyme converts oxalate to formate or formyl CoA.
  • the at least one oxalate catabolism enzyme is selected from an oxalate-CoA ligase, (e.g., ScAAE3 from .S', cerevisiae), an oxalyl-CoA decarboxylase (Oxc, e.g., from O. formigenes). and a formyl-CoA transferase (e.g., Frc, e.g., from O. formigenes)' .
  • an oxalate-CoA ligase e.g., ScAAE3 from .S', cerevisiae
  • Oxc oxalyl-CoA decarboxylase
  • a formyl-CoA transferase e.g., Frc, e.g., from O. formigenes
  • the at least one heterologous gene encoding at least one oxalate catabolism enzyme is selected from a frc gene and an oxc gene In one embodiment, the at least one heterologous gene encoding an oxalate transporter is an oxlT gene. In some embodiments, the at least one heterologous gene encoding at least one oxalate catabolism enzyme is located on a plasmid in the bacterial cell. In some embodiments, the at least one heterologous gene encoding at least one oxalate catabolism enzyme is located on a chromosome in the bacterial cell.
  • the at least one heterologous gene encoding an oxalate transporter is located on a plasmid in the bacterial cell. In some embodiments, the at least one heterologous gene encoding the oxalate transporter is located on a chromosome in the bacterial cell. In some embodiments, the at least one heterologous gene encoding a formate exporter is located on a plasmid in the bacterial cell. In some embodiments, the at least one heterologous gene encoding a formate exporter is located on a chromosome in the bacterial cell.
  • the at least one heterologous gene encoding an oxalate: formate antiporter is located on a plasmid in the bacterial cell. In some embodiments, the at least one heterologous gene encoding an oxalate: formate antiporter is located on a chromosome in the bacterial cell.
  • the engineered bacterial cell is a probiotic bacterial cell.
  • the engineered bacterial cell is a member of a genus selected from the group consisting of Bacteroides, Bifidobacterium, Clostridium, Escherichia, Lactobacillus and Lactococcus .
  • the engineered bacterial cell is of the genus Escherichia.
  • the recombinant bacterial cell is of the species Escherichia coli strain Nissle.
  • the engineered bacterial cell is an auxotroph in a gene that is complemented when the engineered bacterial cell is present in a mammalian gut.
  • the mammalian gut is a human gut.
  • the engineered bacterial cell is an auxotroph in diaminopimelic acid or an enzyme in the thymine biosynthetic pathway.
  • the engineered bacterial cell further comprises a heterologous gene encoding a substance that is toxic to the bacterial cell that is operably linked to an inducible promoter, wherein the inducible promoter is directly or indirectly induced by an environmental condition not naturally present in the mammalian gut.
  • the disclosure provides a pharmaceutical composition comprising a recombinant bacterial cell comprising at least one heterologous gene encoding at least one oxalate catabolism enzyme operably linked to a first inducible promoter and a pharmaceutically acceptable carrier.
  • the disclosure provides a pharmaceutical composition comprising a recombinant bacterial cell comprising at least one heterologous gene encoding at least one oxalate catabolism enzyme operably linked to a first inducible promoter, at least one heterologous gene encoding an oxalate transporter operably linked to a second inducible promoter, which may be the same or different promoter from the first inducible promoter, and a pharmaceutically acceptable carrier.
  • the disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising a recombinant bacterial cell comprising at least one heterologous gene encoding at least one oxalate catabolism enzyme operably linked to a first inducible promoter, at least one heterologous gene encoding a formate exporter operably linked to a second inducible promoter, which may be the same or different promoter from the first inducible promoter, and a pharmaceutically acceptable carrier.
  • the disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising a recombinant bacterial cell comprising at least one heterologous gene encoding at least one oxalate catabolism enzyme operably linked to a first inducible promoter, at least one heterologous gene encoding an oxalate: formate antiporter operably linked to a second inducible promoter, which may be the same or different promoter from the first inducible promoter, and a pharmaceutically acceptable carrier.
  • the first promoter and the second promoter may be separate copies of the same promoter.
  • the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter are each directly induced by environmental conditions. In some embodiments, the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter, are each indirectly induced by environmental conditions. In some embodiments, the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter, are each directly or indirectly induced by environmental conditions found in the gut of a mammal.
  • the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter are each directly or indirectly induced by low-oxygen or anaerobic conditions. In some embodiments, the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter, are each directly or indirectly induced by inflammatory conditions. In some embodiments, the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter, are each an FNR responsive promoter.
  • the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter are each an RNS responsive promoter. In some embodiments, the first inducible promoter, the second inducible promoter, or the first inducible promoter and the second inducible promoter, are each an ROS responsive promoter.
  • the disclosure provides a method for treating a disease or disorder in which oxalate is detrimental in a subject, the method comprising administering a an engineered bacterial cell or a pharmaceutical composition comprising an engineered bacterial cell to the subject, wherein the engineered bacterial cell comprises gene sequence encoding one or more oxalate catabolism enzyme(s).
  • the disclosure provides a method for treating a disease or disorder in which oxalate is detrimental in a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition comprising an engineered bacterial cell to the subject, wherein the engineered bacterial cell comprises gene sequence encoding one or more oxalate transporter(s).
  • the disclosure provides a method for treating a disease or disorder in which oxalate is detrimental in a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition comprising an engineered bacterial cell to the subject, wherein the engineered bacterial cell comprises gene sequence encoding one or more formate exporter(s).
  • the disclosure provides a method for treating a disease or disorder in which oxalate is detrimental in a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition comprising an engineered bacterial cell to the subject, wherein the engineered bacterial cell comprises gene sequence encoding one or more oxalate: formate antiporter(s).
  • the disclosure provides a method for treating a disease or disorder in which oxalate is detrimental in a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition comprising an engineered bacterial cell to the subject, wherein the engineered bacterial cell comprises gene sequence encoding one or more of the following: (i) oxalate catabolism enzyme(s); (ii) one or more oxalate transporter(s); (iii) one or more formate exporter(s); and (iv) one or more oxalate: formate antiporter(s).
  • the disclosure provides a method for treating a disease or disorder in which oxalate is detrimental in a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition comprising an engineered bacterial cell to the subject, wherein the engineered bacterial cell expresses at least one heterologous gene encoding at least one oxalate catabolism enzyme in response to an exogenous environmental condition in the subject, thereby treating the disease or disorder in which oxalate is detrimental in the subject.
  • the engineered bacterial cell further expresses one or more of the following: (i) at least one heterologous gene encoding an importer of oxalate; (ii) at least one heterologous gene encoding an exporter of formate; and/or (iii) at least one heterologous gene encoding an oxalate: formate antiporter.
  • the disclosure provides a method for treating a disorder in which oxalate is detrimental in a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition of the disclosure to the subject, thereby treating the disorder in which oxalate is detrimental in the subject.
  • the disclosure provides a method for decreasing a level of oxalate in plasma of a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition of the disclosure to the subject, thereby decreasing the level of oxalate in the plasma of the subject.
  • the disclosure provides a method for decreasing a level of oxalate in urine of a subject, the method comprising administering an engineered bacterial cell or a pharmaceutical composition of the disclosure to the subject, thereby decreasing the level of oxalate in the urine of the subject.
  • the level of oxalate is decreased in plasma of the subject after administering the engineered bacterial cell or pharmaceutical composition to the subject.
  • the level of oxalate is reduced in urine of the subject after administering the engineered bacterial cell or pharmaceutical composition to the subject.
  • the engineered bacterial cell or pharmaceutical composition is administered orally.
  • the method further comprises isolating a plasma sample from the subject or a urine sample from the subject after administering the engineered bacterial cell or pharmaceutical composition to the subject, and determining the level of oxalate in the plasma sample from the subject or the urine sample from the subject.
  • the method further comprises comparing the level of oxalate in the plasma sample from the subject or the urine sample from the subject to a control level of oxalate.
  • the control level of oxalate is the level of oxalate in the plasma of the subject or in the urine of the subject before administration of the engineered bacterial cell or pharmaceutical composition.
  • the disorder in which oxalate is detrimental is a hyperoxaluria.
  • the hyperoxaluria is primary hyperoxaluria type I.
  • the hyperoxaluria is primary hyperoxaluria type II.
  • the hyperoxaluria is primary hyperoxaluria type III.
  • the hyperoxaluria is enteric hyperoxaluria.
  • the hyperoxaluria is dietary hyperoxaluria.
  • the hyperoxaluria is idiopathic hyperoxaluria.
  • the subject is fed a meal within one hour of administering the pharmaceutical composition. In another embodiment, the subject is fed a meal concurrently with administering the pharmaceutical composition.
  • the recombinant bacterium is capable of decreasing urinary oxalate in the subject after administration by at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, or at least 45%.
  • the decrease is a decrease as compared to a level of urinary oxalate in the subject prior to administration.
  • the decrease is a decrease as compared to a level of urinary oxalate in a subject, or a population of subjects, having hyperoxaluria that has not been treated with the recombinant bacterium.
  • the method further comprises measuring the level of urinary oxalate in the subject prior to administration.
  • the method further comprises measuring the level of urinary oxalate in the subject after administration.
  • the method comprises measuring the level of urinary oxalate in the subject prior to administration and after administration.
  • the recombinant bacterium is capable of decreasing fecal oxalate in the subject after administration by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 85%.
  • the decrease is a decrease as compared to a level of fecal oxalate in the subject prior to administration.
  • the decrease is a decrease as compared to a level of fecal oxalate in a subject, or a population of subjects, having hyperoxaluria that has not been treated with the recombinant bacterium.
  • the method further comprises measuring the level of fecal oxalate in the subject prior to administration. In another embodiment, the method further comprises measuring the level of fecal oxalate in the subject after administration. In one embodiment, the method comprises measuring the level of fecal oxalate in the subject prior to administration and after administration.
  • a method for reducing the levels of oxalate in a subject comprising administering to the subject a pharmaceutical composition comprising a recombinant bacterium comprising: one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked to a directly or indirectly first promoter that is not associated with the oxalate catabolism enzyme gene in nature, wherein the one or more gene sequences comprise a scaciE3 gene, an frc gene, and an oxdC gene, wherein the scaciE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 502, wherein the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises,
  • the endogenous phage comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 292.
  • the modified endogenous colibactin island comprises one or more modified clb sequences selected from the group consisting of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c/6J(SEQ ID NO: 303), c//>7 (SEQ ID NO: 304), clbL (SEQ ID NO: 305), c/ (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO:
  • the modified endogenous colibactin island comprises a deletion of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbE (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c//?./ (SEQ ID NO: 303), c//>7 (SEQ ID NO: 304), clbL (SEQ ID NO: 305), clbM (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO: 309), clbQ
  • the recombinant bacterium does not comprise a gene encoding for antibiotic resistance.
  • the recombinant bacterium has an oxalate consumption activity of at least about 1 pmol/lxlO 9 cell.
  • the recombinant bacterium has an oxalate consumption activity of about 50 to about 600 mg/day under anaerobic conditions. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 211 mg/day under anaerobic conditions. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 211 mg/day under anaerobic conditions when administered to the subject three times per day.
  • the anaerobic conditions are conditions in the intestine and/or colon of the subject.
  • the method reduces acute levels of oxalate in the subject by about two fold. In one embodiment, the method reduces acute levels of oxalate in the subject by about three fold. In one embodiment, the method reduces chronic levels of oxalate in the subject by about two fold. In one embodiment, the method reduces chronic levels of oxalate in the subject by about three fold.
  • the method reduces acute levels of oxalate in the subject to about 25 mg/day, about 30 mg/day, about 40 mg/day, about 50 mg/day, about 60 mg/day, about 70 mg/day, about 80 mg/day, about 90 mg/day, or about 100 mg/day. In one embodiment, the method reduces chronic levels of oxalate in the subject to about 25 mg/day, about 30 mg/day, about 40 mg/day, about 50 mg/day, about 60 mg/day, about 70 mg/day, about 80 mg/day, about 90 mg/day, or about 100 mg/day.
  • the recombinant bacterium is of the genus Escherichia. In one embodiment, the recombinant bacterium is of the species Escherichia coli strain Nissle. [0085] In one embodiment, the pharmaceutical composition is administered orally. In one embodiment, the subject is fed a meal within one hour of administering the pharmaceutical composition. In one embodiment, the subject is fed a meal concurrently with administering the pharmaceutical composition.
  • the subject is a human subject.
  • the first promoter is an inducible promoter, optionally when the inducible promoter is a FNR promoter, optionally wherein the FNR promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 1-12.
  • the inducible promoter is a Pr/Pl promoter.
  • the Pr/Pl promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 19, 22, and 25.
  • the recombinant bacterium further comprises a gene sequence encoding a mutant repressor of the Pr/Pl promoter.
  • the gene sequence encoding a mutant repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 20 and 23.
  • the inducible promoter is a IPTG inducible promoter.
  • the IPTG inducible promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 17.
  • the recombinant bacterium further comprises a gene sequence encoding a repressor of the Lac promoter.
  • the gene sequence encoding a repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 15.
  • the repressor comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 16.
  • the recombinant bacterium is SYNB8802.
  • the subject has hyperoxaluria.
  • the hyperoxaluria is primary hyperoxaluria, dietary hyperoxaluria, or enteric hyperoxaluria.
  • the subject has short bowel syndrome, chronic pancreatitis, inflammatory bowel disease (IBD), cystic fibrosis, kidney disease, and/or Roux-en-Y gastric bypass. In one embodiment, the subject has short bowel syndrome and/or Roux-en-Y gastric bypass.
  • IBD inflammatory bowel disease
  • cystic fibrosis cystic fibrosis
  • kidney disease kidney disease
  • Roux-en-Y gastric bypass the subject has short bowel syndrome and/or Roux-en-Y gastric bypass.
  • the subject has urinary oxalate (Uox) levels of at least 70 mg/day prior to the administering.
  • Uox urinary oxalate
  • the subject exhibits a decrease in Uox levels of at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or 80% after the administering.
  • the subject has eGFR ⁇ 30 mL/min/1.73 m 2 , requires hemodialysis, or has systemic oxalosis prior to the administering.
  • the recombinant bacteria is administered at a dose of about IxlO 11 live recombinant bacteria, about 3x10" live recombinant bacteria, about 4.5x10" live bacteria, about 5x10" live recombinant bacteria, about 6x 10" live recombinant bacteria, about IxlO 12 live recombinant bacteria, or about 2xl0 12 live recombinant bacteria.
  • the administering is about 4.5x10" live recombinant bacteria.
  • the recombinant bacteria is administered once daily, twice daily, or three times daily. In one embodiment, the administering is about 5x10" live recombinant bacteria with meals three times per day.
  • the method further administering a proton pump inhibitor (PPI) to the subject.
  • PPI proton pump inhibitor
  • the PPI is esomeprazole.
  • esomeprazole is administered at 20 mg once daily.
  • esomeprazole is administered at 40 mg once daily.
  • the administering of the PPI is once a day.
  • the pharmaceutical composition further comprises galactose.
  • galactose is D-galactose.
  • galactose is present in the composition at about 0.1 g to about 3 g, about 0.1 g to about 2.5 g, about 0.
  • galactose is present in the composition at about 1.0 g. In some embodiments, galactose is present in the composition at about 0.5 g. In some embodiments, galactose is present in the composition at about 2.0 g.
  • a recombinant bacterium comprising: one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked to a directly or indirectly first promoter that is not associated with the oxalate catabolism enzyme gene in nature, wherein the one or more gene sequences comprise a scaaE3 gene, an frc gene, and an oxdC gene, wherein the scaciE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 502, wherein the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 500, and wherein the oxdC gene comprises a sequence having at least 90%, 91%, 9
  • the endogenous phage comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 292.
  • the modified endogenous colibactin island comprises one or more modified clb sequences selected from the group consisting of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), c/W (SEQ ID NO: 301), c//>J(SEQ ID NO: 302), c/A T (SEQ ID NO: 303), clbL (SEQ ID NO: 304), c/ (SEQ ID NO: 305), clbN (SEQ ID NO: 306), clbO (SEQ ID NO: 307), clbP (SEQ ID NO:
  • the modified endogenous colibactin island comprises a deletion of clb A (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbE (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c//?./ (SEQ ID NO: 303), c/ ⁇ (SEQ ID NO: 304), clbL (SEQ ID NO: 305), clbM (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO: 309), clbQ (SEQ ID NO: 294),
  • the recombinant bacterium does not comprise a gene encoding for antibiotic resistance.
  • the first promoter is an inducible promoter, optionally when the inducible promoter is a FNR promoter, optionally wherein the FNR promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 1-12.
  • the recombinant bacterium has an oxalate consumption activity of at least about Ipmol/lxlO 9 cell. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 50-600 mg/day under anaerobic conditions.
  • the recombinant bacterium is SYNB8802. In one embodiment, the recombinant bacterium is SYNB8802.
  • the recombinant bacterium has an oxalate consumption activity of about 0.2 pmole/hr to about 1.6 pmole/hr, about 0.5 pmole/hr to about 1.5 pmole/hr, or about 1.0 pmole/hr to about 1.5 pmole/hr under anaerobic conditions. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 0.5 pmole/hr to about 1.5 pmole/hr under anaerobic conditions.
  • the recombinant bacterium has an oxalate consumption activity of about 0.2 pmole/hr to about 1.6 pmole/hr, about 0.5 pmole/hr to about 1.5 pmole/hr, or about 1.0 pmole/hr to about 1.5 pmole/hr under anaerobic conditions. In one embodiment, the recombinant bacterium has an oxalate consumption activity of about 0.5 pmole/hr to about 1.5 pmole/hr under anaerobic conditions.
  • the recombinant bacterium is capable of decreasing urinary oxalate in the subject after administration by at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, or at least 45%. In one embodiment, the recombinant bacterium is capable of decreasing fecal oxalate in the subject after administration by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 85%.
  • a method for reducing the levels of oxalate in a subject comprising administering to the subject a pharmaceutical composition comprising a recombinant bacterium comprising: one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked directly or indirectly to a first promoter that is not associated with the oxalate catabolism enzyme gene in nature, wherein the one or more gene sequences comprise a scaciE3 gene, an frc gene, and an oxdC gene, wherein the scaciE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 502, wherein the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises,
  • a method for reducing the levels of oxalate in a subject comprising administering to the subject a pharmaceutical composition comprising a recombinant bacterium comprising: one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked directly or indirectly to a first promoter that is not associated with the oxalate catabolism enzyme gene in nature, wherein the one or more gene sequences comprise a scaaE3 gene, an frc gene, and an oxdC gene, wherein the scaaE3 gene encodes a polypeptide comprising a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 506, wherein the frc gene encodes a polypeptide comprising a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 9
  • the levels of oxalate in a subject are reduced between about 20% and about 45%, about 20% and about 40%, about 20% and about 35%, about 20% and about 30%, about 20% and about 25%, about 25% and about 45%, about 25% and about 40%, about 25% and about 35%, about 25% and about 30%, about 30% and about 45%, about 30% and about 40%, about 30% and about 35%, about 35% and about 45%, about 35% and about 40%, or about 40% to about 45% as compared to a level of oxalate in the subject prior to the administering.
  • the levels of oxalate in a subject are reduced by about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, or about 45% as compared to a level of oxalate in the subject prior to the administering.
  • the levels of oxalate in a subject are reduced about 28% or about 38% as compared to a level of oxalate in the subject prior to the administering.
  • the endogenous phage comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 292.
  • the modified endogenous colibactin island comprises one or more modified clb sequences selected from the group consisting of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c/A/(SEQ ID NO: 303), c//?
  • AT SEQ ID NO: 304
  • clbL SEQ ID NO: 305
  • c/ SEQ ID NO: 306
  • clbN SEQ ID NO: 307
  • clbO SEQ ID NO: 308
  • clbP SEQ ID NO: 309
  • clbQ SEQ ID NO: 310
  • clbR SEQ ID NO: 311)
  • clbS SEQ ID NO: 312).
  • the modified endogenous colibactin island comprises a deletion of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), c (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c//?./ (SEQ ID NO: 303), c/AA (SEQ ID NO: 304), clbL (SEQ ID NO: 305), c/ (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO: 309), clbQ (SEQ ID NO: 310), and
  • the recombinant bacterium does not comprise a gene encoding for antibiotic resistance.
  • the recombinant bacterium has an oxalate consumption activity under anaerobic conditions resulting in the reduced levels of oxalate in the subject.
  • the anaerobic conditions are conditions in the intestine and/or colon of the subject.
  • the recombinant bacterium is of the genus Escherichia. In one embodiment, the recombinant bacterium is of the species Escherichia coli strain Nissle.
  • the pharmaceutical composition is administered orally.
  • the subject is fed a meal within one hour of administering the pharmaceutical composition.
  • the subject is fed a meal concurrently with administering the pharmaceutical composition.
  • the subject is a human subject.
  • the first promoter is an inducible promoter, optionally when the inducible promoter is a FNR promoter, optionally wherein the FNR promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs: 1-12.
  • the recombinant bacterium is SYNB8802.
  • the subject has hyperoxaluria.
  • the hyperoxaluria is primary hyperoxaluria, dietary hyperoxaluria, or enteric hyperoxaluria.
  • the subject has short bowel syndrome, chronic pancreatitis, inflammatory bowel disease (IBD), cystic fibrosis, kidney disease, and/or Roux-en-Y gastric bypass. In one embodiment, the subject has short bowel syndrome and/or Roux-en-Y gastric bypass.
  • IBD inflammatory bowel disease
  • cystic fibrosis cystic fibrosis
  • kidney disease kidney disease
  • Roux-en-Y gastric bypass the subject has short bowel syndrome and/or Roux-en-Y gastric bypass.
  • the subject has urinary oxalate (Uox) levels of at least 70 mg/day prior to the administering.
  • Uox urinary oxalate
  • the subject has eGFR ⁇ 30 mL/min/1.73 m2, requires hemodialysis, or has systemic oxalosis prior to the administering.
  • the method comprises administering to a subject a first dose of the bacteria for a first dosing interval (e.g., 2, 3, or 4 weeks), followed by a second dose of the bacteria that is higher than the first dose for a second dosing interval (e.g. , 2, 3, or 4 weeks). In some embodiments, this is followed by a third dose of the bacteria that is higher than the second dose for a third dosing interval (e.g., 2, 3, or 4 weeks).
  • the genetically engineered bacterium is administered for a first dosing interval, a second dosing interval, and optionally for a third dosing interval.
  • the first dosing interval, the second dosing interval, optionally the third dosing interval comprise(s) administering to the subject a dose of genetically engineered bacterium once per day (QD) for a set amount of days, then administering said dose twice per day (BID) for a set amount of days, and then optionally administering said dose three times per day (TID) for a set amount of days.
  • QD genetically engineered bacterium once per day
  • BID twice per day
  • TID three times per day
  • the second dosing interval comprises administering to the subject the genetically engineered bacterium once per day (QD) for a set amount of days, then administering the full dose twice per day (BID) for a set amount of days, and then the full dose three times per day (TID) for a set amount of days.
  • the third dosing interval comprises administering to the subject a dose of genetically engineered bacterium once per day (QD) for a set amount of days, then administering the dose twice per day (BID) for a set amount of days, and then administering the full dose three times per day (TID) for a set amount of days.
  • the dose administered in the second dosing interval and the dose administered in the third dosing interval are different doses. In some embodiments, the dose administered in the second dosing interval and the dose administered in the third dosing interval are the same doses.
  • a dose of genetically engineered bacterium is administered once per day (QD) for at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, or at least 7 days in the first dosing interval, in the second dosing interval, and in the optional third dosing interval.
  • QD once per day
  • a dose of the genetically engineered bacterium is administered twice per day (BID) for at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, or at least 7 days in the first dosing interval, the second dosing interval, and/or the third dosing interval.
  • BID twice per day
  • a dose of the genetically engineered bacterium is administered three times per day (TID) for at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 7 days, or the remainder of days in the first dosing interval, the second dosing interval, and/or the third dosing interval.
  • TID three times per day
  • the first dosing interval, the second dosing interval, and/or the third dosing interval are at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 8 weeks, at least 9 weeks, at least 10 weeks, or at least 11 weeks.
  • the first dosing interval, the second dosing interval, and/or the third dosing interval combined are at least 6 weeks, at least 7 weeks, at least 8 weeks, at least 9 weeks, at least 10 weeks, at least 11 weeks, at least 12 weeks, at least 13 weeks, at least 14 weeks, or at least 15 weeks.
  • the dose of genetically engineered bacterium administered to the subject is: about IxlO 11 cells in the first dosing interval; and about 3xl0 n cells in the second dosing interval.
  • the genetically engineered bacterium administered to the subject in the first dosing interval is a dose of about IxlO 11 cells.
  • the first dosing interval is 21 days in length, and the genetically engineered bacterium is administered to the subject: a. at a dose of about 1 xlO 11 cells once per day for days 1-3; b. at a dose of about IxlO 11 cells twice per day for days 4-6; c. at a dose of about IxlO 11 cells three times per day for days 10-21, as determined by live cell counting.
  • the second dosing interval is 21 days in length, and the genetically engineered bacterium is administered to the subject at a dose of about 3x10 11 cells, as determined by live cell counting: a. once per day for days 1-3; b. twice per day for days 4-7; and c. three times per day for days 8-21.
  • the second dosing interval is 21 days in length
  • the genetically engineered bacterium is administered to the subject at a dose of about 3x10 11 cells, as determined by live cell counting: a. once per day for days 1-3; b. twice per day for days 4-7; and c. three times per day for days 8-21.
  • the first dosing interval is 6 days in length
  • the genetically engineered bacterium is administered to the subject: a. at a dose of about 1 xlO 11 cells once per day for day 1, at a dose of about IxlO 11 cells twice per day for day 2, and at a dose of about IxlO 11 cells three times per day for days 3-6, as determined by live cell counting.
  • the second dosing interval is 6 days in length
  • the genetically engineered bacterium is administered to the subject: a. at a dose of about 3 xlO 11 cells once per day for day 1, at a dose of about 3xl0 n cells twice per day for day 2, and at a dose of about 3xl0 n cells three times per day for days 3-6, as determined by live cell counting.
  • a dose is considered intolerable is a subject experiences Grade 3 or more severe adverse events or Grade 2 gastrointestinal adverse events that do not improve with continued dosing at the same dose over time.
  • the method comprises administering to a subject a first dose of the bacteria for a first dosing interval (e.g., 2, 3, or 4 weeks), followed by a second dose of the bacteria that is higher than the first dose for a second dosing interval (e.g., 2, 3, or 4 weeks). In some embodiments, this is followed by a third dose of the bacteria that is higher than the second dose for a third dosing interval (e.g., 2, 3, or 4 weeks).
  • the subject tolerates the first dose during the first dosing interval, e.g., after 2, 3, or 4 weeks according to the metrics described herein, the subject escalates to the second dose for a second dosing interval. In some embodiments, where the subject does not tolerate the second dose during the second dosing interval, e.g., after 2, 3, or 4 weeks according to the metrics described herein, the subject de- escalates to the first dose. In some embodiments, where the subject tolerates the second dose during the second dosing interval, e.g., after 2, 3, or 4 weeks according to the metrics described herein, the subject escalates to the third dose for the third dosing interval. In some embodiments, where the subject does not tolerate the third dose during the third dosing interval, e.g., after 2, 3, or 4 weeks according to the metrics described herein, the subject de-escalates to the second dose.
  • the subject tolerates the first dose during a first dosing interval of 3 weeks according to the metrics described herein
  • the subject escalates to the second dose for a second dosing interval of 3 weeks.
  • the subject de-escalates to the first dose.
  • the subject tolerates the second dose during the second dosing interval of 3 weeks according to the metrics described herein
  • the subject escalates to the third dose for a third dosing interval of 3 weeks.
  • the subject de-escalates to the second dose.
  • the recombinant bacteria is administered: at a dose of about IxlO 11 live recombinant bacteria once per day for one day to 28 days, one day to 27 days, one day to 26 days, one day to 25 days, one day to 24 days, one day to 23 days, one day to 22 days, one day to 21 days, one day to 20 days, one day to 19 days, one day to 18 days, one day to 17 days, one day to 16 days, one day to 15 days, one day to 14 days, one day to 13 days, one day to 12 days, one day to 11 days, one day to 10 days, one day to 9 days, one day to 8 days, one day to 7 days, one day to 6 days, one day to 5 days, one day to 4 days, one day to 3 days, one day to 2 days, or one day; or at a dose of about IxlO 11 live recombinant bacteria once per day for 1 week to 4 weeks, 1 week to 3 weeks, 1 week to 2 weeks, 1 week, 2 weeks, 3
  • the recombinant bacteria is administered: at a dose of about IxlO 11 live recombinant bacteria twice per day for one day to 28 days, one day to 27 days, one day to 26 days, one day to 25 days, one day to 24 days, one day to 23 days, one day to 22 days, one day to 21 days, one day to 20 days, one day to 19 days, one day to 18 days, one day to 17 days, one day to 16 days, one day to 15 days, one day to 14 days, one day to 13 days, one day to 12 days, one day to 11 days, one day to 10 days, one day to 9 days, one day to 8 days, one day to 7 days, one day to 6 days, one day to 5 days, one day to 4 days, one day to 3 days, one day to 2 days, or one day; or at a dose of about IxlO 11 live recombinant bacteria twice per day for 1 week to 4 weeks, 1 week to 3 weeks, 1 week to 2 weeks, 1 week, 2 weeks, 3
  • the recombinant bacteria is administered: at a dose of about IxlO 11 live recombinant bacteria three times per day for one day to 28 days, one day to 27 days, one day to 26 days, one day to 25 days, one day to 24 days, one day to 23 days, one day to 22 days, one day to 21 days, one day to 20 days, one day to 19 days, one day to 18 days, one day to 17 days, one day to 16 days, one day to 15 days, one day to 14 days, one day to 13 days, one day to 12 days, one day to 11 days, one day to 10 days, one day to 9 days, one day to 8 days, one day to 7 days, one day to 6 days, one day to 5 days, one day to 4 days, one day to 3 days, one day to 2 days, or one day; or at a dose of about IxlO 11 live recombinant bacteria three times per day for 1 week to 4 weeks, 1 week to 3 weeks, 1 week to 2 weeks, 1 week, 2 weeks
  • the recombinant bacteria is administered: at a dose of about 3xl0 n live recombinant bacteria once per day for one day to 28 days, one day to 27 days, one day to 26 days, one day to 25 days, one day to 24 days, one day to 23 days, one day to 22 days, one day to 21 days, one day to 20 days, one day to 19 days, one day to 18 days, one day to 17 days, one day to 16 days, one day to 15 days, one day to 14 days, one day to 13 days, one day to 12 days, one day to 11 days, one day to 10 days, one day to 9 days, one day to 8 days, one day to 7 days, one day to 6 days, one day to 5 days, one day to 4 days, one day to 3 days, one day to 2 days, or one day; or at a dose of about 3x10 11 live recombinant bacteria once per day for 1 week to 4 weeks, 1 week to 3 weeks, 1 week to 2 weeks, 1 week, 2 weeks, 3
  • the recombinant bacteria is administered: at a dose of about 3xl0 n live recombinant bacteria twice per day for one day to 28 days, one day to 27 days, one day to 26 days, one day to 25 days, one day to 24 days, one day to 23 days, one day to 22 days, one day to 21 days, one day to 20 days, one day to 19 days, one day to 18 days, one day to 17 days, one day to 16 days, one day to 15 days, one day to 14 days, one day to 13 days, one day to 12 days, one day to 11 days, one day to 10 days, one day to 9 days, one day to 8 days, one day to 7 days, one day to 6 days, one day to 5 days, one day to 4 days, one day to 3 days, one day to 2 days, or one day; or at a dose of about 3xl0 n live recombinant bacteria twice per day for 1 week to 4 weeks, 1 week to 3 weeks, 1 week to 2 weeks, 1 week, 2 weeks
  • the recombinant bacteria is administered: at a dose of about 3xl0 n live recombinant bacteria three times per day for one day to 28 days, one day to 27 days, one day to 26 days, one day to 25 days, one day to 24 days, one day to 23 days, one day to 22 days, one day to 21 days, one day to 20 days, one day to 19 days, one day to 18 days, one day to 17 days, one day to 16 days, one day to 15 days, one day to 14 days, one day to 13 days, one day to 12 days, one day to 11 days, one day to 10 days, one day to 9 days, one day to 8 days, one day to 7 days, one day to 6 days, one day to 5 days, one day to 4 days, one day to 3 days, one day to 2 days, or one day; or at a dose of about 3xl0 n live recombinant bacteria three times per day for 1 week to 4 weeks, 1 week to 3 weeks, 1 week to 2 weeks, 1 week,
  • the recombinant bacteria is administered: at a dose of about IxlO 11 live recombinant bacteria once, twice or three times a day for 1 week, 2 weeks, 3 weeks, or 4 weeks; and further at a dose of about 3xl0 n live recombinant bacteria once, twice or three times a day for 1 week, 2 weeks, 3 weeks, or 4 weeks.
  • the recombinant bacteria is administered at a dose of about IxlO 11 live recombinant bacteria once per day on day 1 of treatment, at a dose of about IxlO 11 live recombinant bacteria twice per day on day 2 of treatment, at a dose of about IxlO 11 live recombinant bacteria three times per day on each of days 3, 4, 5, and 6 of treatment, at a dose of about 3xl0 n live recombinant bacteria once per day on day 7 of treatment, at a dose of about 3x 10" live recombinant bacteria twice per day on day 8 of treatment, and at a dose of about 3xl0 n live recombinant bacteria three times per day on day 9 of treatment.
  • the bacteria is administered at a dose of about 3xl0 n live recombinant bacteria three times per day on day 10 of treatment and each day after day 10 of treatment.
  • the method further comprising administering a proton pump inhibitor (PPI) to the subject.
  • PPI proton pump inhibitor
  • the PPI is esomeprazole.
  • esomeprazole is administered at 20 mg once daily.
  • esomeprazole is administered at 40 mg once daily.
  • the administering of the PPI is once a day.
  • the pharmaceutical composition further comprises galactose.
  • galactose is D-galactose.
  • a method for reducing the levels of oxalate in a subject comprising administering to the subject a pharmaceutical composition comprising a recombinant bacterium comprising: one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked directly or indirectly to a first promoter that is not associated with the oxalate catabolism enzyme gene in nature, wherein the one or more gene sequences comprise a scaciE3 gene, an frc gene, and an oxdC gene, wherein the scaciE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO: 502, wherein the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises,
  • the bacteria is administered at a dose of about 3xl0 n live recombinant bacteria three times per day on day 10 of treatment. In one embodiment, the bacteria is administered at a dose of about 3xl0 n live recombinant bacteria three times per day on days 10, 11, and 12 of treatment. In one embodiment, the bacteria is further administered at a dose of about 3xl0 n live recombinant bacteria three times per day on each day after day 12 of treatment.
  • the method further comprising administering a proton pump inhibitor (PPI) to the subject.
  • PPI proton pump inhibitor
  • the PPI is esomeprazole.
  • the administering of the PPI is once a day.
  • the pharmaceutical composition further comprises galactose.
  • galactose is D-galactose.
  • the pharmaceutical composition further comprises bicarbonate.
  • FIG. 1 is a figure summarizing the disease pathogenesis of enteric hyperoxaluria.
  • FIG. 2 depicts the components of strain SYNB8802.
  • FIG. 3 depicts a schematic of chromosomal gene modifications of an exemplary oxalate consuming strain, SYNB8802.
  • the oxalate consuming strain may further contain a deletion of the pks island.
  • FIG. 4 depicts a graph showing the largest population-based study on the relationship of urinary oxalate levels and incident CKD to date.
  • the dataset includes 426,896 patients without CKD at baseline and includes 12,522 with GI malabsorption.
  • higher urine oxalate is associated with higher risk of developing incident CKD.
  • the prevalence of CKD was twice as high in patients with UOx > 80 mg/d compared with ⁇ 20 mg/d.
  • the risk is substantially higher among those with an underlying malabsorptive condition.
  • FIG. 5 depicts a schematic showing the path at arriving at a differential diagnosis to enteric hyperoxaluria (EH).
  • FIG. 6 depicts a graph showing the sites of SYNB8802 action, targeting oxalate through the entire GI tract.
  • FIG. 7 depicts a dosing schematic of a randomized, placebo-controlled parallel arm, inpatient study described in Example 2.
  • Primary endpoint safety and tolerability.
  • Controlled diet Standardized dietary oxalate intake (meals contained an average level of oxalate and low calcium, divided over 3 meals a day during in patient stay).
  • Patient population prior Roux-en-Y gastric bypass, with abnormal GI physiology typical of EH.
  • Disposition 11 patients, 7 received SYNB8802 and 4 received placebo, 1 patient discontinued during placebo treatment.
  • Placebo (Pbo) contains bicarbonate. Patients received placebo containing bicarbonate for the first 3 days during a placebo run-in.
  • Dose frequency was QD for day 1. BID for day 2, TID for days 3-6, QD for day 7, BID for day 8, TID for days 9-12.
  • FIG. 8 depicts a graph showing urinary oxalate values during dosing period in a phase lb SYNB8802 study described in Example 2.
  • Urinary oxalate levels at screening were consistent with diet and patient population (at ⁇ 30), and generally remained consistent with baseline values during the treatment period for placebo patients.
  • dose-related reduction in urinary oxalate levels in response to SYNB8802 were observed. This is a pharmacometrics analysis including data from 7 patients receiving SYNB8802 at both the IxlO 11 and 3xl0 n dose levels and 4 patients receiving placebo.
  • FIG. 9A depicts a graph showing a pharmacometric model with estimated percent change from baseline in 24-hour urinary oxalate. Mean percent change (line) ⁇ 95% confidence interval (gray shading).
  • FIG. 10 depicts a graph showing the mean absolute amount of UOx over time based on 24- hour urine collections as performed in a study depicted in FIG. 7.
  • FIG. 11 depicts a graph showing the effect of SYNB8802 on change from baseline (absolute values) in UOx:creatinine ratio over time based on 24-hour urine collections as performed in a study depicted in FIG. 7.
  • Enteric hyperoxaluria is a metabolic disease and well-recognized cause of recurrent kidney stones, typically caused by a chronic underlying GI disorder associated with malabsorption, which predisposes patients to excess oxalate absorption. Elevated oxalate in the circulation leads to oxalate crystal formation in the kidney, causing excruciating pain and progressive renal damage. There is no FDA-approved treatment for enteric hyperoxaluria. SYNB8802 is a novel, orally administered, non-systemically absorbed drug candidate being developed for the treatment of enteric hyperoxaluria, a we 11 -recognized cause of recurrent kidney stones. Enteric hyperoxaluria is caused by oxalate crystals which can damage kidneys, leading to chronic kidney disease (CKD) and end-stage renal disease (ESRD).
  • CKD chronic kidney disease
  • ESRD end-stage renal disease
  • SYNB8802 was designed using precision genetic engineering of the well-characterized probiotic E. coli Nissle to metabolize oxalate in GI tract, preventing its absorption and resultant crystal formation, lowering levels of urinary oxalate.
  • Non-limiting examples are described in International Patent Application PCT/US2022/021748, filed March 24, 2022 the contents of which is herein incorporated by reference in its entirety.
  • Oxalate arises from a variety of dietary and endogenous sources and is considered an endproduct of human metabolism. Under physiological conditions, the absorbed dietary and endogenously produced oxalate is excreted by the kidneys as urinary oxalate (UOx). (Mitchell T, et al. Dietary oxalate and kidney stone formation Am J Physiol Renal Physiol. 2019;316:F409-13). In a healthy person, only a small fraction of ingested oxalate is absorbed. The contribution of endogenous oxalate production and dietary oxalate absorption to UOx is approximately equal in a healthy person( Holmes R, Goodman H, Assimos D.
  • Kidney Int. 2001;59:270-76 An increase in either gastrointestinal (GI) oxalate absorption or hepatic oxalate production increases plasma oxalate (POx) and thus UOx, and contributes to the risk of stone formation and other adverse renal outcomes (Curhan G, Taylor E. 24-h uric acid excretion and the risk of kidney stones. Kidney Int. 2008;73:489-96). Approximately 85% of kidney stones are due to calcium oxalate supersaturation in the urine.
  • GI gastrointestinal
  • POx plasma oxalate
  • Hyperoxaluria may have a genetic or enteric etiology (Table 1).
  • Enteric hyperoxaluria can result from increased gut oxalate absorption, increased oxalate bioavailability from food, decreased intestinal oxalate degradation, decreased intestinal secretion of oxalate, or increased endogenous production of oxalate.
  • dietary calcium forms a complex with oxalate in the gut lumen and renders it insoluble and therefore unavailable for absorption.
  • Diseases of the GI tract leading to fat malabsorption and increased free fatty acids in the gut can lead to increased soluble oxalate in the colon and increased colonic absorption of oxalate by preventing the formation of the calcium-oxalate complex.
  • EH inflammatory bowel disease
  • cystic fibrosis cystic fibrosis
  • short-bowel syndrome chronic biliary or pancreatic pathologies.
  • IBD inflammatory bowel disease
  • IBD inflammatory bowel disease
  • IBD cystic fibrosis
  • short-bowel syndrome chronic biliary or pancreatic pathologies.
  • the prevalence of EH patients with kidney stones in the United States has been estimated to be ⁇ 250,000, with the most frequent underlying malabsorptive enteric conditions being Roux-n-Y (RnY) gastric bypass (>60%) and IBD (20%) (Tasian G, Wade B, Gaebler J, Kausz A, Medicis J, Wyatt C. Prevalence of kidney stones in patients with enteric disorders. Paper presented at American Society of Nephrology Washington, DC, 2019).
  • UOx urinary oxalate
  • treatment for hyperoxaluria is limited to dietary restrictions, including low oxalate diet, calcium supplements, and a change to IBD therapeutics (if applicable). Treatment has modest efficacy and avoids healthy foods (e.g. green vegetables). Calcium supplements can exacerbate hypercalciuria. Treatment is even less effective for enteric hyperoxaluria.
  • the gut microbiota and certain genetic anomalies can also have an impact on oxalate homeostasis.
  • Certain commensal bacterial strains in the human gut microbiome including Oxalobacter spp., Bifidobacterium spp., and Lactobacillus spp., can degrade oxalate and may be capable of modulating intestinal oxalate secretion.
  • Oxalobacter spp. can degrade oxalate and may be capable of modulating intestinal oxalate secretion.
  • inherited defects in the SLC26 family of anion exchangers may predispose individuals to EH (Freel R, et al., Ileal oxalate absorption and urinary oxalate excretion are enhanced in Slc26a6-null mice. Am J Physiol.
  • Adherence to a low oxalate diet for a prolonged time is challenging, due to the presence of oxalate in many foods (e.g., green vegetables, nuts, grains, fruits, chocolate).
  • oxalate in many foods (e.g., green vegetables, nuts, grains, fruits, chocolate).
  • the absorption of oxalate is also increased with the typical Western diet with a high salt, high fat, and low-calcium content.
  • the disclosure includes engineered and programmed microorganisms, e.g., bacteria, yeast, viruses etc., pharmaceutical compositions thereof, and methods of modulating and treating disorders in which oxalate is detrimental.
  • the microorganism e.g., bacterium, yeast, or virus, has been genetically engineered to comprise heterologous gene sequence(s) encoding one or more oxalate catabolism enzyme(s).
  • the microorganism e.g., bacterium, yeast, or virus
  • the engineered microorganism comprises heterologous gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and is capable of transporting oxalic acid and/or oxalate and/or another related metabolite(s) into the bacterium.
  • the recombinant microorganism and pharmaceutical compositions comprising the microorganism of the disclosure may be used to catabolize oxalate or oxalic acid to treat and/or prevent conditions associated with disorders in which oxalate is detrimental.
  • the disorder in which oxalate is detrimental is a disorder involving the abnormal levels of oxalate, such as primary hyperoxalurias (z.e., PHI, PHII, and PHIII), secondary hyperoxaluria, enteric hyperoxaluria, dietary hyperoxaluria, or idiopathic hyperoxaluria.
  • the engineered microorganism comprise gene sequence(s) encoding one or more of the following: (i) one or more transporter(s) of oxalate; (ii) one or more exporter(s) of formate; (iii) one or more polypeptide (s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)); and (iv) any combination thereof.
  • the microorganism has been engineered to comprise gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and one or more of the following: (i) one or more transporter(s) of oxalate; (ii) one or more exporter(s) of formate; (iii) one or more polypeptide(s) which mediate both the transport (import) of oxalate and the export of formate (e.g., oxalate: formate antiporter(s)); and (iv) any combination thereof.
  • microorganism or “recombinant microorganism” refers to a microorganism, e.g., bacterial or viral cell, or bacteria or virus, that has been genetically modified from its native state.
  • a “recombinant bacterial cell” or “recombinant bacteria” refers to a bacterial cell or bacteria that have been genetically modified from their native state.
  • a recombinant bacterial cell may have nucleotide insertions, nucleotide deletions, nucleotide rearrangements, and nucleotide modifications introduced into their DNA.
  • Recombinant bacterial cells disclosed herein may comprise exogenous nucleotide sequences on plasmids.
  • recombinant bacterial cells may comprise exogenous nucleotide sequences stably incorporated into their chromosome.
  • a “programmed or engineered microorganism” refers to a microorganism, e.g. , bacterial or viral cell, or bacteria or virus, that has been genetically modified from its native state to perform a specific function.
  • a “programmed or engineered bacterial cell” or “programmed or engineered bacteria” or “genetically engineered bacterial cell or bacteria” refers to a bacterial cell or bacteria that has been genetically modified from its native state to perform a specific function, e.g., to metabolize a metabolite, e.g., oxalate.
  • the programmed or engineered bacterial cell has been modified to express one or more proteins, for example, one or more proteins that have a therapeutic activity or serve a therapeutic purpose.
  • the programmed or engineered bacterial cell may additionally have the ability to stop growing or to destroy itself once the protein(s) of interest have been expressed.
  • the term “gene” refers to a nucleic acid fragment that encodes a protein or fragment thereof, optionally including regulatory sequences preceding (5’ non-coding sequences) and following (3’ non-coding sequences) the coding sequence. In one embodiment, a “gene” does not include regulatory sequences preceding and following the coding sequence.
  • a “native gene” refers to a gene as found in nature, optionally with its own regulatory sequences preceding and following the coding sequence.
  • a “chimeric gene” refers to any gene that is not a native gene, optionally comprising regulatory sequences preceding and following the coding sequence, wherein the coding sequences and/or the regulatory sequences, in whole or in part, are not found together in nature. Thus, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory and coding sequences that are derived from the same source, but arranged differently than is found in nature.
  • the term “gene sequence” is meant to refer to a genetic sequence, e.g. , a nucleic acid sequence.
  • the gene sequence or genetic sequence is meant to include a complete gene sequence or a partial gene sequence.
  • the gene sequence or genetic sequence is meant to include sequence that encodes a protein or polypeptide and is also meant to include genetic sequence that does not encode a protein or polypeptide, e.g., a regulatory sequence, leader sequence, signal sequence, or other non-protein coding sequence.
  • heterologous gene or heterologous sequence refers to a nucleotide sequence that is not normally found in a given cell in nature.
  • a heterologous sequence encompasses a nucleic acid sequence that is exogenously introduced into a given cell and can be a native sequence (naturally found or expressed in the cell) or non-native sequence (not naturally found or expressed in the cell) and can be a natural or wild-type sequence or a variant, non-natural, or synthetic sequence.
  • “Heterologous gene” includes a native gene, or fragment thereof, that has been introduced into the host cell in a form that is different from the corresponding native gene.
  • a heterologous gene may include a native coding sequence that is a portion of a chimeric gene to include non-native regulatory regions that is reintroduced into the host cell.
  • a heterologous gene may also include a native gene, or fragment thereof, introduced into a non-native host cell.
  • a heterologous gene may be foreign or native to the recipient cell; a nucleic acid sequence that is naturally found in a given cell but expresses an unnatural amount of the nucleic acid and/or the polypeptide which it encodes; and/or two or more nucleic acid sequences that are not found in the same relationship to each other in nature.
  • the term “endogenous gene” refers to a native gene in its natural location in the genome of an organism.
  • the term “transgene” refers to a gene that has been introduced into the host organism, e.g., host bacterial cell, genome.
  • a “non-native” nucleic acid sequence refers to a nucleic acid sequence not normally present in a microorganism, e.g., an extra copy of an endogenous sequence, or a heterologous sequence such as a sequence from a different species, strain, or substrain of bacteria or virus, or a sequence that is modified and/or mutated as compared to the unmodified sequence from bacteria or virus of the same subtype.
  • the non-native nucleic acid sequence is a synthetic, non-naturally occurring sequence (see, e.g., Purcell et al., 2013).
  • the non-native nucleic acid sequence may be a regulatory region, a promoter, a gene, and/or one or more genes in gene cassette.
  • “non-native” refers to two or more nucleic acid sequences that are not found in the same relationship to each other in nature.
  • the non-native nucleic acid sequence may be present on a plasmid or chromosome.
  • the genetically engineered microorganism of the disclosure comprises a gene and/or gene cassette that is operably linked to a promoter that is not associated with said gene in nature.
  • the genetically engineered bacteria disclosed herein comprise a gene or gene cassette encoding one or more oxalate -metabolizing enzyme(s) described herein and/or one or more oxalate transporter(s), one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s)(e.g., oxalate: formate antiporter(s)) that is operably linked to a directly or indirectly inducible promoter that is not associated with said gene in nature, e.g., an FNR responsive one or more oxalate -metabolizing enzyme(s) described herein and/or one or more oxalate transporter(s), one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s)(e.g., oxalate: formate antiporter(s)) (or other promoter disclosed herein) operably linked to a gene encoding
  • the genetically engineered virus of the disclosure comprises a gene or gene cassette that is operably linked to a directly or indirectly inducible promoter that is not associated with said gene or gene cassette in nature, e.g., a promoter operably linked to a gene and/or gene cassette encoding one or more oxalate- metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s)(e.g., oxalate: formate antiporter(s)).
  • a promoter operably linked to a gene and/or gene cassette encoding one or more oxalate- metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s)(e.g., oxalate:
  • coding region refers to a nucleotide sequence that codes for a specific amino acid sequence.
  • regulatory sequence refers to a nucleotide sequence located upstream (5 ’ non-coding sequences), within, or downstream (3 ’ non-coding sequences) of a coding sequence, and which influences the transcription, RNA processing, RNA stability, or translation of the associated coding sequence. Examples of regulatory sequences include, but are not limited to, promoters, translation leader sequences, effector binding sites, signal sequences, and stem-loop structures.
  • the regulatory sequence comprises a promoter, e.g., an FNR responsive promoter or other promoter disclosed herein.
  • “Operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other.
  • a regulatory element is operably linked with a coding sequence when it is capable of affecting the expression of the gene coding sequence, regardless of the distance between the regulatory element and the coding sequence.
  • operably linked refers to a nucleic acid sequence, e.g., a gene or gene cassette encoding one or more an oxalate catabolism enzyme, that is joined to a regulatory sequence in a manner which allows expression of the nucleic acid sequence, e.g., the gene(s) or gene cassettes encoding one or more oxalate catabolism enzyme(s) and/or one or more oxalate transporter(s), one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s)(e.g., oxalate: formate antiporter(s)).
  • the regulatory sequence acts in cis.
  • a gene may be “directly linked” to a regulatory sequence in a manner which allows expression of the gene.
  • a gene may be “indirectly linked” to a regulatory sequence in a manner which allows expression of the gene.
  • two or more genes may be directly or indirectly linked to a regulatory sequence in a manner which allows expression of the two or more genes.
  • a regulatory region or sequence is a nucleic acid that can direct transcription of a gene of interest and may comprise promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, promoter control elements, protein binding sequences, 5' and 3' untranslated regions, transcriptional start sites, termination sequences, polyadenylation sequences, and introns.
  • a “promoter” as used herein refers to a nucleotide sequence that is capable of controlling the expression of a coding sequence or gene. Promoters are generally located 5’ of the sequence that they regulate. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from promoters found in nature, and/or comprise synthetic nucleotide segments. Those skilled in the art will readily ascertain that different promoters may regulate expression of a coding sequence or gene in response to a particular stimulus, e.g., in a cell- or tissue-specific manner, in response to different environmental or physiological conditions, or in response to specific compounds. Prokaryotic promoters are typically classified into two classes: inducible and constitutive. A “constitutive promoter” refers to a promoter that allows for continual transcription of the coding sequence or gene under its control.
  • Constant promoter refers to a promoter that is capable of facilitating continuous transcription of a coding sequence or gene under its control and/or to which it is operably linked.
  • Constitutive promoters and variants are well known in the art and include, but are not limited to, Ptac promoter, BBa_J23100, a constitutive Escherichia coli o s promoter (e.g., an osmY promoter (International Genetically Engineered Machine (iGEM) Registry of Standard Biological Parts Name BBa_J45992; BBa_J45993)), a constitutive Escherichia coli o 32 promoter (e.g., htpG heat shock promoter (BBa_J45504)), a constitutive Escherichia coli o 70 promoter (e.g., lacq promoter (BBa_J54200; BBa_J56015), E.
  • coli CreABCD phosphate sensing operon promoter (BBa_J64951), GlnRS promoter (BBa_K088007), lacZ promoter (BBa Kl 19000; BBa Kl 19001); M13K07 gene I promoter (BBa_M13101); M13K07 gene II promoter (BBa_M13102), M13K07 gene III promoter (BBa_M13103), M13K07 gene IV promoter (BBa_M13104), M13K07 gene V promoter (BBa_M13105), M13K07 gene VI promoter (BBa_M13106), M13K07 gene VIII promoter
  • BBa_M 13108 M 13110 (BBa_M 13110)
  • a constitutive Bacillus subtilis o A promoter e.g. , promoter veg (BBa_K143013), promoter 43 (BBa_K143013), P UaG (BBa_K823000), Pi epA (BBa_K823002), P veg (BBa_K823003)
  • a constitutive Bacillus subtilis o B promoter e.g., promoter etc (BBa_K143010), promoter gsiB (BBa_K143011)
  • a Salmonella promoter e.g., Pspv2 from Salmonella
  • BBa_Kl 12706 Pspv from Salmonella
  • a bacteriophage T7 promoter e.g., T7 promoter (BBa_I712074; BBa_I719005; BBa_J34814; BBa_J64997; BBa Kl 13010; BBa Kl 13011; BBa Kl 13012; BBa_R0085; BBa_R0180; BBa_R0181; BBa_R0182; BBa_R0183; BBa_Z0251; BBa_Z0252; BBa_Z0253)
  • a bacteriophage SP6 promoter e.g., SP6 promoter (BBa_J64998)
  • an “inducible promoter” refers to a regulatory region that is operably linked to one or more genes, wherein expression of the gene(s) is increased in the presence of an inducer of said regulatory region.
  • An “inducible promoter” refers to a promoter that initiates increased levels of transcription of the coding sequence or gene under its control in response to a stimulus or an exogenous environmental condition.
  • a “directly inducible promoter” refers to a regulatory region, wherein the regulatory region is operably linked to a gene and/or gene cassette encoding one or more oxalate- metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s) (e.g., oxalate: formate antiporter(s)), where, in the presence of an inducer of said regulatory region, the protein or polypeptide is expressed.
  • exporter(s) e.g., of formate
  • antiporter(s) e.g., oxalate: formate antiporter(s)
  • an “indirectly inducible promoter” refers to a regulatory system comprising two or more regulatory regions, for example, a first regulatory region that is operably linked to a first gene encoding a first protein, polypeptide, or factor, e.g., a transcriptional regulator, which is capable of regulating a second regulatory region that is operably linked to a second gene, the second regulatory region may be activated or repressed, thereby activating or repressing expression of the second gene.
  • inducible promoter Both a directly inducible promoter and an indirectly inducible promoter are encompassed by “inducible promoter.”
  • exemplary inducible promoters described herein include oxygen level -dependent promoters (e.g., FNR-inducible promoter), promoters induced by inflammation or an inflammatory response (RNS, ROS promoters), and promoters induced by a metabolite that may or may not be naturally present (e.g., can be exogenously added) in the gut, e.g., arabinose and tetracycline.
  • inducible promoters include, but are not limited to, an FNR responsive promoter, a P ara c promoter, a ParaBAD promoter, a PietR promoter, and a Pi aci promoter, each of which are described in more detail herein. Examples of other inducible promoters are provided herein below.
  • stable bacterium is used to refer to a bacterial host cell carrying non-native genetic material, e.g., a gene and/or gene cassette encoding one or more oxalate -metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s)(e.g., oxalate: formate antiporter(s)), which is incorporated into the host genome or propagated on a self-replicating extra-chromosomal plasmid, such that the non-native genetic material is retained, expressed, and propagated.
  • non-native genetic material e.g., a gene and/or gene cassette encoding one or more oxalate -metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/
  • the stable bacterium is capable of survival and/or growth in vitro, e.g., in medium, and/or in vivo, e.g., in the gut.
  • the stable bacterium may be a genetically engineered bacterium comprising a gene and/or gene cassette encoding one or more oxalate -metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s)(e.g., oxalate: formate antiporter(s)), in which the plasmid or chromosome carrying the gene is stably maintained in the bacterium, such that the one or more oxalate -metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s
  • the term “expression” refers to the transcription and stable accumulation of sense (mRNA) or anti-sense RNA derived from a nucleic acid, and/or to translation of an mRNA into a polypeptide.
  • Plasmid refers to an extrachromosomal nucleic acid, e.g., DNA, construct that is not integrated into a bacterial cell’s genome. Plasmids are usually circular and capable of autonomous replication. Plasmids may be low-copy, medium-copy, or high-copy, as is well known in the art. Plasmids may optionally comprise a selectable marker, such as an antibiotic resistance gene, which helps select for bacterial cells containing the plasmid and which ensures that the plasmid is retained in the bacterial cell.
  • a selectable marker such as an antibiotic resistance gene
  • a plasmid disclosed herein may comprise a nucleic acid sequence encoding a heterologous gene, e.g., a gene and/or gene cassette encoding one or more oxalate-metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s) (e.g., oxalate: formate antiporter(s)).
  • the term “transform” or “transformation” refers to the transfer of a nucleic acid fragment into a host bacterial cell, resulting in genetically-stable inheritance. Host bacterial cells comprising the transformed nucleic acid fragment are referred to as “recombinant” or “transgenic” or “transformed” organisms.
  • genetic modification refers to any genetic change.
  • Exemplary genetic modifications include those that increase, decrease, or abolish the expression of a gene, including, for example, modifications of native chromosomal or extrachromosomal genetic material.
  • Exemplary genetic modifications also include the introduction of at least one plasmid, modification, mutation, base deletion, base addition, base substitution, and/or codon modification of chromosomal or extrachromosomal genetic sequence(s), gene over-expression, gene amplification, gene suppression, promoter modification or substitution, gene addition (either single or multi -copy), antisense expression or suppression, or any other change to the genetic elements of a host cell, whether the change produces a change in phenotype or not.
  • Genetic modification can include the introduction of a plasmid, e.g., a plasmid comprising a gene and/or gene cassette encoding one or more oxalate -metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s) (e.g., oxalate: formate antiporter(s)) operably linked to a promoter, into a bacterial cell.
  • a plasmid e.g., a plasmid comprising a gene and/or gene cassette encoding one or more oxalate -metabolizing enzyme(s) and/or one or more oxalate transporter(s) and/or one or more exporter(s) (e.g., of formate) and/or one or more antiporter(s) (e.g., oxalate: formate anti
  • Genetic modification can also involve a targeted replacement in the chromosome, e.g., to replace a native gene promoter with an inducible promoter, regulated promoter, strong promoter, or constitutive promoter. Genetic modification can also involve gene amplification, e.g., introduction of at least one additional copy of a native gene into the chromosome of the cell. Alternatively, chromosomal genetic modification can involve a genetic mutation.
  • the term “genetic mutation” refers to a change or changes in a nucleotide sequence of a gene or related regulatory region that alters the nucleotide sequence as compared to its native or wild-type sequence. Mutations include, for example, substitutions, additions, and deletions, in whole or in part, within the wild-type sequence. Such substitutions, additions, or deletions can be single nucleotide changes (e.g., one or more point mutations), or can be two or more nucleotide changes, which may result in substantial changes to the sequence. Mutations can occur within the coding region of the gene as well as within the non-coding and regulatory sequence of the gene.
  • genetic mutation is intended to include silent and conservative mutations within a coding region as well as changes which alter the amino acid sequence of the polypeptide encoded by the gene.
  • a genetic mutation in a gene coding sequence may, for example, increase, decrease, or otherwise alter the activity (e.g., enzymatic activity) of the gene’s polypeptide product.
  • a genetic mutation in a regulatory sequence may increase, decrease, or otherwise alter the expression of sequences operably linked to the altered regulatory sequence.
  • the term “genetic modification that reduces export of oxalate from the bacterial cell” refers to a genetic modification that reduces the rate of export or quantity of export of an oxalate from the bacterial cell, as compared to the rate of export or quantity of export of oxalate from a bacterial cell not having said modification, e.g., a wild-type bacterial cell.
  • a recombinant bacterial cell having a genetic modification that reduces export of oxalate from the bacterial cell comprises a genetic mutation in a native gene.
  • a recombinant bacterial cell having a genetic modification that reduces export of oxalate from the bacterial cell comprises a genetic mutation in a native promoter, which reduces or inhibits transcription of a gene encoding an oxalate exporter.
  • a recombinant bacterial cell having a genetic modification that reduces export of oxalate from the bacterial cell comprises a genetic mutation leading to overexpression of a repressor of an exporter of oxalate.
  • a recombinant bacterial cell having a genetic modification that reduces export of oxalate from the bacterial cell comprises a genetic mutation which reduces or inhibits translation of the gene encoding the oxalate exporter.
  • the term “genetic modification that increases import of oxalate into the bacterial cell” refers to a genetic modification that increases the uptake rate or increases the uptake quantity of oxalate into the cytosol of the bacterial cell, as compared to the uptake rate or uptake quantity of the oxalate into the cytosol of a bacterial cell not having said modification, e.g., a wild-type bacterial cell.
  • an engineered bacterial cell having a genetic modification that increases import of oxalate into the bacterial cell refers to a bacterial cell comprising a heterologous gene sequence (native or non-native) encoding one or more importer/transporter(s) of oxalate.
  • the genetically engineered bacteria comprising genetic modification that increases import of oxalate into the bacterial cell comprise gene sequence(s) encoding an oxalate transporter or other metabolite transporter or an antiporter, e.g. an oxalate: formate antiporter, that transports oxalate into the bacterial cell.
  • the transporter can be any transporter that assists or allows import of oxalate into the cell.
  • the oxalate transporter is antiporter, e.g. an oxalate: formate antiporter, e.g., OxlT, e.g. from O. formigenes .
  • the engineered bacterial cell contains gene sequence encoding OxlT, e.g. from O. formigenes.
  • the engineered bacteria comprise more than one copy of gene sequence encoding an oxalate transporter, e.g., an oxalate: formate antiporter, e.g., OxlT, e.g. from O. formigenes .
  • the engineered bacteria comprise gene sequence(s) encoding more than one oxalate transporter, e.g., two or more different oxalate transporters.
  • the term “transporter” is meant to refer to a mechanism, e.g. , protein, proteins, or protein complex, for importing a molecule, e.g., amino acid, peptide (di -peptide, tripeptide, polypeptide, etc.), toxin, metabolite, substrate, as well as other biomolecules into the microorganism from the extracellular milieu.
  • a molecule e.g., amino acid, peptide (di -peptide, tripeptide, polypeptide, etc.), toxin, metabolite, substrate, as well as other biomolecules into the microorganism from the extracellular milieu.
  • the term “transporter” also includes antiporters, which can import and export metabolites, e.g. such as oxalate: formate antiporters described herein.
  • the terms “transporter” and “importer” are used equivalently.
  • oxalate refers to the dianion of the formula C2O4 2 .
  • Oxalate is the conjugate base of oxalic acid.
  • oxalic acid refers to a dicarboxylic acid with the chemical formula H2C2O4.
  • exogenous environmental condition or “exogenous environment signal” refers to settings, circumstances, stimuli, or biological molecules under which a promoter described herein is directly or indirectly induced.
  • exogenous environmental conditions is meant to refer to the environmental conditions external to the engineered microorganism, but endogenous or native to the host subject environment.
  • exogenous and endogenous may be used interchangeably to refer to environmental conditions in which the environmental conditions are endogenous to a mammalian body, but external or exogenous to an intact microorganism cell.
  • the exogenous environmental conditions are specific to the gut of a mammal.
  • the exogenous environmental conditions are specific to the upper gastrointestinal tract of a mammal. In some embodiments, the exogenous environmental conditions are specific to the lower gastrointestinal tract of a mammal. In some embodiments, the exogenous environmental conditions are specific to the small intestine of a mammal. In some embodiments, the exogenous environmental conditions are low-oxygen, microaerobic, or anaerobic conditions, such as the environment of the mammalian gut. In some embodiments, exogenous environmental conditions are molecules or metabolites that are specific to the mammalian gut, e.g., propionate. In some embodiments, the exogenous environmental condition is a tissue-specific or disease-specific metabolite or molecule(s).
  • the exogenous environmental condition is specific to a disease, e.g., hyperoxaluria. In some embodiments, the exogenous environmental condition is a low-pH environment.
  • the genetically engineered microorganism of the disclosure comprises a pH-dependent promoter. In some embodiments, the genetically engineered microorganism of the disclosure comprise an oxygen level-dependent promoter. In some aspects, bacteria have evolved transcription factors that are capable of sensing oxygen levels. Different signaling pathways may be triggered by different oxygen levels and occur with different kinetics.
  • oxygen level-dependent promoter or “oxygen level-dependent regulatory region” refers to a nucleic acid sequence to which one or more oxygen level-sensing transcription factors is capable of binding, wherein the binding and/or activation of the corresponding transcription factor activates downstream gene expression.
  • oxygen level-dependent transcription factors include, but are not limited to, FNR (fumarate and nitrate reductase), ANR, and DNR.
  • FNR fluarate and nitrate reductase
  • ANR anaerobic nitrate respiration
  • DNR dissimilatory nitrate respiration regulator
  • a promoter was derived from the E. coll Nissle fumarate and nitrate reductase gene S (finrS) that is known to be highly expressed under conditions of low or no environmental oxygen (Durand and Storz, 2010; Boysen et al, 2010).
  • the PfhrS promoter is activated under anaerobic conditions by the global transcriptional regulator FNR that is naturally found in Nissle. Under anaerobic conditions, FNR forms a dimer and binds to specific sequences in the promoters of specific genes under its control, thereby activating their expression.
  • PfnrS inducible promoter is adopted to modulate the expression of proteins or RNA.
  • PfnrS is used interchangeably in this application as FNRS, fhrs, FNR, P-FNRS promoter and other such related designations to indicate the promoter PfnrS. Table 2. Examples of transcription factors and responsive genes and regulatory regions
  • the exogenous environmental conditions are in the presence or absence of reactive oxygen species (ROS). In other embodiments, the exogenous environmental conditions are the presence or absence of reactive nitrogen species (RNS).
  • exogenous environmental conditions are biological molecules that are involved in the inflammatory response, for example, molecules present in an inflammatory disorder of the gut.
  • the exogenous environmental conditions or signals exist naturally or are naturally absent in the environment in which the recombinant bacterial cell resides. In some embodiments, the exogenous environmental conditions or signals are artificially created, for example, by the creation or removal of biological conditions and/or the administration or removal of biological molecules.
  • the exogenous environmental condition(s) and/or signal(s) stimulates the activity of an inducible promoter.
  • the exogenous environmental condition(s) and/or signal(s) that serves to activate the inducible promoter is not naturally present within the gut of a mammal.
  • the inducible promoter is stimulated by a molecule or metabolite that is administered in combination with the pharmaceutical composition of the disclosure, for example, tetracycline, arabinose, or any biological molecule that serves to activate an inducible promoter.
  • the exogenous environmental condition(s) and/or signal(s) is added to culture media comprising a recombinant bacterial cell of the disclosure.
  • the exogenous environmental condition that serves to activate the inducible promoter is naturally present within the gut of a mammal (for example, low oxygen or anaerobic conditions, or biological molecules involved in an inflammatory response).
  • the loss of exposure to an exogenous environmental condition inhibits the activity of an inducible promoter, as the exogenous environmental condition is not present to induce the promoter (for example, an aerobic environment outside the gut).
  • “Gut” refers to the organs, glands, tracts, and systems that are responsible for the transfer and digestion of food, absorption of nutrients, and excretion of waste.
  • the gut comprises the gastrointestinal (GI) tract, which starts at the mouth and ends at the anus, and additionally comprises the esophagus, stomach, small intestine, and large intestine.
  • the gut also comprises accessory organs and glands, such as the spleen, liver, gallbladder, and pancreas.
  • the upper gastrointestinal tract comprises the esophagus, stomach, and duodenum of the small intestine.
  • the lower gastrointestinal tract comprises the remainder of the small intestine, i.e., the jejunum and ileum, and all of the large intestine, i.e., the cecum, colon, rectum, and anal canal.
  • Bacteria can be found throughout the gut, e.g., in the gastrointestinal tract, and particularly in the intestines.
  • Microorganism refers to an organism or microbe of microscopic, submicroscopic, or ultramicroscopic size that typically consists of a single cell. Examples of microorganisms include bacteria, viruses, parasites, fungi, certain algae, and protozoa.
  • the microorganism is engineered (“engineered microorganism”) to produce one or more therapeutic molecules, e.g., oxalate catabolism enzyme(s).
  • the engineered microorganism is an engineered bacterium.
  • the engineered microorganism is an engineered virus.
  • Non -pathogenic bacteria refer to bacteria that are not capable of causing disease or harmful responses in a host.
  • non-pathogenic bacteria are Gram-negative bacteria.
  • non-pathogenic bacteria are Gram-positive bacteria.
  • non- pathogenic bacteria do not contain lipopolysaccharides (LPS).
  • LPS lipopolysaccharides
  • non-pathogenic bacteria are commensal bacteria.
  • non-pathogenic bacteria examples include, but are not limited to certain strains belonging to the genus Bacillus, Bacteroides, Bifidobacterium, Brevibacteria, Clostridium, Enterococcus, Escherichia coli, Lactobacillus, Lactococcus, Saccharomyces, and Staphylococcus, e.g., Bacillus coagulans, Bacillus subtilis, Bacteroides fragilis, Bacteroides subtilis, Bacteroides thetaiotaomicron, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Clostridium butyricum, Enterococcus faecium, Escherichia coli, Escherichia coli Nissle, Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus casei, Lactobac
  • Non-pathogenic bacteria also include commensal bacteria, which are present in the indigenous microbiota of the gut.
  • the disclosure further includes non-pathogenic Saccharomyces, such as Saccharomyces boulardii.
  • Naturally pathogenic bacteria may be genetically engineered to reduce or eliminate pathogenicity.
  • Probiotic is used to refer to live, non-pathogenic microorganisms, e.g., bacteria, which can confer health benefits to a host organism that contains an appropriate amount of the microorganism.
  • the host organism is a mammal.
  • the host organism is a human.
  • the probiotic bacteria are Gram-negative bacteria.
  • the probiotic bacteria are Gram-positive bacteria. Some species, strains, and/or subtypes of non-pathogenic bacteria are currently recognized as probiotic bacteria.
  • probiotic bacteria examples include, but are not limited to, certain strains belonging to the genus Bifidobacteria, Escherichia coli, Lactobacillus, and Saccharomyces e.g., Bifidobacterium bifidum, Enterococcus faecium, Escherichia coli strain Nissle, Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus paracasei, and Lactobacillus plantarum, and Saccharomyces boulardii (Dinleyici et al. , 2014; U.S. Patent No. 5,589,168; U.S. Patent No. 6,203,797; U.S.
  • the probiotic may be a variant or a mutant strain of bacterium (Arthur et al., 2012; Cuevas-Ramos etal., 2010; Olier et al., 2012; Nougayrede et al., 2006).
  • Non-pathogenic bacteria may be genetically engineered to enhance or improve desired biological properties, e.g., survivability.
  • Non-pathogenic bacteria may be genetically engineered to provide probiotic properties.
  • Probiotic bacteria may be genetically engineered to enhance or improve probiotic properties.
  • auxotroph refers to an organism that requires a specific factor, e.g., an amino acid, a sugar, or other nutrient) to support its growth.
  • An “auxotrophic modification” is a genetic modification that causes the organism to die in the absence of an exogenously added nutrient essential for survival or growth because it is unable to produce said nutrient.
  • essential gene refers to a gene which is necessary to for cell growth and/or survival. Essential genes are described in more detail infra and include, but are not limited to, DNA synthesis genes (such as thyA), cell wall synthesis genes (such as dapA). and amino acid genes (such as serA and metA).
  • module and “treat” and their cognates refer to an amelioration of a disease, disorder, and/or condition, or at least one discernible symptom thereof.
  • modulate and “treat” refer to an amelioration of at least one measurable physical parameter, not necessarily discernible by the patient.
  • modulate and “treat” refer to inhibiting the progression of a disease, disorder, and/or condition, either physically (e.g., stabilization of a discernible symptom), physiologically (e.g., stabilization of a physical parameter), or both.
  • modulate” and “treat” refer to slowing the progression or reversing the progression of a disease, disorder, and/or condition.
  • prevent and its cognates refer to delaying the onset or reducing the risk of acquiring a given disease, disorder and/or condition or a symptom associated with such disease, disorder, and/or condition.
  • Those in need of treatment may include individuals already having a particular medical disease, as well as those at risk of having, or who may ultimately acquire the disease.
  • the need for treatment is assessed, for example, by the presence of one or more risk factors associated with the development of a disease, the presence or progression of a disease, or likely receptiveness to treatment of a subject having the disease.
  • Disorders in which oxalate is detrimental, e.g., a hyperoxaluria may be caused by inborn genetic mutations for which there are no known cures.
  • Diseases can also be secondary to other conditions, e.g., an intestinal disorder.
  • Treating diseases in which oxalate is detrimental may encompass reducing normal levels of oxalate and/or oxalic acid, reducing excess levels of oxalate and/or oxalic acid, or eliminating oxalate, and/or oxalic acid, and does not necessarily encompass the elimination of the underlying disease.
  • the term “catabolism” refers to the cellular uptake of oxalate, and/or degradation of oxalate into its corresponding oxalyl CoA, and/or the degradation of oxalyl CoA formate and carbon dioxide.
  • the cellular uptake of oxalate occurs in the kidney.
  • the cellular uptake occurs in the liver.
  • the cellular uptake of oxalate occurs in the intestinal tract.
  • the cellular uptake of oxalate occurs in the stomach.
  • the cellular uptake is mediated by a SLC26 transporting protein (see Robijn et al. (2011)).
  • the cellular uptake is mediated by the transport protein SLC26A1. In one embodiment, the cellular uptake is mediated by the transport protein SLC26A6. In one embodiment, the cellular uptake of oxalate is mediated by a paracellular transport system. In one embodiment, the cellular uptake of oxalate is mediated by a transcellular transport system.
  • abnormal catabolism refers to a decrease in the rate of cellular uptake of oxalate. In one embodiment, “abnormal catabolism” refers to any condition(s), disorder(s), disease(s), predisposition(s), and/or genetic mutations(s) that result in daily urinary oxalate excretion over 40 mg per 24 hours. In one embodiment, “abnormal catabolism” refers to an inability and/or decreased capacity of an organ and/or system to process and/or mediate the cellular uptake of oxalate.
  • said inability or decreased capacity of an organ and/or system to process and/or mediate the cellular uptake of oxalate is caused by the increased endogenous production of oxalate.
  • increased endogenous production of oxalate results from the absence of, or a deficiency in, the peroxisomal liver enzyme AGT.
  • increased endogenous production of oxalate results from the absence of, or a deficiency in the enzyme GRHPR.
  • increased endogenous production of oxalate results from the absence of, or a deficiency in the enzyme 4-hydroxy-2 -oxoglutarate aldolase.
  • said inability or decreased capacity of an organ and/or system to process and/or mediate the cellular uptake of oxalate is caused by increased absorption of oxalate.
  • said increased absorption of oxalate results from an increased dietary intake of oxalate.
  • said increased absorption of oxalate results from increased intestinal absorption of oxalate.
  • said increased absorption of oxalate results from excessive intake of oxalate precursors.
  • said increased absorption of oxalate results from a decrease in intestinal oxalate-degrading microorganisms.
  • said increased absorption of oxalate results from genetic variations of intestinal oxalate transporters.
  • a “disorder in which oxalate is detrimental” is a disease or disorder involving the abnormal, e.g., increased, levels of oxalate and/or oxalic acid or molecules directly upstream, such as glyoxylate.
  • the disorder in which oxalate is detrimental is a disorder or disease in which hyperoxaluria is observed in the subject.
  • the disorder in which oxalate is detrimental refers to any condition(s), disorder(s), disease(s), predisposition(s), and/or genetic mutations(s) that result in daily urinary oxalate excretion over 40 mg per 24 hours.
  • the disorder in which oxalate is detrimental is a disorder or disease selected from the group consisting of: PHI, PHII, PHII, secondary hyperoxaluria, enteric hyperoxaluria, syndrome of bacterial overgrowth, Crohn’s disease, inflammatory bowel disease, hyperoxaluria following renal transplantation, hyperoxaluria after a jejunoileal bypass for obesity, hyperoxaluria after gastric ulcer surgery, chronic mesenteric ischemia, gastric bypass, cystic fibrosis, short bowel syndrome, biliary/pancreatic diseases (e.g., chronic pancreatitis).
  • PHI a disorder or disease selected from the group consisting of: PHI, PHII, PHII, secondary hyperoxaluria, enteric hyperoxaluria, syndrome of bacterial overgrowth, Crohn’s disease, inflammatory bowel disease, hyperoxaluria following renal transplantation, hyperoxaluria after a jejunoileal bypass for obesity, hyperoxaluria after gastric ulcer surgery, chronic
  • a "pharmaceutical composition” refers to a preparation of genetically engineered microorganism of the disclosure, e.g., genetically engineered bacteria or virus, with other components such as a physiologically suitable carrier and/or excipient.
  • the pharmaceutical composition is a frozen liquid composition.
  • the pharmaceutical composition is a lyophilized composition.
  • physiologically acceptable carrier and “pharmaceutically acceptable carrier” which may be used interchangeably refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered bacterial or viral compound.
  • An adjuvant is included under these phrases.
  • excipient refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient.
  • examples include, but are not limited to, calcium bicarbonate, sodium bicarbonate calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils, polyethylene glycols, and surfactants, including, for example, polysorbate 20.
  • terapéuticaally effective dose and “therapeutically effective amount” are used to refer to an amount of a compound that results in prevention, delay of onset of symptoms, or amelioration of symptoms of a condition, e.g., a disorder in which oxalate is detrimental.
  • a therapeutically effective amount may, for example, be sufficient to treat, prevent, reduce the severity, delay the onset, and/or reduce the risk of occurrence of one or more symptoms of a disease or condition associated with daily urinary oxalate excretion over 40 mg per 24 hours.
  • a therapeutically effective amount, as well as a therapeutically effective frequency of administration can be determined by methods known in the art and discussed below.
  • bacteriostatic or “cytostatic” refers to a molecule or protein which is capable of arresting, retarding, or inhibiting the growth, division, multiplication or replication of recombinant bacterial cell of the disclosure.
  • bactericidal refers to a molecule or protein which is capable of killing the recombinant bacterial cell of the disclosure.
  • toxin refers to a protein, enzyme, or polypeptide fragment thereof, or other molecule which is capable of arresting, retarding, or inhibiting the growth, division, multiplication or replication of the recombinant bacterial cell of the disclosure, or which is capable of killing the recombinant bacterial cell of the disclosure.
  • the term “toxin” is intended to include bacteriostatic proteins and bactericidal proteins.
  • the term “toxin” is intended to include, but not limited to, lytic proteins, bacteriocins (e.g., microcins and colicins), gyrase inhibitors, polymerase inhibitors, transcription inhibitors, translation inhibitors, DNases, and RNases.
  • anti-toxin refers to a protein or enzyme which is capable of inhibiting the activity of a toxin.
  • anti -toxin is intended to include, but not limited to, immunity modulators, and inhibitors of toxin expression. Examples of toxins and antitoxins are known in the art and described in more detail infra.
  • oxalate catabolic or catabolism enzyme or “oxalate catabolic or catabolism enzyme” or “oxalate metabolic enzyme” refers to any enzyme that is capable of metabolizing oxalate or capable of reducing accumulated oxalate or that can lessen, ameliorate, or prevent one or more diseases, or disease symptoms in which oxalate is detrimental.
  • oxalate enzymes include, but are not limited to, formyl -CoA: oxalate CoA-transferase (also called formyl -CoA transferase), e.g., Frc from O. formigenes.
  • oxalyl-CoA synthetase also called oxalate- CoA ligase
  • Saccharomyces cerevisiae acyl-activating enzyme 3 ScAAE3 from Saccharomyces cerevisiae
  • Oxalyl-CoA Decarboxylase e.g., Oxc from O. formigenes (also referred to herein is oxdC or oxalate decarboxylase)
  • acetyl-CoA: oxalate CoA-transferase (ACOCT) e.g., YfdE from E.
  • Catabolism enzymes also include alanine glyoxalate aminotransferase (AGT, encoded by the AGXT gene, e.g.
  • glyoxylate/hydroxypyruvate reductase GRHPR; an enzyme having glyoxylate reductase (GR), hydroxypyruvate reductase (HPR), and D-glycerate dehydrogenase (DGDH) activities, e.g., the human form
  • DGDH D-glycerate dehydrogenase
  • 4-hydroxy 2 -oxoglutarate aldolase encoded by the HOGA1 gene, e.g. in humans, and which breaks down 4-hydroxy 2 -oxoglutarate into pyruvate and glyoxalate.
  • Functional deficiencies in these proteins result in the accumulation of oxalate or its corresponding a-keto acid in cells and tissues.
  • Oxalate metabolic enzymes of the present disclosure include both wild-type or modified oxalate metabolic enzymes and can be produced using recombinant and synthetic methods or purified from nature sources.
  • Oxalate metabolic enzymes include full-length polypeptides and functional fragments thereof, as well as homologs and variants thereof, oxalate metabolic enzymes include polypeptides that have been modified from the wild-type sequence, including, for example, polypeptides having one or more amino acid deletions, insertions, and/or substitutions and may include, for example, fusion polypeptides and polypeptides having additional sequence, e.g., regulatory peptide sequence, linker peptide sequence, and other peptide sequence.
  • conventional hyperoxaluria treatment or “conventional hyperoxaluria therapy” refers to treatment or therapy that is currently accepted, considered current standard of care, and/or used by most healthcare professionals for treating a disease or disorders in which oxalate is detrimental. It is different from alternative or complementary therapies, which are not as widely used.
  • polypeptide includes “polypeptide” as well as “polypeptides,” and refers to a molecule composed of amino acid monomers linearly linked by amide bonds (z. e. , peptide bonds).
  • polypeptide refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product.
  • polypeptides include peptides, “dipeptides,” “tripeptides, “oligopeptides,” “protein,” “amino acid chain,” or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of “polypeptide,” and the term “polypeptide” may be used instead of, or interchangeably with any of these terms.
  • polypeptide is also intended to refer to the products of post-expression modifications of the polypeptide, including but not limited to glycosylation, acetylation, phosphorylation, amidation, derivatization, proteolytic cleavage, or modification by non-naturally occurring amino acids.
  • a polypeptide may be derived from a natural biological source or produced by recombinant technology.
  • polypeptide is produced by the genetically engineered bacteria or virus of the current disclosure.
  • a polypeptide of the disclosure may be of a size of about 3 or more, 5 or more, 10 or more, 20 or more, 25 or more, 50 or more, 75 or more, 100 or more, 200 or more, 500 or more, 1,000 or more, or 2,000 or more amino acids.
  • Polypeptides may have a defined three-dimensional structure, although they do not necessarily have such structure. Polypeptides with a defined three- dimensional structure are referred to as folded, and polypeptides, which do not possess a defined three-dimensional structure, but rather can adopt a large number of different conformations, are referred to as unfolded.
  • peptide or “polypeptide” may refer to an amino acid sequence that corresponds to a protein or a portion of a protein or may refer to an amino acid sequence that corresponds with non-protein sequence, e.g., a sequence selected from a regulatory peptide sequence, leader peptide sequence, signal peptide sequence, linker peptide sequence, and other peptide sequence.
  • polypeptide or a fragment, variant, or derivative thereof refers to a polypeptide that is not in its natural milieu. No particular level of purification is required.
  • Recombinantly produced polypeptides and proteins expressed in host cells including but not limited to bacterial or mammalian cells, are considered isolated for purposed of the disclosure, as are native or recombinant polypeptides which have been separated, fractionated, or partially or substantially purified by any suitable technique.
  • Recombinant peptides, polypeptides or proteins refer to peptides, polypeptides or proteins produced by recombinant DNA techniques, i.e.
  • fragments include polypeptides having an amino acid sequence sufficiently similar to the amino acid sequence of the original peptide and include any polypeptides, which retain at least one or more properties of the corresponding original polypeptide.
  • Fragments of polypeptides of the present disclosure include proteolytic fragments, as well as deletion fragments.
  • Fragments also include specific antibody or bioactive fragments or immunologically active fragments derived from any polypeptides described herein. Variants may occur naturally or be non-naturally occurring. Non-naturally occurring variants may be produced using mutagenesis methods known in the art. Variant polypeptides may comprise conservative or non-conservative amino acid substitutions, deletions or additions.
  • Polypeptides also include fusion proteins.
  • the term “variant” includes a fusion protein, which comprises a sequence of the original peptide or sufficiently similar to the original peptide.
  • the term “fusion protein” refers to a chimeric protein comprising amino acid sequences of two or more different proteins. Typically, fusion proteins result from well known in vitro recombination techniques. Fusion proteins may have a similar structural function (but not necessarily to the same extent), and/or similar regulatory function (but not necessarily to the same extent), and/or similar biochemical function (but not necessarily to the same extent) and/or immunological activity (but not necessarily to the same extent) as the individual original proteins which are the components of the fusion proteins.
  • “Derivatives” include but are not limited to peptides, which contain one or more naturally occurring amino acid derivatives of the twenty standard amino acids. “Similarity” between two peptides is determined by comparing the amino acid sequence of one peptide to the sequence of a second peptide. An amino acid of one peptide is similar to the corresponding amino acid of a second peptide if it is identical or a conservative amino acid substitution. Conservative substitutions include those described in Dayhoff, M. O., ed., The Atlas of Protein Sequence and Structure 5, National Biomedical Research Foundation, Washington, D.C. (1978), and in Argos, EMBO J. 8 (1989), 779-785.
  • amino acids belonging to one of the following groups represent conservative changes or substitutions: -Ala, Pro, Gly, Gin, Asn, Ser, Thr; - Cys, Ser, Tyr, Thr; -Vai, He, Leu, Met, Ala, Phe; -Lys, Arg, His; -Phe, Tyr, Trp, His; and -Asp, Glu.
  • the term “sufficiently similar” means a first amino acid sequence that contains a sufficient or minimum number of identical or equivalent amino acid residues relative to a second amino acid sequence such that the first and second amino acid sequences have a common structural domain and/or common functional activity.
  • amino acid sequences that comprise a common structural domain that is at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100%, identical are defined herein as sufficiently similar.
  • variants will be sufficiently similar to the amino acid sequence of the peptides of the disclosure. Such variants generally retain the functional activity of the peptides of the present disclosure.
  • Variants include peptides that differ in amino acid sequence from the native and wt peptide, respectively, by way of one or more amino acid deletion(s), addition(s), and/or substitution(s). These may be naturally occurring variants as well as artificially designed ones.
  • linker refers to synthetic or non-native or non-naturally-occurring amino acid sequences that connect or link two polypeptide sequences, e.g., that link two polypeptide domains.
  • synthetic refers to amino acid sequences that are not naturally occurring. Exemplary linkers are described herein. Additional exemplary linkers are provided in US 20140079701, the contents of which are herein incorporated by reference in its entirety.
  • codon-optimized refers to the modification of codons in the gene or coding regions of a nucleic acid molecule to reflect the typical codon usage of the host organism without altering the polypeptide encoded by the nucleic acid molecule. Such optimization includes replacing at least one, or more than one, or a significant number, of codons with one or more codons that are more frequently used in the genes of the host organism.
  • a “codon-optimized sequence” refers to a sequence, which was modified from an existing coding sequence, or designed, for example, to improve translation in an expression host cell or organism of a transcript RNA molecule transcribed from the coding sequence, or to improve transcription of a coding sequence.
  • Codon optimization includes, but is not limited to, processes including selecting codons for the coding sequence to suit the codon preference of the expression host organism. Many organisms display a bias or preference for use of particular codons to code for insertion of a particular amino acid in a growing polypeptide chain. Codon preference or codon bias, differences in codon usage between organisms, is allowed by the degeneracy of the genetic code, and is well documented among many organisms. Codon bias often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, inter alia, the properties of the codons being translated and the availability of particular transfer RNA (tRNA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization.
  • mRNA messenger RNA
  • tRNA transfer RNA
  • the phrase “and/or,” when used between elements in a list, is intended to mean either (1) that only a single listed element is present, or (2) that more than one element of the list is present.
  • “A, B, and/or C” indicates that the selection may be A alone; B alone; C alone; A and B; A and C; B and C; or A, B, and C.
  • the phrase “and/or” may be used interchangeably with “at least one of’ or “one or more of’ the elements in a list.
  • Ranges provided herein are understood to be shorthand for all of the values within the range.
  • a range of 1 to 50 is understood to include any number, combination of numbers, or subrange from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
  • the genetically engineered microorganisms, or programmed microorganisms, such as genetically engineered bacteria of the disclosure are capable of producing one or more enzymes for metabolizing an oxalate and/or a metabolite thereof.
  • the disclosure provides a bacterial cell that comprises one or more heterologous gene sequence(s) encoding an oxalate catabolism enzyme or other protein that results in a decrease in oxalate levels.
  • the genetically engineered bacteria are obligate anaerobic bacteria. In certain embodiments, the genetically engineered bacteria are facultative anaerobic bacteria. In certain embodiments, the genetically engineered bacteria are aerobic bacteria. In some embodiments, the genetically engineered bacteria are Gram-positive bacteria. In some embodiments, the genetically engineered bacteria are Gram -positive bacteria and lack LPS. In some embodiments, the genetically engineered bacteria are Gram-negative bacteria. In some embodiments, the genetically engineered bacteria are Gram-positive and obligate anaerobic bacteria. In some embodiments, the genetically engineered bacteria are Gram-positive and facultative anaerobic bacteria. In some embodiments, the genetically engineered bacteria are non-pathogenic bacteria.
  • the genetically engineered bacteria are commensal bacteria. In some embodiments, the genetically engineered bacteria are probiotic bacteria. In some embodiments, the genetically engineered bacteria are naturally pathogenic bacteria that are modified or mutated to reduce or eliminate pathogenicity.
  • Exemplary bacteria include, but are not limited to, Bacillus, Bacteroides, Bifidobacterium, Brevibacteria, Caulobacter, Clostridium, Enterococcus, Escherichia coli, Lactobacillus, Lactococcus, Listeria, Mycobacterium, Saccharomyces, Salmonella, Staphylococcus, Streptococcus, Vibrio, Bacillus coagulans, Bacillus subtilis, Bacteroides fragilis, Bacteroides subtilis, Bacteroides thetaiotaomicron, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve UCC2003, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Clostridium acetobutylicum, Clostridium butyricum, Clostridium butyricum M-55,
  • the genetically engineered bacteria are selected from the group consisting of Enterococcus faecium, Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus johnsonii, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Lactococcus lactis, and Oxalobacter formigenes bacterial cell. Saccharomyces boulardii.
  • the genetically engineered bacteria are selected from Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides subtilis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium lactis, Clostridium butyricum, Escherichia coli, Escherichia coli Nissle, Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus reuteri, and Lactococcus lactis bacterial cell.
  • the bacterial cell is a Bacteroides fragilis bacterial cell.
  • the bacterial cell is a Bacteroides thetaiotaomicron bacterial cell. In one embodiment, the bacterial cell is a Bacteroides subtilis bacterial cell. In one embodiment, the bacterial cell is a Bifidobacterium bifidum bacterial cell. In one embodiment, the bacterial cell is a Bifidobacterium infantis bacterial cell. In one embodiment, the bacterial cell is a Bifidobacterium lactis or B. infantis bacterial cell. In one embodiment, the bacterial cell is a Clostridium butyricum bacterial cell. In one embodiment, the bacterial cell is an Escherichia coli bacterial cell.
  • the bacterial cell is a Lactobacillus acidophilus bacterial cell. In one embodiment, the bacterial cell is a Lactobacillus plantarum bacterial cell. In one embodiment the bacterial cell is a Bifidobacterium lactis bacterial cell. In one embodiment, the bacterial cell is a Clostridium butyricum bacterial cell. In one embodiment, the bacterial cell is an Escherichia coli bacterial cell. In one embodiment, the bacterial cell is a Lactobacillus acidophilus bacterial cell. In one embodiment, the bacterial cell is a Lactobacillus plantarum bacterial cell. In one embodiment, the bacterial cell is a Lactobacillus reuteri bacterial cell.
  • the bacterial cell is a Lactococcus lactis bacterial cell. In one embodiment, the bacterial cell is a Oxalobacter formigenes bacterial cell. In another embodiment, the bacterial cell does not include Oxalobacter formigenes.
  • the genetically engineered bacteria are Escherichia coli strain Nissle 1917 (E. coli Nissle), a Gram -negative bacterium of the Enterobacteriaceae family that has evolved into one of the best characterized probiotics (Ukena et al. , 2007).
  • the strain is characterized by its complete harmlessness (Schultz, 2008), and has GRAS (generally recognized as safe) status (Reister et al., 2014, emphasis added).
  • Genomic sequencing confirmed that E. coli Nissle lacks prominent virulence factors (e.g., E. coli a-hemolysin, P-fimbrial adhesins) (Schultz, 2008).
  • E. coli Nissle does not carry pathogenic adhesion factors, does not produce any enterotoxins or cytotoxins, is not invasive, and not uropathogenic (Sonnenbom et al. , 2009).
  • E. coli Nissle was packaged into medicinal capsules, called Mutaflor, for therapeutic use.
  • E. coli Nissle has since been used to treat ulcerative colitis in humans in vivo (Rembacken et al.
  • the recombinant bacterial cell of the disclosure does not colonize the subject having the disorder in which oxalate is detrimental.
  • genes from one or more different species can be introduced into one another, e.g., an oxalate catabolism gene from Lactococcus lactis can be expressed in Escherichia coli. Unmodified E. coli Nissle and the genetically engineered bacteria of the disclosure may be destroyed, e.g., by defense factors in the gut or blood serum (Sonnenbom et al. , 2009).
  • the residence time is calculated for a human subject.
  • residence time in vivo is calculated for the genetically engineered bacteria disclosed herein.
  • the bacterial cell is a genetically engineered bacterial cell. In another embodiment, the bacterial cell is a recombinant bacterial cell. In some embodiments, the disclosure comprises a colony of bacterial cells disclosed herein.
  • the disclosure provides a recombinant bacterial culture which comprises bacterial cells disclosed herein.
  • the disclosure provides a recombinant bacterial culture which reduces levels of oxalate or oxalic acid in the media of the culture.
  • the levels of the oxalate or oxalic acid are reduced by about 50%, about 75%, or about 100% in the media of the cell culture after a period of time, e.g., 1 hour, e.g., under inducing conditions.
  • the levels of the oxalate or oxalic acid are reduced by about two-fold, three-fold, fourfold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, or ten-fold in the media of the cell culture after a period of time, e.g., 1 hour, e.g., under inducing conditions. In one embodiment, the levels of the oxalate or oxalic acid are reduced below the limit of detection in the media of the cell culture. [0248] In some embodiments of the above described genetically engineered bacteria, the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a plasmid in the bacterium.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a plasmid in the bacterium and operatively linked on the plasmid to a promoter that is induced under low-oxygen or anaerobic conditions, such as any of the promoters disclosed herein.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present in the bacterial chromosome.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present in the bacterial chromosome and is operatively linked in the chromosome to the promoter that is induced under low-oxygen or anaerobic conditions, such as any of the promoters disclosed herein.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a plasmid in the bacterium and operatively linked on the plasmid to the promoter that is induced under inflammatory conditions, such as any of the promoters disclosed herein.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present in the bacterial chromosome and is operatively linked in the chromosome to the promoter that is induced under inflammatory conditions, such as any of the promoters disclosed herein.
  • the genetically engineered bacteria comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) further comprise gene sequence(s) encoding an oxalate transporter. In some embodiments, the genetically engineered bacteria comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) further comprise gene sequence(s) encoding a formate exporter. In some embodiments, the genetically engineered bacteria comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) further comprise gene sequence(s) encoding an oxalate: formate antiporter.
  • the genetically engineered bacteria comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) further comprise gene sequence(s) encoding one or more of the following: an oxalate transporter, a formate exporter, and/or an oxalate: formate antiporter.
  • the genetically engineered bacteria comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter, and/or formate exporter, and/or oxalate: formate antiporter is an auxotroph.
  • the genetically engineered bacteria is an auxotroph selected from a cysE, glnA, ilvD, leuB, lysA, serA, metA, glyA, hisB, ilvA, pheA, proA, thrC, trpC, tyrA, thyA, uraA, dapA, dapB, dapD, dapE, dapF, flhD, metB, metC, proAB, and thi l auxotroph.
  • the engineered bacteria have more than one auxotrophy, for example, they may be a tdhyA and dapA auxotroph.
  • the genetically engineered bacteria comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter, and/or formate exporter, and/or oxalate: formate antiporter further comprise gene sequence(s) encoding a secretion protein or protein complex for secreting a biomolecule, such as any of the secretion systems disclosed herein.
  • the genetically engineered bacteria comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter, and/or formate exporter, and/or oxalate: formate antiporter further comprise gene sequence(s) encoding one or more antibiotic gene(s), such as any of the antibiotic genes disclosed herein.
  • the genetically engineered bacteria comprising a gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter, and/or formate exporter, and/or oxalate: formate antiporter further comprise a kill-switch circuit, such as any of the kill-switch circuits provided herein.
  • the genetically engineered bacteria further comprise one or more genes encoding one or more recombinase(s) under the control of an inducible promoter, and an inverted toxin sequence.
  • the genetically engineered bacteria further comprise one or more genes encoding an antitoxin.
  • the engineered bacteria further comprise one or more genes encoding one or more recombinase(s) under the control of an inducible promoter and one or more inverted excision genes, wherein the excision gene(s) encode an enzyme that deletes an essential gene.
  • the genetically engineered bacteria further comprise one or more genes encoding an antitoxin.
  • the engineered bacteria further comprise one or more genes encoding a toxin under the control of a promoter having a TetR repressor binding site and a gene encoding the TetR under the control of an inducible promoter that is induced by arabinose, such as P ara BAD.
  • the genetically engineered bacteria further comprise one or more genes encoding an antitoxin.
  • the genetically engineered bacteria is an auxotroph comprising the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and further comprises a kill-switch circuit, such as any of the kill-switch circuits described herein.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a plasmid in the bacterium. In some embodiments, the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present in the bacterial chromosome. In some embodiments, the genetically engineered bacteria comprise one or more gene and/or gene cassette(s) encoding one or more oxalate transporter(s) that transports oxalate into the bacterial cell. In some embodiments, the gene sequence(s) encoding an oxalate transporter is present on a plasmid in the bacterium.
  • the gene sequence(s) encoding an oxalate transporter is present in the bacterial chromosome.
  • the gene sequence encoding a secretion protein or protein complex for secreting a biomolecule is present on a plasmid in the bacterium.
  • the gene sequence encoding a secretion protein or protein complex for secreting a biomolecule is present in the bacterial chromosome.
  • the gene sequence(s) encoding an antibiotic resistance gene is present on a plasmid in the bacterium.
  • the gene sequence(s) encoding an antibiotic resistance gene is present in the bacterial chromosome.
  • O. formi genes was the first oxalate-degrading obligate anaerobe to be described in humans and has served as the paradigm organism in which anaerobic oxalate degradation has been studied.
  • O. formigenes has three enzymes involved in the catabolism of oxalic acid.
  • First extracellular oxalate is taken up by the membrane-associated oxalate-formate antiporter, OxlT, encoded by the oxlT gene.
  • the fire gene encodes fbrmyl-CoA transferase, Frc, which activates the intracellular oxalate to form oxalyl-CoA.
  • oxalate catabolism enzyme refers to an enzyme involved in the catabolism of oxalate to its corresponding oxalyl-CoA molecule, the catabolism of oxalyl-CoA to formate and carbon dioxide, or the catabolism of oxalate to another metabolite.
  • Enzymes involved in the catabolism of oxalate are well known to those of skill in the art.
  • the formyl coenzyme A transferase FRC encoded by the frc gene
  • transfers a coenzyme A moiety to oxalic acid, forming oxalyl-CoA see, e.g., Sidhu et al., J. Bacterial. 179: 3378-81 (1997), the entire contents of which are expressly incorporated herein by reference).
  • the oxalyl -CoA is subject to a reaction mediated by the oxalyl-CoA decarboxylase OXC (encoded by the oxc gene), which leads to the formation of formate and carbon dioxide (see, e.g., Lung et al., J. Bacterial. 176: 2468-72 (1994), the entire contents of which are expressly incorporated herein by reference).
  • OXC encoded by the oxc gene
  • E0SNC8 are a formyl-CoA transferase and an oxalyl-CoA decarboxylase that have been shown to be functional homologs of the O. formigenes FRC and OXC enzymes (see, e.g., Toyota et al., J. Bact. 190: 2256-64 (2008); Werther et al., FEBSJ. 277: 2628-40 (2010); Fontenot et al., J. Bact. 195: 1446-55 (2013)).
  • acetyl-CoA:oxalate CoA-transferase converts acetyl- CoA and oxalate to oxalyl-CoA and acetate.
  • the acetyl-CoA: oxalate CoA- transferase is YfdE from E. coli (e.g., described in Function and X-ray crystal structure of Escherichia coli YfdE; PLoS One. 2013 Jul 23 ;8(7):e67901).
  • Acetyl-CoA substrate a very ubiquitous metabolite in bacteria, such as E.
  • coli, and acetate produced can for example diffuse into the extracellular space without the need of a transporter.
  • acetyl-CoA:oxalate CoA-transferase reaction can be followed by oxalyl-CoA decarboxylase OXC (encoded by the oxc gene), which leads to the formation of formate and carbon dioxide.
  • Formate can exit the cell, for example through a formate exporter, including but not limited to, OxlT from O. formigenes .
  • OCL oxalyl-CoA synthetase
  • OCL oxalyl-CoA synthetase
  • oxalate-CoA ligase is Saccharomyces cerevisiae acyl- activating enzyme 3 (ScAAE3) (e.g., described in Foster and Nakata, An oxalyl-CoA synthetase is important for oxalate metabolism in Saccharomyces cerevisiae. FEBS Lett.
  • oxalate-CoA ligase can be followed by oxalyl-CoA decarboxylase OXC (encoded by the oxc gene), which leads to the formation of formate and carbon dioxide.
  • Formate can exit the cell, for example through a formate exporter, including but not limited to, OxlT from O. formigenes .
  • the genetically engineered bacteria of the disclosure comprise one or more gene(s) and/or gene cassette(s) encoding at least one oxalate catabolism enzyme.
  • the engineered bacteria comprise one or more gene(s) and/or gene cassette(s) encoding at least one oxalate catabolism enzyme and are capable of converting oxalate into oxalyl-CoA.
  • the engineered bacteria comprise one or more gene(s) and/or gene cassette(s) encoding at least one oxalate catabolism enzyme and are capable of converting oxalyl-CoA into formate and carbon dioxide.
  • the engineered bacteria comprise one or more gene(s) and/or gene cassette(s) encoding at least one oxalate catabolism enzyme and are capable of converting oxalate into oxalyl-CoA, and oxalyl-CoA into formate and carbon dioxide.
  • the engineered bacteria of the disclosure comprise one or more gene(s) and or gene cassette encoding one or more oxalate catabolism enzyme(s) which convert oxalate and formyl CoA into oxalyl-CoA and formate.
  • the engineered bacteria of the disclosure comprise one or more gene(s) and/or gene cassette(s) encoding one or more oxalate catabolism enzyme(s) which convert oxalate and acetyl-coA into oxalyl-CoA and acetate. In some embodiments, the engineered bacteria of the disclosure comprise one or more gene(s) and/or gene cassette(s) encoding one or more oxalate catabolism enzyme(s) which convert oxalate and CoA into oxalyl-CoA (e.g., by converting one ATP to AMP plus diphosphate).
  • the engineered bacteria of the disclosure comprise one or more gene(s) and/or gene cassette(s) encoding one or more oxalate catabolism enzyme(s) which convert oxalyl-CoA to carbon dioxide and formyl-CoA.
  • the engineered bacteria produce formate as a result of oxalate catabolism.
  • the engineered bacteria produce formate and carbon dioxide as a result of oxalate catabolism.
  • the engineered bacteria produce acetate as a result of oxalate catabolism.
  • the engineered bacteria produce acetate and carbon dioxide as a result of oxalate catabolism.
  • the engineered bacteria produce formate, acetate, and carbon dioxide as a result of oxalate catabolism.
  • the genetically engineered bacteria comprise gene sequence(s) encoding one or more oxalate catabolism enzyme (s).
  • the one or more oxalate catabolism enzyme(s) increases the rate of oxalate and/or oxalyl-CoA catabolism in the cell.
  • the one or more oxalate catabolism enzyme(s) decreases the level of oxalate in the cell.
  • the one or more oxalate catabolism enzyme(s) decreases the level of oxalyl- CoA in the cell.
  • the one or more oxalate catabolism enzyme(s) decreases the level of oxalic acid in the cell.
  • the one or more oxalate catabolism enzyme(s) increases the level of oxalyl -CoA in the cell as compared to the level of its corresponding oxalate in the cell. In some embodiments, the one or more oxalate catabolism enzyme(s) increases the level of formate and carbon dioxide in the cell as compared to the level of its corresponding oxalyl -CoA in the cell. In some embodiments, the one or more oxalate catabolism enzyme(s) decreases the level of the oxalate and/or oxalyl CoA as compared to the level of oxalate in the cell.
  • Enzymes involved in the catabolism of oxalate may be expressed or modified in the bacteria of the disclosure in order to enhance catabolism of oxalate. Specifically, when at least one oxalate catabolism enzyme is expressed in the engineered bacterial cells of the disclosure, the engineered bacterial cells convert more oxalate into oxalyl-CoA, or convert more oxalyl-CoA into formate and carbon dioxide when the catabolism enzyme is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the genetically engineered bacteria comprising a heterologous gene encoding an oxalate catabolism enzyme can catabolize oxalate and/or oxalyl-CoA to treat disorders in which oxalate is detrimental, such as PHI, PHII, PHIII, and secondary hyperoxaluria, enteric hyperoxaluria, and idiopathic hyperoxaluria.
  • the bacterial cell of the disclosure comprises at least one heterologous gene encoding at least one oxalate catabolism enzyme. In one embodiment, the bacterial cell of the disclosure comprises at least one heterologous gene encoding an importer of oxalate and at least one heterologous gene encoding at least one oxalate catabolism enzyme. In one embodiment, the bacterial cell of the disclosure comprises at least one heterologous gene encoding an exporter of formate and at least one heterologous gene encoding at least one oxalate catabolism enzyme. In one embodiment, the bacterial cell of the disclosure comprises at least one heterologous gene encoding an oxalate: formate antiporter and at least one heterologous gene encoding at least one oxalate catabolism enzyme.
  • the disclosure provides a bacterial cell that comprises at least one heterologous gene encoding at least one oxalate catabolism enzyme operably linked to a first promoter.
  • the bacterial cell comprises at least one gene encoding at least one oxalate catabolism enzyme from a different organism, e.g., a different species of bacteria.
  • the bacterial cell comprises more than one copy of a native gene encoding an oxalate catabolism enzyme.
  • the bacterial cell comprises at least one native gene encoding at least one oxalate catabolism enzyme, as well as at least one copy of at least one gene encoding an oxalate catabolism enzyme from a different organism, e.g., a different species of bacteria.
  • the bacterial cell comprises at least one, two, three, four, five, or six copies of a gene encoding an oxalate catabolism enzyme.
  • the bacterial cell comprises multiple copies of a gene encoding an oxalate catabolism enzyme.
  • Oxalate catabolism enzymes are known in the art.
  • AN oxalate catabolism enzyme is encoded by at least one gene encoding at least one oxalate catabolism enzyme derived from a bacterial species.
  • an oxalate catabolism enzyme is encoded by a gene encoding an oxalate catabolism enzyme derived from a non-bacterial species.
  • an oxalate catabolism enzyme is encoded by a gene derived from a eukaryotic species, e.g., a yeast species or a plant species.
  • an oxalate catabolism enzyme is encoded by a gene derived from a human.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is derived from an organism of the genus or species that includes, but is not limited to, Bifidobacterium, Bordetella, Bradyrhizobium, Burkholderia, Clostridium, Enterococcus, Escherichia, Eubacterium, Lactobacillus, Magnetospirillium, Mycobacterium, Neurospora, Oxalobacter, e.g., Oxalobacter formigenes, Ralstonia, Rhodopseudomonas, Shigella, Thermoplasma, and Thauera, e.g., Bifidobacterium animalis, Bifidobacterium bifidum.
  • Bifidobacterium infantis Bifidobacterium lactis, Bifidobacterium longum, Bordatella bronchiseptica, Bordatella parapertussis, Burkholderia fungorum, Burkholderia xenovorans, Bradyrhizobium japonicum, Clostridium acetobutylicum, Clostridium difficile, Clostridium scindens, Clostridium sporogenes, Clostridium tentani, Enterococcus faecalis.
  • one or more oxalate catabolism enzyme(s) encoded by the genetically engineered bacteria are derived from O. formigenes, e.g., oxc and frc described above.
  • one or more oxalate catabolism enzyme(s) encoded by the engineered bacteria are derived from Enteroccoccus faecalis.
  • An inducible oxalate catabolism system has been described in Enterococcus faecalis, which comprised homologs to O. formigenes Frc and Oxc (Hokama et al., Oxalate-degrading Enterococcus faecalis. Microbiol. Immunol. 44, 235-240).
  • one or more oxalate catabolism enzyme(s) encoded by the engineered bacteria are derived from are from Eubacterium lentum.
  • the oxalate -degrading proteins oxalyl-CoA decarboxylase and formyl-CoA transferase were reportedly isolated from this strain (Ito, H., Kotake, T., and Masai, M. (1996). In vitro degradation of oxalic acid by human feces. Int. J. Urol. 3, 207- 211.).
  • one or more oxalate catabolism enzyme(s) encoded by the engineered bacteria are derived from Providencia rettgeri, which have shown to have homologs to O. formigenes Frc and Oxc (e.g., as described in Abratt and Reid, Oxalate -degrading bacteria of the human gut as probiotics in the management of kidney stone disease; Adv Appl Microbiol. 2010;72:63-87, and references therein).
  • one or more oxalate catabolism enzyme(s) encoded by the engineered bacteria are derived from E. coli, e.g. from the yfdXWUVE operon.
  • the ydfU is thought to be a oxc homolog.
  • one or more oxalate catabolism enzyme(s) encoded by the engineered bacteria are derived from Lactobacillus and/or Bifidobacterium species.
  • one or more oxalate catabolism enzyme(s) are derived from oxc and frc homologs Lactobacillus and/or Bifidobacterium species.
  • Non-limiting examples of such Lactobacillus species include Lactobacillus, plantarum, Lactobacillus brevis, Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus gasseri, Lactobacillus rhamnosus, and Lactobacillus salivarius.
  • Non-limiting examples of such Bifidobacterium species include Bifidobacterium infantis, Bifidobacterium animalis, Bifidobacterium breve, Bifidobacterium longum, Bifidobacterium lactis, and Bifidobacterium adolescentis .
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) has been codon-optimized for use in the recombinant bacterial cell of the disclosure. In one embodiment, the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) has been codon-optimized for use in Escherichia coli. In one embodiment, the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) has not been codon-optimized for use in Escherichia coli.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) has been codon-optimized for use in Lactococcus.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed in the recombinant bacterial cells of the disclosure, the bacterial cells catabolize more oxalate or oxalyl-CoA than unmodified bacteria of the same bacterial subtype under the same conditions (e.g., culture or environmental conditions).
  • the genetically engineered bacteria comprising at least one heterologous gene encoding at least one oxalate catabolism enzyme may be used to catabolize excess oxalate, oxalic acid, and/or oxalyl-CoA to treat a disorder in which oxalate is detrimental, such as PHI, PHII, PHIII, and secondary hyperoxaluria, enteric hyperoxaluria, and idiopathic hyperoxaluria.
  • a disorder in which oxalate is detrimental such as PHI, PHII, PHIII, and secondary hyperoxaluria, enteric hyperoxaluria, and idiopathic hyperoxaluria.
  • the present disclosure further comprises genes encoding functional fragments of an oxalate catabolism enzyme or functional variants of an oxalate catabolism enzyme.
  • the term “functional fragment thereof’ or “functional variant thereof’ of an oxalate catabolism enzyme relates to an element having qualitative biological activity in common with the wild-type oxalate catabolism enzyme from which the fragment or variant was derived.
  • a functional fragment or a functional variant of a mutated oxalate catabolism enzyme is one which retains essentially the same ability to catabolize oxalyl-CoA as the oxalate catabolism enzyme from which the functional fragment or functional variant was derived.
  • a polypeptide having oxalate catabolism enzyme activity may be truncated at the N-terminus or C-terminus and the retention of oxalate catabolism enzyme activity assessed using assays known to those of skill in the art, including the exemplary assays provided herein.
  • the recombinant bacterial cell of the disclosure comprises a heterologous gene encoding an oxalate catabolism enzyme functional variant.
  • the recombinant bacterial cell of the disclosure comprises a heterologous gene encoding an oxalate catabolism enzyme functional fragment.
  • oxalate catabolism can be assessed by expressing the protein, functional variant, or fragment thereof, in a recombinant bacterial cell that lacks endogenous oxalate catabolism enzyme activity.
  • Oxalate catabolism activity can be assessed by quantifying oxalate degradation in the culture media as described by Federici et al., Appl. Environ. Microbiol. 70: 5066-73 (2004), the entire contents of which are expressly incorporated herein by reference.
  • Formyl- CoA transferase and oxalyl-CoA decarboxylase activities can be measured by capillary electrophoresis as described in Turroni et al., J. Appl. Microbiol. 103: 1600-9 (2007).
  • percent (%) sequence identity or “percent (%) identity,” also including “homology,” is defined as the percentage of amino acid residues or nucleotides in a candidate sequence that are identical with the amino acid residues or nucleotides in the reference sequences after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • Optimal alignment of the sequences for comparison may be produced, besides manually, by means of the local homology algorithm of Smith and Waterman, 1981, Ads App. Math. 2, 482, by means of the local homology algorithm of Neddleman and Wunsch, 1970, J. Mol. Biol. 48, 443, by means of the similarity search method of Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85, 2444, or by means of computer programs which use these algorithms (GAP, BESTFIT, FASTA, BLAST P, BLAST N and TFASTA in Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Drive, Madison, Wis.).
  • the gene or protein is at least 90%, 91%, 92%, 93%, 94$, 95%, 96%, 97%, 98%, 99% or 100% identical to a gene or protein disclosed herein.
  • the present disclosure encompasses genes encoding an oxalate catabolism enzyme comprising amino acids in its sequence that are substantially the same as an amino acid sequence described herein.
  • Amino acid sequences that are substantially the same as the sequences described herein include sequences comprising conservative amino acid substitutions, as well as amino acid deletions and/or insertions.
  • a conservative amino acid substitution refers to the replacement of a first amino acid by a second amino acid that has chemical and/or physical properties (e.g., charge, structure, polarity, hydrophobicity/hydrophilicity) that are similar to those of the first amino acid.
  • Conservative substitutions include replacement of one amino acid by another within the following groups: lysine (K), arginine (R) and histidine (H); aspartate (D) and glutamate (E); asparagine (N), glutamine (Q), serine (S), threonine (T), tyrosine (Y), K, R, H, D and E; alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), phenylalanine (F), tryptophan (W), methionine (M), cysteine (C) and glycine (G); F, W and Y; C, S and T.
  • contemplated is replacing a basic amino acid with another basic amino acid (e.g., replacement among Lys, Arg, His), replacing an acidic amino acid with another acidic amino acid (e.g., replacement among Asp and Glu), replacing a neutral amino acid with another neutral amino acid (e.g., replacement among Ala, Gly, Ser, Met, Thr, Leu, He, Asn, Gin, Phe, Cys, Pro, Trp, Tyr, Vai).
  • the gene encoding an oxalate catabolism enzyme is mutagenized; mutants exhibiting increased activity are selected; and the mutagenized gene encoding the oxalate catabolism enzyme is isolated and inserted into the bacterial cell of the disclosure.
  • spontaneous mutants that arise that allow bacteria to grow on oxalate as the sole carbon source can be screened for and selected.
  • the gene comprising the modifications described herein may be present on a plasmid or chromosome.
  • Non-limiting examples of oxalate catabolism enzymes of the disclosure are listed in Table 3.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) comprises a formyl -Co A: oxalate CoA -transferase sequence.
  • the formyl -CoA: oxalate CoA-transferase is frc, e.g., from O. formigenes .
  • the frc gene has at least about 80% identity with the entire sequence of SEQ ID NO:
  • the frc gene has at least about 90% identity with the entire sequence of SEQ ID NO: 500. Accordingly, in one embodiment, the frc gene has at least about 95% identity with the entire sequence of SEQ ID NO: 500. Accordingly, in one embodiment, the frc gene has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with the entire sequence of SEQ ID NO: 500. In another embodiment, the frc gene comprises the sequence of SEQ ID NO: 500. In yet another embodiment the frc gene consists of the sequence of SEQ ID NO: 500.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) comprises a oxalyl-CoA decarboxylase sequence.
  • the oxalyl-CoA decarboxylase is oxc, e.g., from O. formigenes. Accordingly, in one embodiment, the oxc gene has at least about 80% identity with the entire sequence of SEQ ID NO: 501. Accordingly, in one embodiment, the oxc gene has at least about 90% identity with the entire sequence of SEQ ID NO:
  • the oxc gene has at least about 95% identity with the entire sequence of SEQ ID NO: 501. Accordingly, in one embodiment, the oxc gene has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with the entire sequence of SEQ ID NO: 501.
  • the oxc gene comprises the sequence of SEQ ID NO: 501.
  • the oxc gene consists of the sequence of SEQ ID NO: 501.
  • the oxc gene consists of the sequence of SEQ ID NO: 501.
  • the at least one gene encoding the at least one oxalate catabolism enzyme comprises an oxalate-CoA ligase sequence.
  • the oxalate-CoA ligase is ScAAE3 from S. cerevisiae. Accordingly, in one embodiment, the ScAAE3 gene has at least about 80% identity with the entire sequence of SEQ ID NO: 502. Accordingly, in one embodiment, the ScAAE3 gene has at least about 90% identity with the entire sequence of SEQ ID NO: 502. Accordingly, in one embodiment, the ScAAE3 gene has at least about 95% identity with the entire sequence of SEQ ID NO: 502.
  • the ScAAE3 gene has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with the entire sequence of SEQ ID NO: 502.
  • the ScAAE3 gene comprises the sequence of SEQ ID NO: 502.
  • the ScAAE3 gene consists of the sequence of SEQ ID NO: 502.
  • the at least one gene encoding the at least one oxalate catabolism enzyme comprises an acetyl-CoA:oxalate CoA-transferase sequence.
  • the acetyl- CoA:oxalate CoA-transferase is YfdE from E. coli from S. cerevisiae. Accordingly, in one embodiment, the YfdE gene has at least about 80% identity with the entire sequence of SEQ ID NO: 503. Accordingly, in one embodiment, the YfdE gene has at least about 90% identity with the entire sequence of SEQ ID NO: 503.
  • the YfdE gene has at least about 95% identity with the entire sequence of SEQ ID NO: 503. Accordingly, in one embodiment, the YfdE gene has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with the entire sequence of SEQ ID NO: 503. In another embodiment, the YfdE gene comprises the sequence of SEQ ID NO: 503. In yet another embodiment the YfdE gene consists of the sequence of SEQ ID NO: 503.
  • Table 4 lists non-limiting examples of oxalate catabolism enzyme polypeptide sequences.
  • one or more polypeptide (s) encoded by the oxalate catabolism cassette(s) and expressed by the genetically engineered bacteria comprises a formyl-CoA transferase, e.g. fire from O. formigenes.
  • the polypeptide (s) have at least about 80% identity with SEQ ID NO: 504.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria have at least about 85% identity with SEQ ID NO: 504.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria have at least about 90% identity with SEQ ID NO: 504. In one embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria have at least about 95% identity with SEQ ID NO: 504. In another embodiment, one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassete(s) and expressed by the genetically engineered bacteria have at least about 96%, 97%, 98%, or 99% identity with SEQ ID NO: 504.
  • one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 504.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria comprise the sequence of SEQ ID NO: 504.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria consist of the sequence of SEQ ID NO: 504.
  • one or more polypeptide (s) encoded by the oxalate catabolism cassette(s) and expressed by the engineered bacteria comprises a oxalyl-CoA decarboxylase, e.g. oxc from O. formigenes.
  • the polypeptide(s) have at least about 80% identity with SEQ ID NO: 505.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s and expressed by the engineered bacteria have at least about 85% identity with SEQ ID NO: 505.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 90% identity with SEQ ID NO: 505. In one embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 95% identity with SEQ ID NO: 505. In another embodiment, one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 96%, 97%, 98%, or 99% identity with SEQ ID NO: 505.
  • one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 505.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria comprise the sequence of SEQ ID NO: 505.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria consist of the sequence of SEQ ID NO: 505.
  • one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria comprises an oxalate-CoA ligase, e.g. ScAAE3 from S cerevisiae.
  • the polypeptide(s) have at least about 80% identity with SEQ ID NO: 506.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s and expressed by the engineered bacteria have at least about 85% identity with SEQ ID NO: 506.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 90% identity with SEQ ID NO: 506. In one embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 95% identity with SEQ ID NO: 506. In another embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 96%, 97%, 98%, or 99% identity with SEQ ID NO: 506.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 506.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria comprise the sequence of SEQ ID NO: 506.
  • one or more polypeptide(s) encoded by the oxalate catabolism cassette(s) and expressed by the genetically engineered bacteria consist of the sequence of SEQ ID NO: 506.
  • one or more polypeptide (s) encoded by the oxalate catabolism cassette(s) and expressed by the engineered bacteria comprises an Acetyl-CoA:oxalate CoA-transferase from, e.g. YfdE from E. coli. In one embodiment the polypeptide(s) have at least about 80% identity with SEQ ID NO: 507. In another embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s and expressed by the engineered bacteria have at least about 85% identity with SEQ ID NO: 507.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 90% identity with SEQ ID NO: 507. In one embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 95% identity with SEQ ID NO: 507. In another embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 96%, 97%, 98%, or 99% identity with SEQ ID NO: 507.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 507.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria comprise the sequence of SEQ ID NO: 507.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria consist of the sequence of with SEQ ID NO: 507.
  • one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria comprises a formyl CoA transferase, e.g., yfdW from E. coli.
  • the polypeptide(s) have at least about 80% identity with SEQ ID NO: 508.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s and expressed by the engineered bacteria have at least about 85% identity with SEQ ID NO: 508.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 90% identity with SEQ ID NO: 508. In one embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 95% identity with SEQ ID NO: 508. In another embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 96%, 97%, 98%, or 99% identity with SEQ ID NO: 508.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 508.
  • one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered comprise the sequence of SEQ ID NO: 508.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria consist of the sequence of SEQ ID NO: 508.
  • one or more polypeptide (s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria comprises a oxalyl-CoA decarboxylase, e.g., yfdU from E. coli.
  • the polypeptide (s) have at least about 80% identity with SEQ ID NO: 509.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s and expressed by the engineered bacteria have at least about 85% identity with SEQ ID NO: 509.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 90% identity with SEQ ID NO: 509. In one embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 95% identity with SEQ ID NO: 509. In another embodiment, one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 96%, 97%, 98%, or 99% identity with SEQ ID NO: 509.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 509.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria comprise the sequence of SEQ ID NO: 509.
  • one or more polypeptide(s) encoded by the oxalate catabolism gene(s) or gene cassette(s) and expressed by the engineered bacteria consist of the sequence of SEQ ID NO: 509.
  • the recombinant bacteria comprise a nucleotide sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 538.
  • the recombinant bacteria comprise the sequence of SEQ ID NO: 538.
  • the recombinant bacteria consists of the sequence of SEQ ID NO: 538.
  • the recombinant bacteria comprise a nucleotide sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 539.
  • the recombinant bacteria comprise the sequence of SEQ ID NO: 539.
  • the recombinant bacteria consists of the sequence of SEQ ID NO: 539.
  • the recombinant bacteria comprise a nucleotide sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 538 and SEQ ID NO: 539.
  • the recombinant bacteria comprise the sequence of SEQ ID NO: 538 and SEQ ID NO: 539.
  • the recombinant bacteria consists of the sequence of SEQ ID NO: 538 and SEQ ID NO: 539.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is directly operably linked to a first promoter.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is indirectly operably linked to a first promoter.
  • the promoter is not operably linked with the at least one gene encoding the oxalate catabolism enzyme in nature.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed under the control of a constitutive promoter. In another embodiment, the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed under the control of an inducible promoter. In some embodiments, the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed under the control of a promoter that is directly or indirectly induced by exogenous environmental conditions.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed under the control of a promoter that is directly or indirectly induced by low-oxygen or anaerobic conditions, such as the environmental conditions of a mammalian gut, wherein expression of the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is activated under low-oxygen or anaerobic environments, such as the environment of a mammalian gut.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed under the control of a promoter that is directly or indirectly induced by inflammatory conditions.
  • Exemplary inducible promoters described herein include oxygen level-dependent promoters (e.g., FNR-inducible promoter), promoters induced by inflammation or an inflammatory response (RNS, ROS promoters), and promoters induced by a metabolite that may or may not be naturally present (e.g., can be exogenously added) in the gut, e.g., arabinose and tetracycline.
  • inducible promoters include, but are not limited to, an FNR responsive promoter, a P ara c promoter, a P ara BAD promoter, a P etR promoter, and a P aci promoter, each of which are described in more detail herein. Inducible promoters are described in more detail infra.
  • the at least one gene encoding the at least one oxalate catabolism enzyme may be present on a plasmid or chromosome in the bacterial cell.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is located on a plasmid in the bacterial cell.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is located in the chromosome of the bacterial cell.
  • a native copy of the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is located in the chromosome of the bacterial cell, and at least one gene encoding at least one oxalate catabolism enzyme from a different species of bacteria is located on a plasmid in the bacterial cell.
  • a native copy of the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is located on a plasmid in the bacterial cell, and at least one gene encoding the at least one oxalate catabolism enzyme from a different species of bacteria is located on a plasmid in the bacterial cell.
  • a native copy of the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is located in the chromosome of the bacterial cell, and at least one gene encoding the at least one oxalate catabolism enzyme from a different species of bacteria is located in the chromosome of the bacterial cell.
  • the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed on a low-copy plasmid. In some embodiments, the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is expressed on a high-copy plasmid. In some embodiments, the high-copy plasmid may be useful for increasing expression of the at least one oxalate catabolism enzyme, thereby increasing the catabolism of oxalate, oxalic acid, and/or oxalyl- CoA.
  • a recombinant bacterial cell of the disclosure comprising at least one gene encoding at least one oxalate catabolism enzyme expressed on a high-copy plasmid does not increase oxalate catabolism or decrease oxalate and/or oxalic acid levels as compared to a recombinant bacterial cell comprising the same gene expressed on a low-copy plasmid in the absence of a heterologous importer of oxalate and additional copies of a native importer of oxalate.
  • an importer of oxalate into the recombinant bacterial cell
  • a low-copy plasmid comprising the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) in conjunction in order to enhance the stability of expression of the oxalate catabolism enzyme, while maintaining high oxalate catabolism and to reduce negative selection pressure on the transformed bacterium.
  • the importer of oxalate is used in conjunction with a high-copy plasmid.
  • Oxalobacter formigenes The uptake of oxalate into the anaerobic bacterium, Oxalobacter formigenes, has been found to occur via the oxalate transporter OxlT (see, e.g., Ruan et al., J Biol. Chem. 267: 10537-43 (1992), the entire contents of which are expressly incorporated herein by reference).
  • OxlT catalyzes the exchange of extracellular oxalate, a divalent anion, for intracellular formate, a monovalent cation that is derived from the decarboxylation of oxalate, thus generating a proton-motive force.
  • Other proteins that mediate the import of oxalate are well known to those of skill in the art.
  • Oxalate transporters e.g., oxalate importers
  • the bacterial cells import more oxalate into the cell when the importer is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the genetically engineered bacteria comprising one or more heterologous gene sequence(s) encoding an importer of oxalate may be used to import oxalate into the bacteria so that any gene sequence(s) encoding an oxalate catabolism enzyme(s) expressed in the organism can be used to treat disorders in which oxalate is detrimental, such as PHI, PHII, PHIII, and secondary hyperoxaluria, enteric hyperoxaluria, and idiopathic hyperoxaluria.
  • the bacterial cell of the disclosure comprises a heterologous gene sequence(s) encoding a transporter (importer) of oxalate.
  • the bacterial cell of the disclosure comprises a heterologous gene sequence(s) encoding transporter of oxalate and one or more heterologous gene sequence(s) encoding one or more oxalate catabolism enzyme(s). In one embodiment, the bacterial cell of the disclosure comprises a heterologous gene sequence(s) encoding transporter of oxalate and one or more heterologous gene sequence(s) encoding one or more polypeptides selected from a formate exporter, an oxalate: formate antiporter, and combinations thereof.
  • the bacterial cell of the disclosure comprises a heterologous gene sequence(s) encoding a transporter of oxalate, one or more heterologous gene sequence(s) encoding one or more oxalate catabolism enzyme(s), and one or more heterologous gene sequence(s) encoding one or more polypeptides selected from a formate exporter, an oxalate: formate antiporter, and combinations thereof.
  • the disclosure provides a bacterial cell that comprises one or more heterologous gene sequence(s) encoding an oxalate catabolism enzyme operably linked to a first promoter and one or more heterologous gene sequence(s) encoding an transporter (importer) of oxalate.
  • the disclosure provides a bacterial cell that comprises one or more heterologous gene sequence(s) encoding a transporter (importer) of oxalate operably linked to the first promoter.
  • the disclosure provides a bacterial cell that comprises one or more heterologous gene sequence(s) encoding one or more oxalate catabolism enzyme(s) operably linked to a first promoter and one or more heterologous gene sequence(s) encoding a transporter (importer) of oxalate operably linked to a second promoter.
  • the first promoter and the second promoter are separate copies of the same promoter. In another embodiment, the first promoter and the second promoter are different promoters.
  • the bacterial cell comprises one or more gene sequence(s) encoding an transporter (importer) of oxalate from a different organism, e.g., a different species of bacteria.
  • the bacterial cell comprises one or more native gene sequence(s) encoding an transporter (importer) of oxalate.
  • the one or more native gene sequence(s) encoding an transporter (importer) of oxalate is not modified.
  • the bacterial cell comprises more than one copy of one or more native gene sequence(s) encoding a transporter (importer) of oxalate.
  • the bacterial cell comprises a copy of one or more gene sequence(s) encoding a native transporter (importer) of oxalate, as well as one or more copy of one or more heterologous gene sequence(s) encoding a transporter of oxalate from a different bacterial species.
  • the bacterial cell comprises one or more, two, three, four, five, or six copies of the one or more heterologous gene sequence(s) encoding a transporter of oxalate.
  • the bacterial cell comprises multiple copies of the one or more heterologous gene sequence(s) encoding a transporter of oxalate.
  • the transporter of oxalate is encoded by an transporter of oxalate gene derived from a bacterial genus or species, including but not limited to, Oxalobacter.
  • the transporter of oxalate gene is derived from a bacteria of the species Oxalobacter formi genes .
  • the transporter is the OxlT Oxalate: Formate Antiporter from Oxalobacter formigenes
  • transporter of oxalate is encoded by a gene selected from the oxalate: formate antiporter (OFA) family.
  • OFA formate antiporter
  • the OFA family members belong to the major facilitator superfamily and are widely distributed in nature, being present in the bacterial, archaeal, and eukaryotic kingdoms (see., e.g., Pao et al., Major Facilitator Superfamily Microbiol . Mol. Biol . Rev. March 1998 vol 62 no. 1 1-34).
  • the transporter is a homolog and/or ortholog of the Oxalobacter formigenes oxalate: formate antiporter.
  • the transporter is a bacterially derived homolog and/or ortholog of the Oxalobacter formigenes oxalate: formate antiporter (OxlT).
  • the present disclosure further comprises genes encoding functional fragments of an transporter of oxalate or functional variants of an transporter of oxalate.
  • functional fragment thereof’ or “functional variant thereof’ of an transporter of oxalate relates to an element having qualitative biological activity in common with the wild-type transporter of oxalate from which the fragment or variant was derived.
  • a functional fragment or a functional variant of a mutated transporter of oxalate protein is one which retains essentially the same ability to import oxalate into the bacterial cell as does the transporter protein from which the functional fragment or functional variant was derived.
  • the recombinant bacterial cell of the disclosure comprises one or more heterologous gene sequence(s) encoding a functional fragment of a transporter of oxalate.
  • the recombinant bacterial cell of the disclosure comprises one or more heterologous gene sequence(s) encoding a functional variant of a transporter of oxalate.
  • Assays for testing the activity of a transporter of oxalate, an transporter of oxalate functional variant, or an transporter of oxalate functional fragment are well known to one of ordinary skill in the art.
  • oxalate import can be assessed by preparing detergent-extracted proteoliposomes from recombinant bacterial cells expressing the protein, functional variant, or fragment thereof, and determining [ 14 C]oxalate uptake as described in Abe et al., J. Biol. Chem. 271: 6789-93 (1996), the entire contents of which are expressly incorporated herein by reference.
  • the genes encoding the transporter of oxalate have been codon-optimized for use in the host organism. In one embodiment, the genes encoding the transporter of oxalate have been codon-optimized for use in Escherichia coli.
  • the present disclosure also encompasses genes encoding a transporter of oxalate comprising amino acids in its sequence that are substantially the same as an amino acid sequence described herein.
  • Amino acid sequences that are substantially the same as the sequences described herein include sequences comprising conservative amino acid substitutions, as well as amino acid deletions and/or insertions.
  • the one or more gene sequence(s) encoding a transporter of oxalate is mutagenized; mutants exhibiting increased oxalate transport are selected; and the mutagenized one or more gene sequence(s) encoding an transporter of oxalate is isolated and inserted into the bacterial cell of the disclosure.
  • the one or more gene sequence(s) encoding an transporter of oxalate is mutagenized; mutants exhibiting decreased oxalate transport are selected; and the mutagenized one or more gene sequence(s) encoding an transporter of oxalate is isolated and inserted into the bacterial cell of the disclosure.
  • the transporter modifications described herein may be present on a plasmid or chromosome.
  • Table 5 lists polypeptide and polynucleotide sequences for a non-limiting example of an Oxalate: formate antiporter.
  • the oxalate importer is the oxalate: formate antiporter OxlT.
  • the OxlT gene has at least about 80% identity to SEQ ID NO: 510. Accordingly, in one embodiment, the OxlT gene has at least about 90% identity to SEQ ID NO: 510. Accordingly, in one embodiment, the OxlT gene has at least about 95% identity to SEQ ID NO: 510. Accordingly, in one embodiment, the OxlT gene has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 510.
  • the OxlT gene comprises the sequence of SEQ ID NO: 510. In yet another embodiment the OxlT gene consists of the sequence of SEQ ID NO: 510.
  • one or more polypeptide (s) encoded by one or more gene(s) or gene cassette(s) and expressed by the genetically engineered bacteria is the oxalate: formate antiporter OxlT.
  • the polypeptide (s) have at least about 80% identity with SEQ ID NO: 511.
  • one or more polypeptide(s) encoded by one or more gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 85% identity with SEQ ID NO: 511.
  • one or more polypeptide(s) encoded by one or more gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 90% identity with SEQ ID NO: 511.
  • one or more polypeptide(s) encoded by one or more gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 95% identity with SEQ ID NO: 511. In another embodiment, one or more polypeptide (s) encoded by one or more gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 96%, 97%, 98%, or 99% identity with SEQ ID NO: 511.
  • one or more polypeptide(s) encoded by one or more gene(s) or gene cassette(s) and expressed by the engineered bacteria have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 511.
  • one or more polypeptide(s) encoded by one or more gene(s) or gene cassette(s) and expressed by the engineered bacteria comprise the sequence of SEQ ID NO: 511.
  • one or more polypeptide(s) encoded by one or more gene(s) or gene cassette(s) and expressed by the engineered bacteria consist of the sequence of SEQ ID NO: 511.
  • the bacterial cell comprises one or more heterologous gene sequence(s) encoding at least one oxalate catabolism enzyme(s) operably linked to a first promoter and one or more heterologous gene sequence (s) encoding an importer of oxalate.
  • the one or more heterologous gene sequence(s) encoding an importer of oxalate is operably linked to the first promoter.
  • the one or more heterologous gene sequence(s) encoding an importer of oxalate is operably linked to a second promoter.
  • the one or more gene sequence(s) encoding an importer of oxalate is directly operably linked to the second promoter.
  • the one or more gene sequence(s) encoding an importer of oxalate is indirectly operably linked to the second promoter.
  • expression of one or more gene sequence(s) encoding an importer of oxalate is controlled by a different promoter than the promoter that controls expression of the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s).
  • expression of the one or more gene sequence(s) encoding an importer of oxalate is controlled by the same promoter that controls expression of the one or more oxalate catabolism enzyme(s).
  • one or more gene sequence(s) encoding an importer of oxalate and the oxalate catabolism enzyme are divergently transcribed from a promoter region.
  • expression of each of genes encoding the gene sequence(s) encoding an importer of oxalate and the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s) is controlled by different promoters.
  • the promoter is not operably linked with the one or more gene sequence(s) encoding an importer of oxalate in nature.
  • the one or more gene sequence(s) encoding an importer of oxalate is controlled by its native promoter.
  • the one or more gene sequence(s) encoding an importer of oxalate is controlled by an inducible promoter.
  • the one or more gene sequence(s) encoding the importer of oxalate is controlled by a promoter that is stronger than its native promoter.
  • the one or more gene sequence(s) encoding an importer of oxalate is controlled by a constitutive promoter.
  • the promoter is an inducible promoter. Inducible promoters are described in more detail infra.
  • the one or more gene sequence(s) encoding an importer of oxalate is located on a plasmid in the bacterial cell. In another embodiment, the one or more gene sequence(s) encoding an importer of oxalate is located in the chromosome of the bacterial cell. In yet another embodiment, a native copy of the one or more gene sequence(s) encoding an importer of oxalate is located in the chromosome of the bacterial cell, and a copy of one or more gene sequence(s) encoding an importer of oxalate from a different species of bacteria is located on a plasmid in the bacterial cell.
  • a native copy of the one or more gene sequence(s) encoding an importer of oxalate is located on a plasmid in the bacterial cell, and a copy of one or more gene sequence(s) encoding an importer of oxalate from a different species of bacteria is located on a plasmid in the bacterial cell.
  • a native copy of the one or more gene sequence(s) encoding an importer of oxalate is located in the chromosome of the bacterial cell, and a copy of the one or more gene sequence(s) encoding an importer of oxalate from a different species of bacteria is located in the chromosome of the bacterial cell.
  • the at least one native gene encoding the importer of oxalate in the bacterial cell is not modified, and one or more additional copies of the native importer of oxalate are inserted into the genome.
  • the one or more additional copies of the native importer that is inserted into the genome are under the control of the same inducible promoter that controls expression of the one or more gene sequence(s) encoding the oxalate catabolism enzyme, e.g., the FNR responsive promoter, or a different inducible promoter than the one that controls expression of the at least one oxalate catabolism enzyme, or a constitutive promoter.
  • the at least one native gene encoding the importer is not modified, and one or more additional copies of the importer from a different bacterial species is inserted into the genome of the bacterial cell.
  • the one or more additional copies of the importer inserted into the genome of the bacterial cell are under the control of the same inducible promoter that controls expression of the one or more gene sequence(s) encoding the oxalate catabolism enzyme, e.g., the FNR responsive promoter, or a different inducible promoter than the one that controls expression of the gene sequence(s) encoding the one or more oxalate catabolism enzyme(s), or a constitutive promoter.
  • the bacterial cells import 10% more oxalate into the bacterial cell when the importer is expressed than unmodified bacteria of the same bacterial subtype under the same conditions. In another embodiment, when the importer of oxalate is expressed in the recombinant bacterial cells of the disclosure, the bacterial cells import 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% more oxalate into the bacterial cell when the importer is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the bacterial cells import two-fold more oxalate into the cell when the importer is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the bacterial cells import three-fold, four-fold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, or ten-fold more oxalate into the cell when the importer is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the bacterial cell comprises a genetic mutation in one or more endogenous gene(s) encoding a transporter (importer) of formate, wherein the genetic mutation reduces influx of formate into the bacterial cell.
  • a transporter importer
  • such mutations may decrease intracellular formate concentrations and increase the flux through oxalate catabolism pathways.
  • FocA of E. coli catalyzes bidirectional formate transport and may function by a channel-type mechanism (Flake et al. , Unexpected oligomeric structure of the FocA formate channel of Escherichia coli '. a paradigm for the formate-nitrite transporter family of integral membrane proteins". FEMS microbiology letters.
  • FocA may be able to switch its mode of operation from a passive export channel at high external pH to a secondary active formate/H importer at low pH.
  • the genetically engineered bacteria may comprise a mutation and/or deletion in FocA, rendering it non-functional.
  • Formate is a major metabolite in the anaerobic fermentation of glucose by many intestinal bacteria.
  • Several types of formate import and export proteins are known in the art.
  • FocA acts as a passive exporter for formate anions generated in the cytoplasm.
  • formate is subsequently reduced by formate dehydrogenase into carbon dioxide.
  • Another form of formate dehydrogenase and/or formate lyase also exists in the cytoplasm in E. coli.
  • a functional switch of transport mode occurs when the pH of the growth medium drops below 6.8. With ample protons available in the periplasm, the cell switches to active import of formate and again uses FocA for the task.
  • OxlT allows the exchange of oxalate with the intracellular formate derived from oxalate decarboxylation.
  • the overall effect of these associated activities is generation of a proton-motive force to support membrane functions, including ATP synthesis, accumulation of growth substrates and extrusion of waste products.
  • exporter of formate in some embodiments also encompasses a transporter of oxalate, e.g.
  • Formate exporters and/or formate exporters with coupled oxalate import functions may be expressed or modified in the bacteria in order to enhance formate export (and in cases when coupled to oxalate import, thereby enhance oxalate import).
  • the bacterial cells export more formate outside of the cell when the exporter is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the bacterial cell comprises one or more gene sequence(s) encoding an exporter of formate.
  • the bacterial cell comprises a heterologous gene encoding an exporter of formate and at least one heterologous gene or gene cassette encoding at least one oxalate catabolism enzyme.
  • the disclosure provides a bacterial cell that comprises one or more gene sequence(s) encoding one or more oxalate catabolism enzyme(s) operably linked to a first promoter and one or more gene sequence(s) encoding an exporter of formate.
  • the one or more gene sequence(s) encoding an exporter of formate is operably linked to the first promoter.
  • the one or more gene sequence(s) encoding one or more oxalate catabolism enzyme(s) is operably is linked to a first promoter
  • the one or more gene sequence(s) encoding an exporter of formate is operably linked to a second promoter.
  • the first promoter and the second promoter are separate copies of the same promoter.
  • the first promoter and the second promoter are different promoters.
  • the bacterial cell comprises one or more gene sequence(s) encoding an exporter of formate from a different organism, e.g., a different species of bacteria.
  • the bacterial cell comprises at least one native gene sequence(s) encoding an exporter of formate.
  • the at least one native gene sequence(s) encoding an exporter of formate is not modified.
  • the bacterial cell comprises more than one copy of at least one gene native sequence(s) encoding an exporter of formate.
  • the bacterial cell comprises a copy one or more gene sequence(s) encoding a native exporter of formate, as well as at least one copy of at least one heterologous gene sequence(s) encoding an exporter of formate from a different bacterial species.
  • the bacterial cell comprises at least one, two, three, four, five, or six copies of the at least one heterologous gene sequences encoding an exporter of formate.
  • the bacterial cell comprises multiple copies of one or more heterologous gene sequence(s) encoding an exporter of formate.
  • the exporter of formate is encoded by an exporter of formate gene derived from a bacterial genus or species, including but not limited to, Bifidobacterium, Bordetella, Bradyrhizobium, Burkholderia, Clostridium, Enterococcus, Escherichia, Eubacterium, Lactobacillus, Magnetospirillium, Mycobacterium, Neurospora, Oxalobacter, e.g., Oxalobacter formigenes, Ralstonia, Rhodopseudomonas, Shigella, Thermoplasma, and Thauera, e.g., Bifidobacterium animalis, Bifidobacterium bifidum.
  • a bacterial genus or species including but not limited to, Bifidobacterium, Bordetella, Bradyrhizobium, Burkholderia, Clostridium, Enterococcus, Escherichia, Eubacterium, Lactobac
  • Bifidobacterium infantis Bifidobacterium lactis, Bifidobacterium longum, Bordatella bronchiseptica, Bordatella parapertussis, Burkholderia fungorum, Burkholderia xenovorans, Bradyrhizobium japonicum, Clostridium acetobutylicum, Clostridium difficile, Clostridium scindens, Clostridium sporogenes, Clostridium tentani, Enterococcus faecalis.
  • the present disclosure further comprises genes encoding functional fragments of an exporter of formate or functional variants of an exporter of formate.
  • the term “functional fragment thereof’ or “functional variant thereof’ of an exporter of formate relates to an element having qualitative biological activity in common with the wild-type exporter of formate from which the fragment or variant was derived.
  • a functional fragment or a functional variant of a mutated exporter of formate protein is one which retains essentially the same ability to import formate into the bacterial cell as does the exporter protein from which the functional fragment or functional variant was derived.
  • the engineered bacterial cell comprises at least one heterologous gene encoding a functional fragment of an exporter of formate.
  • the engineered bacterial cell comprises at least one heterologous gene encoding a functional variant of an exporter of formate.
  • Assays for testing the activity of an exporter of formate, an exporter of formate functional variant, or an exporter of formate functional fragment are well known to one of ordinary skill in the art.
  • formate export can be assessed by expressing the protein, functional variant, or fragment thereof, in an engineered bacterial cell that lacks an endogenous formate exporter and assessing formate levels in the media after expression of the protein.
  • Methods for measuring formate export are well known to one of ordinary skill in the art (see, e.g., Wraight et al., Structure and mechanism of a pentameric formate channel Nat Struct Mol Biol. 2010 Jan; 17(1): 31-37).
  • the genes encoding the exporter of formate have been codon-optimized for use in the host organism. In one embodiment, the genes encoding the exporter of formate have been codon-optimized for use in Escherichia coli.
  • the present disclosure also encompasses genes encoding an exporter of formate comprising amino acids in its sequence that are substantially the same as an amino acid sequence described herein.
  • Amino acid sequences that are substantially the same as the sequences described herein include sequences comprising conservative amino acid substitutions, as well as amino acid deletions and/or insertions.
  • the at least one gene encoding an exporter of formate is mutagenized; mutants exhibiting increased formate transport are selected; and the mutagenized at least one gene encoding an exporter of formate is isolated and inserted into the bacterial cell.
  • increasing export of formate may also allow increased oxalate import.
  • the at least one gene encoding an exporter of formate is mutagenized; mutants exhibiting decreased formate transport are selected; and the mutagenized at least one gene encoding an exporter of formate is isolated and inserted into the bacterial cell.
  • the exporter modifications described herein may be present on a plasmid or chromosome.
  • the formate exporter is OxlT.
  • the OxlT gene has at least about 80% identity to SEQ ID NO: 510. Accordingly, in one embodiment, the OxlT gene has at least about 90% identity to SEQ ID NO: 510. Accordingly, in one embodiment, the OxlT gene has at least about 95% identity to SEQ ID NO: 510. Accordingly, in one embodiment, the OxlT gene has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 510. In another embodiment, the OxlT gene comprises the sequence of SEQ ID NO: 510.
  • the OxlT gene consists of the sequence of SEQ ID NO: 510. [0330] In one embodiment, the OxlT gene encodes a polypeptide which has at least about 80% identity to SEQ ID NO: 511. Accordingly, in one embodiment, the OxlT gene encodes a polypeptide which has at least about 90% identity to SEQ ID NO: 511. Accordingly, in one embodiment, the OxlT gene encodes a polypeptide which has at least about 95% identity to SEQ ID NO: 511.
  • the OxlT gene encodes a polypeptide which has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 511.
  • the OxlT gene encodes a polypeptide which comprises the sequence of SEQ ID NO: 511.
  • the OxlT gene encodes a polypeptide which consists of the sequence of SEQ ID NO: 511.
  • the bacterial cell comprises one or more heterologous gene sequence(s) encoding at least one oxalate catabolism enzyme operably linked to a first promoter and one or more heterologous gene sequence(s) encoding an exporter of formate.
  • the one or more heterologous gene sequence(s) encoding an exporter of formate are operably linked to the first promoter.
  • the one or more heterologous gene sequence(s) encoding an exporter of formate are operably linked to a second promoter.
  • one or more heterologous gene sequence(s) encoding an exporter of formate are directly operably linked to the second promoter.
  • the one or more heterologous gene sequence(s) encoding an exporter of formate are indirectly operably linked to the second promoter.
  • expression one or more gene sequence(s) encoding an exporter of formate is controlled by a different promoter than the promoter that controls expression of the at least one gene encoding the at least one oxalate catabolism enzyme. In some embodiments, expression of the one or more gene sequence(s) encoding an exporter of formate is controlled by the same promoter that controls expression of the at least one oxalate catabolism enzyme. In some embodiments, the one or more gene sequence(s) encoding an exporter of formate and the oxalate catabolism enzyme are divergently transcribed from a promoter region.
  • expression of each of genes encoding the one or more gene sequence(s) encoding an exporter of formate and the one or more gene sequence(s) encoding the at least one oxalate catabolism enzyme is controlled by different promoters.
  • the promoter is not operably linked with the one or more gene sequence(s) encoding an exporter of formate in nature.
  • the one or more gene sequence(s) encoding the exporter of formate is controlled by its native promoter.
  • the one or more gene sequence(s) encoding the exporter of formate is controlled by an inducible promoter.
  • the one or more gene sequence(s) encoding the exporter of formate is controlled by a promoter that is stronger than its native promoter. In some embodiments, the one or more gene sequence(s) encoding the exporter of formate is controlled by a constitutive promoter.
  • the promoter is an inducible promoter. Inducible promoters are described in more detail infra.
  • the one or more gene sequence(s) encoding an exporter of formate is located on a plasmid in the bacterial cell. In another embodiment, the one or more gene sequence(s) encoding an exporter of formate is located in the chromosome of the bacterial cell. In yet another embodiment, a native copy of the one or more gene sequence(s) encoding an exporter of formate is located in the chromosome of the bacterial cell, and a copy of at least one gene encoding an exporter of formate from a different species of bacteria is located on a plasmid in the bacterial cell.
  • a native copy of the one or more gene sequence(s) encoding an exporter of a formate is located on a plasmid in the bacterial cell, and a copy of at least one gene encoding an exporter of formate from a different species of bacteria is located on a plasmid in the bacterial cell.
  • a native copy of the one or more gene sequence(s) encoding an exporter of formate is located in the chromosome of the bacterial cell, and a copy of the one or more gene sequence(s) encoding an exporter of formate from a different species of bacteria is located in the chromosome of the bacterial cell.
  • the at least one native gene encoding the exporter in the bacterial cell is not modified, and one or more additional copies of the native exporter are inserted into the genome.
  • the one or more additional copies of the native exporter that is inserted into the genome are under the control of the same inducible promoter that controls expression of the at least one gene encoding the oxalate catabolism enzyme, e.g., the FNR responsive promoter, or a different inducible promoter than the one that controls expression of the at least one oxalate catabolism enzyme, or a constitutive promoter.
  • the at least one native gene encoding the exporter is not modified, and one or more additional copies of the exporter from a different bacterial species is inserted into the genome of the bacterial cell.
  • the one or more additional copies of the exporter inserted into the genome of the bacterial cell are under the control of the same inducible promoter that controls expression of the at least one gene encoding the oxalate catabolism enzyme, e.g., the FNR responsive promoter, or a different inducible promoter than the one that controls expression of the at least one gene encoding the at least one oxalate catabolism enzyme, or a constitutive promoter.
  • the bacterial cells when the exporter of formate is expressed in the engineered bacterial cells, the bacterial cells export 10% more formate out of the bacterial cell when the exporter is expressed than unmodified bacteria of the same bacterial subtype under the same conditions. In another embodiment, when the exporter of formate is expressed in the engineered bacterial cells, the bacterial cells export 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% more formate out of the bacterial cell when the exporter is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the bacterial cells when the exporter of formate is expressed in the engineered bacterial cells, the bacterial cells export two-fold more formate out of the cell when the exporter is expressed than unmodified bacteria of the same bacterial subtype under the same conditions. In yet another embodiment, when the exporter of formate is expressed in the engineered bacterial cells, the bacterial cells export three-fold, four-fold, five-fold, six-fold, seven-fold, eightfold, nine-fold, or ten-fold more formate out of the cell when the exporter is expressed than unmodified bacteria of the same bacterial subtype under the same conditions.
  • the bacterial cell comprises a mutation or deletion in an exporter of oxalate, rendering the exporter less functional or non-functional.
  • a mutation may prevent intracellular oxalate from being exported and increase the catabolism of oxalate.
  • the genetically engineered bacteria further comprise a mutation or deletion in one or more endogenous formate exporters, e.g., FocA.
  • such genetically engineered bacteria comprising a mutation in FocA comprise one or more gene sequence(s) encoding a formate: oxalate antiporter, e.g., OxlT.
  • one or more endogenous formate exporter(s) are mutagenized or deleted, e.g. , (e.g. , FocA) to reduce or prevent the export of formate without the concurrent import of oxalate through a formate: oxalate antiporter, e.g., OxlT.
  • Such a mutation may increase the uptake and catabolism of oxalate in the bacterial cell.
  • formate dehydrogenase and/or formate lyase is mutated or deleted, e.g. to prevent the catabolism of formate in the bacterial cell.
  • mutations may increase intracellular formate concentrations, allowing an increase in the flux through a formate oxalate antiporter, and thereby allowing increased oxalate uptake.
  • the genetically engineered bacteria comprise one or more E. coli Nissle bacteriophage, e.g., Phage 1, Phage 2, and Phage 3. In some embodiments, the genetically engineered bacteria comprise one or modifications or mutations in one or more of Phage 1 , 2 or 3. In some embodiments, the genetically engineered bacteria comprise a modification or mutation in Phage 3. Non-limiting examples of such mutations or modifications are described in International Patent Application PCT/US2018/038840, filed August 31, 2016 the contents of which is herein incorporated by reference in its entirety. In some embodiments, the mutations include deletions, insertions, substitutions and inversions and are located in or encompass one or more Phage 3 genes.
  • the one or more insertions comprise an antibiotic cassette.
  • the mutation is a deletion.
  • the genetically engineered bacteria comprise one or more deletions, which are located in or comprise one or more genes selected from ECOLIN_09965, ECOLIN_09970, ECOLIN_09975, ECOLIN_09980, ECOLIN_09985, ECOLIN_09990, ECOLIN 09995, ECOLINJOOOO, ECOLIN_10005, ECOLINJOOIO, ECOLIN_10015, ECOLIN_10020, ECOLIN_10025, ECOLIN_10030, ECOLIN_10035, ECOLIN_10040, ECOLIN_10045, ECOLIN_10050, ECOLIN_10055, ECOLIN_10065, ECOLIN_10070, ECOLIN_10075, ECOLIN_10080, ECOLIN_10085, ECOLIN_10090, ECOLIN_10095, ECOLIN IOIOO, ECOLIN_10105
  • the genetically engineered bacteria comprise a complete or partial deletion of one or more of ECOLIN 10110, ECOLIN 10115, ECOLIN_10120, ECOLIN 10125, ECOLIN_10130, ECOLIN_10135, ECOLIN_10140, ECOLIN_10145, ECOLIN_10150, ECOLIN_10160, ECOLIN_10165, ECOLIN_10170, and ECOLIN_10175.
  • the deletion is a complete deletion of ECOLIN_10110, ECOLIN 10115, ECOLIN_10120, ECOLIN_10125, ECOLIN_10130, ECOLIN_10135, ECOLIN_10140, ECOLIN_10145, ECOLIN_10150, ECOLIN_10160, ECOLIN_10165, and ECOLIN 10170, and a partial deletion of ECOLIN 10175.
  • the sequence of SEQ ID NO: 292 is deleted from the Phage 3 genome.
  • a sequence comprising SEQ ID NO: 292 is deleted from the Phage 3 genome.
  • Colibactin Island also known as pks island
  • the engineered microorganism e.g., engineered bacterium
  • colibactin island a modified pks island
  • Non-limiting examples are described in International Patent Application PCT/US2021/061579, filed 12/31/2021, the contents of which is herein incorporated by reference in its entirety.
  • the engineered microorganism e.g., engineered bacterium, comprises a modified clb sequence selected from one or more of the clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbl, clb J, clbK, clbL, clbM, clbN, clbO, clbP, clbQ, clbll.
  • a modified clb sequence selected from one or more of the clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbl, clb J, clbK, clbL, clbM, clbN, clbO, clb
  • the modified clb sequence is an insertion, a substitution, and/or a deletion as compared to the control.
  • the modified clb sequence is a deletion of the clb island, e.g., clb A, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbl, clbJ, clbK, clbE clbM, clbN, clbO, clbP, clbQ, clbR, and clbS.
  • the clb island e.g., clb A, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbl, clbJ, clbK, clbE clbM, clbN, clbO, clbP, clbQ,
  • the colibactin deletion is the whole island except for the clbS gene, e.g., a deletion of clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbl, clb J, clbK, clbL, clbM, clbN, clbO, clbP, clbQ, and clbR.
  • the clbS gene e.g., a deletion of clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbl, clb J, clbK, clbL, clbM, clbN, clbO, clbP
  • the modified endogenous colibactin island comprises one or more modified clb sequences selected from clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), c//?./ (SEQ ID NO: 303), clbK (SEQ ID NO: 304), clbL (SEQ ID NO: 305), c/ (SEQ ID NO: 306), c/WV(SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO: 309)
  • the modified endogenous colibactin island comprises a deletion of clbA (SEQ ID NO: 294), clbB (SEQ ID NO: 295), clbC (SEQ ID NO: 296), clbD (SEQ ID NO: 297), clbE (SEQ ID NO: 298), clbF (SEQ ID NO: 299), clbG (SEQ ID NO: 300), clbH (SEQ ID NO: 301), clbl (SEQ ID NO: 302), clb J (SEQ ID NO: 303), clbK (SEQ ID NO: 304), clbL (SEQ ID NO: 305), clbM (SEQ ID NO: 306), clbN (SEQ ID NO: 307), clbO (SEQ ID NO: 308), clbP (SEQ ID NO: 309), clbQ (SEQ ID NO:
  • the bacterial cell comprises a stably maintained plasmid or chromosome carrying the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s), e.g., selected from formyl-CoA:oxalate CoA-transferase, e.g.,frc (from O. formigenes), oxalyl-CoA synthetase, e.g., ScAAE3 (from .S' cerevisiae), oxalyl-CoA decarboxylase, e.g., selected from oxc (from ().
  • oxalate catabolism enzyme(s) e.g., selected from formyl-CoA:oxalate CoA-transferase, e.g.,frc (from O. formigenes), oxalyl-CoA synthetase, e.g., ScAAE3 (from .S' cere
  • bacterial cell comprises two or more distinct oxalate catabolism enzymes, e.g., formyl- CoA: oxalate CoA-transferase, e.g., frc (from O.
  • the genetically engineered bacteria comprise multiple copies of the same oxalate catabolism enzyme gene and/or gene cassette. In some embodiments, the genetically engineered bacteria comprise multiple copies of different oxalate catabolism enzyme genes.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a plasmid and operably linked to a directly or indirectly inducible promoter. In some embodiments, the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a plasmid and operably linked to a promoter that is induced under low-oxygen or anaerobic conditions. In some embodiments, the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a chromosome and operably linked to a directly or indirectly inducible promoter.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present in the chromosome and operably linked to a promoter that is induced under low-oxygen or anaerobic conditions. In some embodiments, the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is present on a plasmid and operably linked to a promoter that is induced by exposure to tetracycline or arabinose.
  • the bacterial cell comprises a stably maintained plasmid or chromosome carrying the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes, such that the transporter, e.g., OxlT from O. formigenes, can be expressed in the host cell, and the host cell is capable of survival and/or growth in vitro, e.g., in medium, and/or in vivo, e.g., in the gut.
  • transporter e.g., OxlT from O. formigenes
  • bacterial cell comprises two or more distinct copies of the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes .
  • the genetically engineered bacteria comprise multiple copies of the same gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g. , OxlT from O. formigenes.
  • the at least one gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes is present on a plasmid and operably linked to a directly or indirectly inducible promoter.
  • the gene and/or gene cassette encoding one or more transporter(s) of oxalate e.g., OxlT from O. formigenes
  • a plasmid and operably linked to a promoter that is induced under low-oxygen or anaerobic conditions.
  • the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes. is present on a chromosome and operably linked to a directly or indirectly inducible promoter.
  • the gene and/or gene cassette encoding one or more transporter(s) of oxalate e.g., OxlT from O. formigenes
  • the gene and/or gene cassette encoding one or more transporter(s) of oxalate is present in the chromosome and operably linked to a promoter that is induced under low-oxygen or anaerobic conditions.
  • the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes is present on a plasmid and operably linked to a promoter that is induced by exposure to tetracycline.
  • the promoter that is operably linked to the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and the promoter that is operably linked to the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes. is directly induced by exogenous environmental conditions.
  • the promoter is indirectly induced by exogenous environmental conditions.
  • the promoter is directly or indirectly induced by exogenous environmental conditions specific to the gut of a mammal.
  • the promoter is directly or indirectly induced by exogenous environmental conditions specific to the small intestine of a mammal.
  • the promoter is directly or indirectly induced by low-oxygen or anaerobic conditions such as the environment of the mammalian gut.
  • the promoter is directly or indirectly induced by molecules or metabolites that are specific to the gut of a mammal, e.g., propionate.
  • the promoter is directly or indirectly induced by a molecule that is co-administered with the bacterial cell.
  • the bacterial cell comprises a gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s), e.g., selected from formyl -CoA: oxalate CoA-transferase, e.g., frc (from O. formigenes), oxalyl-CoA synthetase, e.g., ScAAE3 (from .S', cerevisiae), oxalyl-CoA decarboxylase, e.g., oxc (from O.
  • oxalate catabolism enzyme(s) e.g., selected from formyl -CoA: oxalate CoA-transferase, e.g., frc (from O. formigenes), oxalyl-CoA synthetase, e.g., ScAAE3 (from .S', cerevisiae), oxalyl-Co
  • the bacterial cell comprises gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g. , OxlT from O. formigenes, is expressed under the control of the fumarate and nitrate reductase regulator (FNR) promoter.
  • FNR fumarate and nitrate reductase regulator
  • FNR is a major transcriptional activator that controls the switch from aerobic to anaerobic metabolism (Unden et al. , 1997). In the anaerobic state, FNR dimerizes into an active DNA binding protein that activates hundreds of genes responsible for adapting to anaerobic growth. In the aerobic state, FNR is prevented from dimerizing by oxygen and is inactive.
  • FNR responsive promoters include, but are not limited to, the FNR responsive promoters listed in the chart, below.
  • the FNR responsive promoter comprises SEQ ID NO: 1. In one embodiment, the FNR responsive promoter comprises SEQ ID NO: 2. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 3. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 4. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 5. Additional FNR responsive promoters are shown below in Table 7.
  • the FNR responsive promoter comprises SEQ ID NO: 6. In one embodiment, the FNR responsive promoter comprises SEQ ID NO: 7. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 1. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 8. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 9. In one embodiment, the FNR responsive promoter comprises SEQ ID NO: 2. In one embodiment, the FNR responsive promoter comprises SEQ ID NO: 3. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 4. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 5. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 10. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 11. In another embodiment, the FNR responsive promoter comprises SEQ ID NO: 12.
  • the genetically engineered bacteria comprise a gene and/or gene cassette(s) encoding one or more oxalate catabolism enzyme(s), e.g., selected from formyl-CoA: oxalate CoA-transferase, e.g., Frc (from O. formigenes), oxalyl-CoA synthetase, e.g., ScAAE3 (from .S', cerevisiae), oxalyl-CoA decarboxylase, e.g., Oxc (from ().
  • oxalate catabolism enzyme(s) e.g., selected from formyl-CoA: oxalate CoA-transferase, e.g., Frc (from O. formigenes), oxalyl-CoA synthetase, e.g., ScAAE3 (from .S', cerevisiae), oxalyl-
  • the genetically engineered bacteria comprise a gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O.
  • the mammalian gut is a human mammalian gut.
  • the bacterial cell comprises an oxygen-level dependent transcriptional regulator, e.g., FNR, ANR, or DNR, and corresponding promoter from a different bacterial species.
  • the heterologous oxygen-level dependent transcriptional regulator and promoter increase the transcription of genes operably linked to said promoter, e.g., the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s), and/or the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes in a low-oxygen or anaerobic environment, as compared to the native gene(s) and promoter in the bacteria under the same conditions.
  • the non-native oxygen-level dependent transcriptional regulator is an FNR protein from N. gonorrhoeae (see, e.g., Isabella et al., 2011).
  • the corresponding wild-type transcriptional regulator is left intact and retains wild-type activity. In alternate embodiments, the corresponding wild-type transcriptional regulator is deleted or mutated to reduce or eliminate wildtype activity.
  • the genetically engineered bacteria comprise a wild-type oxygen-level dependent transcriptional regulator, e.g., FNR, ANR, or DNR, and corresponding promoter that is mutated relative to the wild-type promoter from bacteria of the same subtype.
  • the mutated promoter enhances binding to the wild-type transcriptional regulator and increases the transcription of genes operably linked to said promoter, e.g. , the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s), and/or the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g. , OxlT from O.
  • the genetically engineered bacteria comprise a wild-type oxygen -level dependent promoter, e.g., FNR, ANR, or DNR promoter, and corresponding transcriptional regulator that is mutated relative to the wild-type transcriptional regulator from bacteria of the same subtype.
  • a wild-type oxygen -level dependent promoter e.g., FNR, ANR, or DNR promoter
  • the mutated transcriptional regulator enhances binding to the wild-type promoter and increases the transcription of genes operably linked to said promoter, e.g., the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s), and/or the gene and/or gene cassette encoding one or more transporter(s) of oxalate, e.g., OxlT from O. formigenes in a low-oxygen or anaerobic environment, as compared to the wild-type transcriptional regulator under the same conditions.
  • the mutant oxygen-level dependent transcriptional regulator is an FNR protein comprising amino acid substitutions that enhance dimerization and FNR activity (see, e.g., Moore et al., 2006).
  • the bacterial cells disclosed herein comprise multiple copies of the endogenous gene encoding the oxygen level -sensing transcriptional regulator, e.g., the FNR gene.
  • the gene encoding the oxygen level-sensing transcriptional regulator is present on a plasmid.
  • the gene encoding the oxygen level-sensing transcriptional regulator and the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) are present on different plasmids.
  • the gene encoding the oxygen level-sensing transcriptional regulator and the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or the gene encoding a transporter of an oxalate are present on different plasmids. In some embodiments, the gene encoding the oxygen level-sensing transcriptional regulator and the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or the gene and/or gene cassette encoding one or more transporter(s) of oxalate are present on the same plasmid.
  • the gene encoding the oxygen level-sensing transcriptional regulator is present on a chromosome. In some embodiments, the gene encoding the oxygen level-sensing transcriptional regulator and the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or the gene and/or gene cassette encoding one or more a transporter(s) of oxalate are present on different chromosomes.
  • the gene encoding the oxygen levelsensing transcriptional regulator and the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or the gene and/or gene cassette encoding one or more transporter(s) of oxalate are present on the same chromosome.
  • expression of the transcriptional regulator is controlled by a different promoter than the promoter that controls expression of the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter.
  • expression of the transcriptional regulator is controlled by the same promoter that controls expression of the oxalate catabolism enzyme(s) and/or Oxalate transporter(s).
  • the transcriptional regulator and the oxalate catabolism enzyme(s) are divergently transcribed from a promoter region.
  • the genetically engineered bacteria comprise a gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s)that is expressed under the control of an inducible promoter.
  • the genetically engineered bacterium that expresses one or more oxalate catabolism enzyme(s) and/or oxalate transporter(s) is under the control of a promoter that is activated by inflammatory conditions.
  • the gene and/or gene cassette for producing the oxalate catabolism enzyme(s) and/or oxalate transporter is expressed under the control of an inflammatory-dependent promoter that is activated in inflammatory environments, e.g., a reactive nitrogen species or RNS promoter.
  • RNS reactive nitrogen species
  • RNS can cause deleterious cellular effects such as nitrosative stress.
  • RNS includes, but is not limited to, nitric oxide (NO*), peroxynitrite or peroxynitrite anion (ONOO-), nitrogen dioxide (*NO2), dinitrogen trioxide (N2O3), peroxynitrous acid (ONOOH), and nitroperoxycarbonate (ONOOCO2-) (unpaired electrons denoted by •).
  • NO* nitric oxide
  • ONOO- nitrogen dioxide
  • N2O3 dinitrogen trioxide
  • ONOOH peroxynitrous acid
  • ONOOCO2- nitroperoxycarbonate
  • Bacteria have evolved transcription factors that are capable of sensing RNS levels. Different RNS signaling pathways are triggered by different RNS levels and occur with different kinetics.
  • transcription factors that sense RNS and their corresponding RNS-responsive genes, promoters, and/or regulatory regions include, but are not limited to, those shown in Table 8.
  • the genetically engineered bacteria of the disclosure comprise a tunable regulatory region that is directly or indirectly controlled by a transcription factor that is capable of sensing at least one reactive nitrogen species.
  • the tunable regulatory region is operatively linked to a gene and/or gene cassette capable of directly or indirectly driving the expression of one or more oxalate catabolism enzyme(s), oxalate transporter(s), thus controlling expression of the oxalate catabolism enzyme, oxalate transporter(s), relative to RNS levels.
  • the tunable regulatory region is a RNS-inducible regulatory region
  • the payload is one or more oxalate catabolism enzyme(s), oxalate transporter(s), such as any of the oxalate catabolism enzymes, and/or oxalate transporter(s) provided herein;
  • a RNS- sensing transcription factor binds to and/or activates the regulatory region and drives expression of the oxalate catabolism enzyme and/or oxalate transporter gene or gene cassette.
  • inflammation is ameliorated, RNS levels are reduced, and production of the oxalate catabolism enzyme(s) and oxalate transporter(s) is decreased or eliminated.
  • the genetically engineered bacteria comprise a gene and/or gene cassette for producing one or more oxalate catabolism enzyme(s) and/or oxalate transporter(s) that is expressed under the control of an inducible promoter.
  • the genetically engineered bacterium that expresses one or more oxalate catabolism enzyme(s) and/or oxalate transporter(s) under the control of a promoter that is activated by conditions of cellular damage.
  • the gene and/or gene cassette for producing one or more oxalate catabolism enzyme(s) is expressed under the control of a cellular damaged-dependent promoter that is activated in environments in which there is cellular or tissue damage, e.g., a reactive oxygen species or ROS promoter.
  • ROS reactive oxygen species
  • H2O2 hydrogen peroxide
  • ROOH organic peroxide
  • OH- hydroxyl radical
  • *OH hydroxyl radical
  • superoxide or superoxide anion (’O2-), singlet oxygen (102), ozone (03), carbonate radical, peroxide or peroxyl radical (»O2- 2), hypochlorous acid (HOC1), hypochlorite ion (OC1-), sodium hypochlorite (NaOCl), nitric oxide (NO*), and peroxynitrite or peroxynitrite anion (ONOO-) (unpaired electrons denoted by •).
  • Bacteria have evolved transcription factors that are capable of sensing ROS levels. Different ROS signaling pathways are triggered by different ROS levels and occur with different kinetics (Marinho et al., 2014).
  • ROS -inducible regulatory region refers to a nucleic acid sequence to which one or more ROS-sensing transcription factors is capable of binding, wherein the binding and/or activation of the corresponding transcription factor activates downstream gene expression; in the presence of ROS, the transcription factor binds to and/or activates the regulatory region.
  • the ROS-inducible regulatory region comprises a promoter sequence.
  • the transcription factor senses ROS and subsequently binds to the ROS-inducible regulatory region, thereby activating downstream gene expression.
  • the transcription factor is bound to the ROS-inducible regulatory region in the absence of ROS; in the presence of ROS, the transcription factor undergoes a conformational change, thereby activating downstream gene expression.
  • the ROS-inducible regulatory region may be operatively linked to a gene sequence or gene sequence, e.g., a sequence or sequences encoding one or more oxalate catabolism enzyme(s).
  • a transcription factor e.g., OxyR
  • ROS induces expression of the gene or gene cassette.
  • transcription factors that sense ROS include, but are not limited to, those shown in Table 9.
  • the genetically engineered bacteria comprise a tunable regulatory region that is directly or indirectly controlled by a transcription factor that is capable of sensing at least one reactive oxygen species.
  • the tunable regulatory region is operatively linked to a gene or gene cassette capable of directly or indirectly driving the expression of an oxalate catabolism enzyme, thus controlling expression of the oxalate catabolism enzyme(s) relative to ROS levels.
  • the tunable regulatory region is a ROS-inducible regulatory region, and the molecule is an oxalate catabolism enzyme; when ROS is present, e.g., in an inflamed tissue, a ROS-sensing transcription factor binds to and/or activates the regulatory region and drives expression of the gene sequence and/or gene cassette sequence for one or more the oxalate catabolism enzyme(s) and/or oxalate transporter(s) thereby producing the oxalate catabolism enzyme(s) and/or oxalate transporter(s). Subsequently, when inflammation is ameliorated, ROS levels are reduced, and production of the oxalate catabolism enzyme(s) and/or oxalate transporter(s) is decreased or eliminated.
  • nucleic acid sequences of several exemplary OxyR-regulated regulatory regions are shown in Table 10.
  • genetically engineered bacteria comprise a nucleic acid sequence that is at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99% homologous to the DNA sequence of SEQ ID NO: 370, 371, 372, or 373, or a functional fragment thereof.
  • the genetically engineered bacteria of the disclosure comprise a gene encoding a ROS-sensing transcription factor, e.g., the oxyR gene, that is controlled by its native promoter, an inducible promoter, a promoter that is stronger than the native promoter, e.g., the GlnRS promoter or the P(Bla) promoter, or a constitutive promoter.
  • a ROS-sensing transcription factor e.g., the oxyR gene
  • a promoter that is stronger than the native promoter e.g., the GlnRS promoter or the P(Bla) promoter
  • expression of the ROS- sensing transcription factor is controlled by a different promoter than the promoter that controls expression of the therapeutic molecule.
  • expression of the ROS-sensing transcription factor is controlled by the same promoter that controls expression of the therapeutic molecule.
  • the ROS-sensing transcription factor and therapeutic molecule are divergently transcribed from a promoter region.
  • thermoregulators may be advantageous because of strong transcriptional control without the use of external chemicals or specialized media.
  • Thermoregulated protein expression using the mutant cI857 repressor and the pL and/or pR phage X promoters have been used to engineer recombinant bacterial strains.
  • a gene of interest cloned downstream of the X promoters can be efficiently regulated by the mutant thermolabile cI857 repressor of bacteriophage X.
  • cI857 binds to the oL or oR regions of the pR promoter and inhibits transcription by RNA polymerase.
  • the functional cI857 dimer is destabilized, binding to the oL or oR DNA sequences is abrogated, and mRNA transcription is initiated.
  • thermoregulated promoter may be induced in culture, e.g., grown in a flask, fermenter or other appropriate culture vessel, e.g., used during cell growth, cell expansion, fermentation, recovery, purification, formulation, and/or manufacture.
  • Bacteria comprising gene sequences or gene cassetes either indirectly or directly operably linked to a temperature sensitive system or promoter may, for example, could be induced by temperatures between 37°C and 42°C.
  • the cultures may be grown aerobically. Alternatively, the cultures are grown anaerobically.
  • the bacteria described herein comprise one or more gene sequence(s) or gene cassete(s) which are directly or indirectly operably linked to a temperature regulated promoter.
  • the gene sequence(s) or gene cassete(s) are induced in vitro during growth, preparation, or manufacturing of the strain prior to in vivo administration.
  • the gene sequence(s) are induced upon or during in vivo administration.
  • the gene sequence(s) are induced during in vitro growth, preparation, or manufacturing of the strain prior to in vivo administration and upon or during in vivo administration.
  • the genetically engineered bacteria further comprise gene sequence (s) encoding a transcription factor which is capable of binding to the temperature sensitive promoter.
  • the transcription factor is a repressor of transcription.
  • the thermoregulated promoter is operably linked to a construct having gene sequence(s) or gene cassete(s) encoding one or more protein(s) of interest jointly with a second promoter, e.g., a second constitutive or inducible promoter.
  • a second promoter e.g., a second constitutive or inducible promoter.
  • two promoters are positioned proximally to the construct and drive its expression, wherein the thermoregulated promoter is induced under a first set of exogenous conditions, and the second promoter is induced under a second set of exogenous conditions.
  • the first and second conditions may be two sequential culture conditions (z.e., during preparation of the culture in a flask, fermenter or other appropriate culture vessel, e.g., thermoregulation and arabinose or IPTG).
  • the first inducing conditions may be culture conditions, e.g., permissive temperature
  • the second inducing conditions may be in vivo conditions.
  • in vivo conditions include low-oxygen, microaerobic, or anaerobic conditions, presence of gut metabolites, and/or metabolites administered in combination with the bacterial strain.
  • one or more thermoregulated promoters drive expression of one or more protein(s) of interest in combination with an oxygen regulated promoter, e.g., FNR, driving the expression of the same gene sequence(s).
  • the thermoregulated promoter drives the expression of one or more protein(s) of interest from a low-copy plasmid or a high copy plasmid or a biosafety system plasmid described herein. In some embodiments, the thermoregulated promoter drives the expression of one or more protein(s) of interest from a construct which is integrated into the bacterial chromosome. Exemplary insertion sites are described herein.
  • the genetically engineered bacteria comprise one or more gene sequence(s) having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with any of the sequences of SEQ ID NO: 19.
  • the genetically engineered bacteria comprise one or more gene sequence(s) having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with any of the sequences of SEQ ID NO: 22.
  • the genetically engineered bacteria comprise one or more gene sequence(s) having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with any of the sequences of SEQ ID NO: 25.
  • the thermoregulated construct further comprises a gene encoding mutant cI857 repressor, which is divergently transcribed from the same promoter as the one or more one or more protein(s) of interest.
  • the genetically engineered bacteria comprise one or more gene sequence(s) having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with any of the sequences of SEQ ID NO: 20.
  • the genetically engineered bacteria comprise one or more gene sequence(s) encoding a polypeptide having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with the polypeptide encoded by any of the sequences of SEQ ID NO: 21.
  • the thermoregulated construct further comprises a gene encoding mutant cI38 repressor, which is divergently transcribed from the same promoter as the one or more one or more protein(s) of interest.
  • the genetically engineered bacteria comprise one or more gene sequence(s) having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with any of the sequences of SEQ ID NO: 23.
  • the genetically engineered bacteria comprise one or more gene sequence(s) encoding a polypeptide having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with the polypeptide encoded by any of the sequences of SEQ ID NO: 24. [0373] SEQ ID NOs: 19-25 are shown in Table 11.
  • essential gene refers to a gene which is necessary to for cell growth and/or survival.
  • Bacterial essential genes are well known to one of ordinary skill in the art, and can be identified by directed deletion of genes and/or random mutagenesis and screening (see, for example, Zhang and Lin, 2009, DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes, Nucl. Acids Res., 37:D455-D458 and Gerdes et al., Essential genes on metabolic maps, Curr. Opin. Biotechnol., 17(5):448-456, the entire contents of each of which are expressly incorporated herein by reference).
  • An “essential gene” may be dependent on the circumstances and environment in which an organism lives. For example, a mutation of, modification of, or excision of an essential gene may result in the recombinant bacteria of the disclosure becoming an auxotroph.
  • An auxotrophic modification is intended to cause bacteria to die in the absence of an exogenously added nutrient essential for survival or growth because they lack the gene(s) necessary to produce that essential nutrient.
  • auxotrophic modification is intended to cause bacteria to die in the absence of an exogenously added nutrient essential for survival or growth because they lack the gene(s) necessary to produce that essential nutrient.
  • any of the genetically engineered bacteria described herein also comprise a deletion or mutation in one or more gene(s) required for cell survival and/or growth.
  • the bacterial cell comprises a genetic mutation in one or more endogenous gene(s) encoding an oxalate biosynthesis gene, wherein the genetic mutation reduces biosynthesis of oxalate in the bacterial cell.
  • the essential gene is an oligonucleotide synthesis gene, for example, thyA.
  • the essential gene is a cell wall synthesis gene, for example, dapA.
  • the essential gene is an amino acid gene, for example, serA or MetA.
  • Any gene required for cell survival and/or growth may be targeted, including but not limited to, cysE, glnA, ilvD, leuB, lysA, serA, metA, glyA, hisB, ilvA, pheA, proA, thrC, trpC, tyrA, thyA, uraA, dapA, dapB, dapD, dapE, dapF, flhD, metB, metC, proAB, and thil, as long as the corresponding wild-type gene product is not produced in the bacteria.
  • Table 12 lists depicts exemplary bacterial genes which may be disrupted or deleted to produce an auxotrophic strain. These include, but are not limited to, genes required for oligonucleotide synthesis, amino acid synthesis, and cell wall synthesis.
  • Table 13 shows the survival of various amino acid auxotrophs in the mouse gut, as detected 24 hrs and 48 hrs post-gavage. These auxotrophs were generated using BW25113, a non-Nissle strain of /'.'. coli.
  • thymine is a nucleic acid that is required for bacterial cell growth; in its absence, bacteria undergo cell death.
  • the thyA gene encodes thymidylate synthetase, an enzyme that catalyzes the first step in thymine synthesis by converting dUMP to dTMP (Sat et al., 2003).
  • the bacterial cell of the disclosure is a thyA auxotroph in which the thyA gene is deleted and/or replaced with an unrelated gene.
  • a thyA auxotroph can grow only when sufficient amounts of thymine are present, e.g., by adding thymine to growth media in vitro, or in the presence of high thymine levels found naturally in the human gut in vivo.
  • the bacterial cell of the disclosure is auxotrophic in a gene that is complemented when the bacterium is present in the mammalian gut. Without sufficient amounts of thymine, the thyA auxotroph dies.
  • the auxotrophic modification is used to ensure that the bacterial cell does not survive in the absence of the auxotrophic gene product (e.g., outside of the gut).
  • Diaminopimelic acid is an amino acid synthetized within the lysine biosynthetic pathway and is required for bacterial cell wall growth (Meadow et al., 1959; Clarkson et al., 1971).
  • any of the genetically engineered bacteria described herein is a dapD auxotroph in which dapD is deleted and/or replaced with an unrelated gene.
  • a dapD auxotroph can grow only when sufficient amounts of DAP are present, e.g., by adding DAP to growth media in vitro. Without sufficient amounts of DAP, the dapD auxotroph dies.
  • the auxotrophic modification is used to ensure that the bacterial cell does not survive in the absence of the auxotrophic gene product (e.g., outside of the gut).
  • the genetically engineered bacterium of the present disclosure is a uraA auxotroph in which uraA is deleted and/or replaced with an unrelated gene.
  • the uraA gene codes for UraA, a membrane-bound transporter that facilitates the uptake and subsequent metabolism of the pyrimidine uracil (Andersen et al., 1995).
  • a uraA auxotroph can grow only when sufficient amounts of uracil are present, e.g., by adding uracil to growth media in vitro. Without sufficient amounts of uracil, the uraA auxotroph dies.
  • auxotrophic modifications are used to ensure that the bacteria do not survive in the absence of the auxotrophic gene product (e.g., outside of the gut).
  • an auxotrophic bacterial strain may receive DNA from a non-auxotrophic strain, which repairs the genomic deletion and permanently rescues the auxotroph. Therefore, engineering a bacterial strain with more than one auxotroph may greatly decrease the probability that DNA transfer will occur enough times to rescue the auxotrophy.
  • the genetically engineered bacteria comprise a deletion or mutation in two or more genes required for cell survival and/or growth.
  • essential genes include, but are not limited to yhbV, yagG, hemB, secD, secF, ribD, ribE, thiL, dxs, ispA, dnaX, adk, hemH, IpxH, cysS, fold, rplT, infC, thrS, nadE, gapA, yeaZ, aspS, argS, pgsA, yejM, metG,folE, yejM, gyrA, nrdA, nrdB, folC, accD, fabB, gltX, ligA, zipA, dapE, dapA, der, hisS, ispG, suhB, tadA, acpS, era, rnc, ftsB, eno, pyrG, chpR, I
  • the genetically engineered bacterium of the present disclosure is a synthetic ligand-dependent essential gene (SLiDE) bacterial cell.
  • SLiDE bacterial cells are synthetic auxotrophs with a mutation in one or more essential genes that only grow in the presence of a particular ligand (see Lopez and Anderson “Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21 (DE3 Biosafety Strain,” ACS Synthetic Biology (2015) DOI: 10.1021/acssynbio.5b00085, the entire contents of which are expressly incorporated herein by reference).
  • the SLiDE bacterial cell comprises a mutation in an essential gene.
  • the essential gene is selected from the group consisting of pheS, dnaN, tyrS, metG and adk.
  • the essential gene is dnaN comprising one or more of the following mutations: H191N, R240C, I317S, F319V, L340T, V347I, and S345C.
  • the essential gene is dnaN comprising the mutations H191N, R240C, I317S, F319V, L340T, V347I, and S345C.
  • the essential gene is pheS comprising one or more of the following mutations: F125G, P183T, P184A, R186A, and I188L. In some embodiments, the essential gene is pheS comprising the mutations F125G, P183T, P184A, R186A, and I188L. In some embodiments, the essential gene is tyrS comprising one or more of the following mutations: L36V, C38A and F40G. In some embodiments, the essential gene is tyrS comprising the mutations L36V, C38A and F40G. In some embodiments, the essential gene is metG comprising one or more of the following mutations: E45Q, N47R, I49G, and A51C.
  • the essential gene is metG comprising the mutations E45Q, N47R, I49G, and A51C. In some embodiments, the essential gene is adk comprising one or more of the following mutations: I4L, L5I and L6G. In some embodiments, the essential gene is adk comprising the mutations I4L, L5I and L6G.
  • the genetically engineered bacterium is complemented by a ligand.
  • the ligand is selected from the group consisting of benzothiazole, indole, 2- aminobenzothiazole, indole -3 -butyric acid, indole-3 -acetic acid, and L-histidine methyl ester.
  • bacterial cells comprising mutations in metG are complemented by benzothiazole, indole, 2-aminobenzothiazole, indole -3 -butyric acid, indole-3 -acetic acid or L-histidine methyl ester.
  • Bacterial cells comprising mutations in dnaN are complemented by benzothiazole, indole or 2- aminobenzothiazole.
  • Bacterial cells comprising mutations in pheS are complemented by benzothiazole or 2-aminobenzothiazole.
  • Bacterial cells comprising mutations in tyrS are complemented by benzothiazole or 2- aminobenzothiazole.
  • Bacterial cells comprising mutations in adk I4L, L5I and L6G are complemented by benzothiazole or indole.
  • the genetically engineered bacterium comprises more than one mutant essential gene that renders it auxotrophic to a ligand.
  • the bacterial cell comprises mutations in two essential genes.
  • the bacterial cell comprises mutations in tyrS (L36V, C38A, and F40G) and metG (E45Q, N47R, I49G, and A51C).
  • the bacterial cell comprises mutations in three essential genes.
  • the bacterial cell comprises mutations in tyrS (L36V, C38A, and F40G), metG (E45Q, N47R, I49G, and A51C), and pheS (F125G, P183T, P184A, R186A, and I188L).
  • the genetically engineered bacterium is a conditional auxotroph whose essential gene(s) is replaced using the arabinose system described herein.
  • the genetically engineered bacterium of the disclosure is an auxotroph and also comprises kill-switch circuitry, such as any of the kill -switch components and systems described herein.
  • the recombinant bacteria may comprise a deletion or mutation in an essential gene required for cell survival and/or growth, for example, in a DNA synthesis gene, for example, thyA, cell wall synthesis gene, for example, dapA and/or an amino acid gene, for example, serA o Met A or z/vC, and may also comprise a toxin gene that is regulated by one or more transcriptional activators that are expressed in response to an environmental condition(s) and/or signal(s) (such as the described arabinose system) or regulated by one or more recombinases that are expressed upon sensing an exogenous environmental condition(s) and/or signal(s) (such as the recombinase systems described herein).
  • the genetically engineered bacterium of the disclosure is an auxotroph and also comprises kill-switch circuitry, such as any of the kill-switch components and systems described herein, as well as another biosecurity system, such a conditional origin of replication (see Wright et al., supra).
  • the disclosure provides an isolated plasmid comprising a first nucleic acid encoding a first payload operably linked to a first inducible promoter, and a second nucleic acid encoding a second payload operably linked to a second inducible promoter.
  • the disclosure provides an isolated plasmid further comprising a third nucleic acid encoding a third payload operably linked to a third inducible promoter.
  • the disclosure provides a plasmid comprising four, five, six, or more nucleic acids encoding four, five, six, or more payloads operably linked to inducible promoters.
  • the first, second, third, fourth, fifth, sixth, etc. “payload(s)” can be an oxalate catabolism enzyme, a transporter of oxalate, or other sequence described herein.
  • the nucleic acid encoding the first payload and the nucleic acid encoding the second payload are operably linked to the first inducible promoter.
  • the nucleic acid encoding the first payload is operably linked to a first inducible promoter and the nucleic acid encoding the second payload is operably linked to a second inducible promoter.
  • the first inducible promoter and the second inducible promoter are separate copies of the same inducible promoter.
  • the first inducible promoter and the second inducible promoter are different inducible promoters.
  • the nucleic acid encoding the third payload and the nucleic acid encoding the first and second payloads are all operably linked to the same inducible promoter.
  • the nucleic acid encoding the first payload is operably linked to a first inducible promoter
  • the nucleic acid encoding the second payload is operably linked to a second inducible promoter
  • the nucleic acid encoding the third payload is operably linked to a third inducible promoter.
  • the first, second, and third inducible promoters are separate copies of the same inducible promoter. In other embodiments, the first inducible promoter, the second inducible promoter, and the third inducible promoter are different inducible promoters. In some embodiments, the first promoter, the second promoter, and the optional third promoter, or the first promoter and the second promoter and the optional third promoter, are each directly or indirectly induced by low-oxygen or anaerobic conditions. In other embodiments, the first promoter, the second promoter, and the optional third promoter, or the first promoter and the second promoter and the optional third promoter, are each a fumarate and nitrate reduction regulator (FNR) responsive promoter.
  • FNR fumarate and nitrate reduction regulator
  • first promoter, the second promoter, and the optional third promoter, or the first promoter and the second promoter and the optional third promoter are each a ROS-inducible regulatory region. In other embodiments, the first promoter, the second promoter, and the optional third promoter, or the first promoter and the second promoter and the optional third promoter are each a RNS-inducible regulatory region.
  • the heterologous gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) is operably linked to a constitutive promoter.
  • the constitutive promoter is a lac promoter.
  • the constitutive promoter is a Tet promoter.
  • the constitutive promoter is a constitutive Escherichia coli o 32 promoter.
  • the constitutive promoter is a constitutive Escherichia coli o 70 promoter.
  • the constitutive promoter is a constitutive Bacillus suhtilis o A promoter.
  • the constitutive promoter is a constitutive Bacillus suhtilis o B promoter.
  • the constitutive promoter is a Salmonella promoter. In other embodiments, the constitutive promoter is a bacteriophage T7 promoter. In other embodiments, the constitutive promoter is and a bacteriophage SP6 promoter. In any of the above-described embodiments, the plasmid further comprises a heterologous gene encoding a transporter oxalate, and/or a kill switch construct, which may be operably linked to a constitutive promoter or an inducible promoter.
  • the isolated plasmid comprises at least one heterologous oxalate catabolism enzyme gene operably linked to a first inducible promoter; a heterologous gene encoding a TetR protein operably linked to a P ara BAD promoter, a heterologous gene encoding AraC operably linked to a P ara c promoter, a heterologous gene encoding an antitoxin operably linked to a constitutive promoter, and a heterologous gene encoding a toxin operably linked to a PietR promoter.
  • the isolated plasmid comprises at least one heterologous gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) operably linked to a first inducible promoter; a heterologous gene encoding a TetR protein and an anti-toxin operably linked to a P ara BAD promoter, a heterologous gene encoding AraC operably linked to a P ara c promoter, and a heterologous gene encoding a toxin operably linked to a PietR promoter.
  • a first nucleic acid encoding one or more oxalate catabolism enzyme(s) comprises a Formyl CoA: oxalate CoA transferase (e.g., frc) gene.
  • the frc gene is from O. formi genes .
  • the frc gene has at least about 90% identity to SEQ ID NO: 500.
  • the frc gene comprises SEQ ID NO: 500.
  • a first nucleic acid encoding one or more oxalate catabolism enzyme(s) comprises an Oxalate-CoA ligase (e.g., ScAAE3) gene.
  • the ScAAE3 gene is from S.
  • the ScAAE3 gene has at least about 90% identity to SEQ ID NO: 502.
  • the ScAAE3gene comprises SEQ ID NO: 502.
  • a first nucleic acid encoding one or more oxalate catabolism enzyme(s) comprises an acetyl-CoA: oxalate CoA- transferase (e.g., YfdE) gene.
  • the YfdE gene is from E. coli.
  • the YfdE gene has at least about 90% identity to SEQ ID NO: 503.
  • the YfdE gene comprises SEQ ID NO: 503.
  • a first nucleic acid encoding one or more oxalate catabolism enzyme(s) comprises a Oxalyl-CoA Decarboxylase (e.g., oxc) gene.
  • the frc and/or ScAAE3 and/or YfdE gene(s) are co-expressed with a Oxalyl-CoA Decarboxylase (e.g., oxc) gene.
  • the oxc gene is from O. formi genes .
  • the oxc gene has at least about 90% identity to SEQ ID NO: 501.
  • the oxc gene comprises SEQ ID NO: 501.
  • a second nucleic acid encoding a transporter of oxalate comprises OxlT.
  • the OxlT transporter is from O. formigenes.
  • the OxlT transporter has at least about 90% identity to SEQ ID NO: 510.
  • the OxlT transporter comprises SEQ ID NO: 510.
  • the plasmid is a high-copy plasmid. In another embodiment, the plasmid is a low-copy plasmid.
  • the disclosure provides a recombinant bacterial cell comprising an isolated plasmid described herein. In another embodiment, the disclosure provides a pharmaceutical composition comprising the recombinant bacterial cell.
  • the bacterial cell further comprises a genetic mutation in an endogenous gene encoding an exporter of oxalate, wherein the genetic mutation reduces export of oxalate from the bacterial cell.
  • the bacterial cell further comprises a genetic mutation in an endogenous gene encoding an oxalate biosynthesis gene, wherein the genetic mutation reduces biosynthesis of oxalate in the bacterial cell.
  • any of the gene(s) or gene cassette(s) of the present disclosure may be integrated into the bacterial chromosome at one or more integration sites.
  • One or more copies of the gene for example, an oxalate catabolism gene, oxalate transporter gene, and/or oxalate binding protein gene
  • gene cassette for example, a gene cassette comprising an oxalate catabolism gene and/or an oxalate transporter gene may be integrated into the bacterial chromosome.
  • Having multiple copies of the gene or gene cassette integrated into the chromosome allows for greater production of the payload, e.g., one or more oxalate catabolism enzyme(s) and/or oxalate transporter gene(s) and other enzymes of a gene cassette, and also permits fine-tuning of the level of expression.
  • the payload e.g., one or more oxalate catabolism enzyme(s) and/or oxalate transporter gene(s) and other enzymes of a gene cassette
  • circuits described herein such as any of the kill-switch circuits, in addition to the therapeutic gene(s) or gene cassette(s) could be integrated into the bacterial chromosome at one or more different integration sites to perform multiple different functions.
  • FIG. 3 depicts the genotype of SYNB8802.
  • SYNB8802 is a strain of modified live probiotic bacterium (Escherichia coli Nissle 1917 [EcN]) that has been modified to treat EH by consuming oxalate within the gastrointestinal tract.
  • the locations of the genomic modification sites in SYNB8802 are shown, with kbp designation indicating the chromosomal position relative to the 0/5.4 Mb reference marker.
  • the chromosomal origin of replication is shown as a red line (ori). Italicized gene names in parenthesis refer to the upstream and downstream genes surrounding the inserted genes.
  • SYNB8802 was developed by engineering a pathway for oxalate degradation in a probiotic strain of EcN using the oxalate degradation capabilities of the human commensal microorganism Oxalobacter formigenes.
  • the following modifications to the genome of EcN have been made to enhance oxalate degradation under the low oxygen conditions found in the gut, while augmenting biologic containment through thymidine auxotrophy: (1) Insertion of one gene encoding an oxalate/formate antiporter (OxlT) derived from Oxalobacter formigenes under the regulatory control of an anaerobic-inducible promoter (PfhrS) and the anaerobic-responsive transcriptional activator FNR.
  • OxlT oxalate/formate antiporter
  • the first gene is an oxalyl-CoA synthetase (ScaaE3) derived from Saccharomyces cerevisiae.
  • the second gene is an oxalate decarboxylase (OxdC) derived from Oxalobacter formigenes.
  • the third gene (frc) is a formyl- CoA transferase derived from Oxalobacter formigenes .
  • the genetically engineered bacteria comprise a stably maintained plasmid or chromosome carrying a gene for producing an oxalate catabolism enzyme and/or oxalate transporter such that the oxalate catabolism enzyme and/or oxalate transporter can be expressed in the host cell, and the host cell is capable of survival and/or growth in vitro, e.g. , in medium, and/or in vivo.
  • a bacterium may comprise multiple copies of the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter(s).
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter(s) is expressed on a low-copy plasmid.
  • the low- copy plasmid may be useful for increasing stability of expression.
  • the low- copy plasmid may be useful for decreasing leaky expression under non-inducing conditions.
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter(s) is expressed on a high-copy plasmid.
  • the high- copy plasmid may be useful for increasing expression of the oxalate catabolism enzyme(s) and/or oxalate transporter(s).
  • the gene and/or gene cassette encoding one or more oxalate catabolism enzyme(s) and/or oxalate transporter(s) is expressed on a chromosome.
  • the bacteria are genetically engineered to include multiple mechanisms of action (MOAs), e.g., circuits producing multiple copies of the same product (e.g., to enhance copy number) or circuits performing multiple different functions.
  • MOAs mechanisms of action
  • the genetically engineered bacteria may include four copies of the gene and/or gene cassette encoding one or more particular oxalate catabolism enzyme(s) and/or oxalate transporter(s) inserted at four different insertion sites.
  • the genetically engineered bacteria may include three copies of the gene encoding a particular oxalate catabolism enzyme and/or oxalate transporter inserted at three different insertion sites and three copies of the gene encoding a different oxalate catabolism enzyme and/or oxalate transporter inserted at three different insertion sites.
  • the genetically engineered bacteria of the disclosure produce at least about 1.5 -fold, at least about 2-fold, at least about 10-fold, at least about 15 -fold, at least about 20- fold, at least about 30-fold, at least about 50-fold, at least about 100-fold, at least about 200-fold, at least about 300-fold, at least about 400-fold, at least about 500-fold, at least about 600-fold, at least about 700-fold, at least about 800-fold, at least about 900-fold, at least about 1,000-fold, or at least about 1,500-fold more of the oxalate catabolism enzyme(s) and/or oxalate transporter(s) and/or transcript of the gene(s) in the operon as compared to unmodified bacteria of the same subtype under the same conditions.
  • qPCR quantitative PCR
  • Primers specific for oxalate catabolism enzyme and/or oxalate transporter gene(s) may be designed and used to detect mRNA in a sample according to methods known in the art.
  • a fluorophore is added to a sample reaction mixture that may contain oxalate catabolism enzyme mRNA, and a thermal cycler is used to illuminate the sample reaction mixture with a specific wavelength of light and detect the subsequent emission by the fluorophore.
  • the reaction mixture is heated and cooled to predetermined temperatures for predetermined time periods. In certain embodiments, the heating and cooling is repeated for a predetermined number of cycles. In some embodiments, the reaction mixture is heated and cooled to 90-100° C, 60-70° C, and 30-50° C for a predetermined number of cycles. In a certain embodiment, the reaction mixture is heated and cooled to 93-97° C, 55-65° C, and 35-45° C for a predetermined number of cycles. In some embodiments, the accumulating amplicon is quantified after each cycle of the qPCR. The number of cycles at which fluorescence exceeds the threshold is the threshold cycle (CT). At least one CT result for each sample is generated, and the CT result(s) may be used to determine mRNA expression levels of the oxalate catabolism enzyme and/or oxalate transporter gene(s).
  • CT threshold cycle
  • qPCR quantitative PCR
  • Primers specific for oxalate catabolism enzyme and/or oxalate transporter gene(s) may be designed and used to detect mRNA in a sample according to methods known in the art.
  • a fluorophore is added to a sample reaction mixture that may contain oxalate catabolism enzyme and/or oxalate transporter mRNA, and a thermal cycler is used to illuminate the sample reaction mixture with a specific wavelength of light and detect the subsequent emission by the fluorophore.
  • the reaction mixture is heated and cooled to predetermined temperatures for predetermined time periods. In certain embodiments, the heating and cooling is repeated for a predetermined number of cycles. In some embodiments, the reaction mixture is heated and cooled to 90-100° C, 60-70° C, and 30-50° C for a predetermined number of cycles. In a certain embodiment, the reaction mixture is heated and cooled to 93-97° C, 55-65° C, and 35-45° C for a predetermined number of cycles. In some embodiments, the accumulating amplicon is quantified after each cycle of the qPCR. The number of cycles at which fluorescence exceeds the threshold is the threshold cycle (CT). At least one CT result for each sample is generated, and the CT result(s) may be used to determine mRNA expression levels of the oxalate catabolism enzyme and/or oxalate transporter gene(s).
  • CT threshold cycle
  • compositions comprising the genetically engineered microorganisms of the disclosure may be used to treat, manage, ameliorate, and/or prevent diseases or disorders in which oxalate is detrimental in a subject.
  • the disorder in which oxalate is detrimental is a disorder that results in daily urinary oxalate excretion over 40 mg per 24 hours.
  • Pharmaceutical compositions of the disclosure comprising one or more genetically engineered bacteria, and/or one or more genetically engineered virus, alone or in combination with prophylactic agents, therapeutic agents, and/or pharmaceutically acceptable carriers are provided.
  • the pharmaceutical composition comprises one species, strain, or subtype of bacteria that are engineered to comprise one or more of the genetic modifications described herein, e.g., selected from expression of at least one oxalate catabolism enzyme, oxalate importer/transporter and/or formate exporter and/or oxalate: formate antiporter, auxotrophy, killswitch, knock-out, etc.
  • the pharmaceutical composition comprises two or more species, strains, and/or subtypes of bacteria that are each engineered to comprise the genetic modifications described herein, e.g., one oxalate catabolism enzyme, oxalate importer/transporter and/or formate exporter and/or oxalate: formate antiporter, auxotrophy, kill-switch, knock-out, etc.
  • the pharmaceutical compositions of the disclosure may be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active ingredients into compositions for pharmaceutical use.
  • compositions are known in the art (see, e.g., "Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, PA).
  • the pharmaceutical compositions are subjected to tabletting, lyophilizing, direct compression, conventional mixing, dissolving, granulating, levigating, emulsifying, encapsulating, entrapping, or spray drying to form tablets, granulates, nanoparticles, nanocapsules, microcapsules, microtablets, pellets, or powders, which may be enterically coated or uncoated. Appropriate formulation depends on the route of administration.
  • the genetically engineered microorganisms may be formulated into pharmaceutical compositions in any suitable dosage form (e.g., liquids, capsules, sachet, hard capsules, soft capsules, tablets, enteric coated tablets, suspension powders, granules, or matrix sustained release formations for oral administration) and for any suitable type of administration (e.g., oral, topical, injectable, intravenous, sub-cutaneous, immediate-release, pulsatile-release, delayed-release, or sustained release). Suitable dosage amounts for the genetically engineered bacteria may range from about 10 4 to 10 12 bacteria.
  • the composition may be administered once or more daily, weekly, or monthly.
  • the composition may be administered before, during, or following a meal.
  • the pharmaceutical composition is administered before the subject eats a meal. In one embodiment, the pharmaceutical composition is administered currently with a meal. In on embodiment, the pharmaceutical composition is administered after the subject eats a meal.
  • the genetically engineered bacteria or genetically engineered virus may be formulated into pharmaceutical compositions comprising one or more pharmaceutically acceptable carriers, thickeners, diluents, buffers, buffering agents, surface active agents, neutral or cationic lipids, lipid complexes, liposomes, penetration enhancers, carrier compounds, and other pharmaceutically acceptable carriers or agents.
  • the pharmaceutical composition may include, but is not limited to, the addition of calcium bicarbonate, sodium bicarbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils, polyethylene glycols, and surfactants, including, for example, polysorbate 20.
  • the genetically engineered bacteria of the disclosure may be formulated in a solution of sodium bicarbonate, e.g., 1 molar solution of sodium bicarbonate or another concentration described herein (to buffer an acidic cellular environment, such as the stomach, for example).
  • the genetically engineered bacteria may be administered and formulated as neutral or salt forms.
  • Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
  • the genetically engineered microorganisms may be administered intravenously, e.g., by infusion or injection.
  • the genetically engineered microorganisms of the disclosure may be administered intrathecally. In some embodiments, the genetically engineered microorganisms of the disclosure may be administered orally.
  • the genetically engineered microorganisms disclosed herein may be administered topically and formulated in the form of an ointment, cream, transdermal patch, lotion, gel, shampoo, spray, aerosol, solution, emulsion, or other form well known to one of skill in the art. See, e.g., "Remington's Pharmaceutical Sciences," Mack Publishing Co., Easton, PA.
  • viscous to semi-solid or solid forms comprising a carrier or one or more excipients compatible with topical application and having a dynamic viscosity greater than water are employed.
  • suitable formulations include, but are not limited to, solutions, suspensions, emulsions, creams, ointments, powders, liniments, salves, etc., which may be sterilized or mixed with auxiliary agents (e.g., preservatives, stabilizers, wetting agents, buffers, or salts) for influencing various properties, e.g., osmotic pressure.
  • suitable topical dosage forms include sprayable aerosol preparations wherein the active ingredient in combination with a solid or liquid inert carrier, is packaged in a mixture with a pressurized volatile (e.g., a gaseous propellant, such as freon) or in a squeeze bottle.
  • a pressurized volatile e.g., a gaseous propellant, such as freon
  • Moisturizers or humectants can also be added to pharmaceutical compositions and dosage forms. Examples of such additional ingredients are well known in the art.
  • the pharmaceutical composition comprising the recombinant bacteria of the disclosure may be formulated as a hygiene product.
  • the hygiene product may be an antibacterial formulation, or a fermentation product such as a fermentation broth.
  • Hygiene products may be, for example, shampoos, conditioners, creams, pastes, lotions, and lip balms.
  • the genetically engineered microorganisms disclosed herein may be administered orally and formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, etc.
  • Pharmacological compositions for oral use can be made using a solid excipient, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries if desired, to obtain tablets or dragee cores.
  • Suitable excipients include, but are not limited to, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose compositions such as maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carbomethylcellulose; and/or physiologically acceptable polymers such as polyvinylpyrrolidone (PVP) or polyethylene glycol (PEG). Disintegrating agents may also be added, such as cross-linked polyvinylpyrrolidone, agar, alginic acid or a salt thereof such as sodium alginate.
  • fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol
  • cellulose compositions such as maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carbo
  • Tablets or capsules can be prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone, hydroxypropyl methylcellulose, carboxymethylcellulose, polyethylene glycol, sucrose, glucose, sorbitol, starch, gum, kaolin, and tragacanth); fillers (e.g., lactose, microcrystalline cellulose, or calcium hydrogen phosphate); lubricants (e.g., calcium, aluminum, zinc, stearic acid, polyethylene glycol, sodium lauryl sulfate, starch, sodium benzoate, L-leucine, magnesium stearate, talc, or silica); disintegrants (e.g., starch, potato starch, sodium starch glycolate, sugars, cellulose derivatives, silica powders); or wetting agents (e.g, sodium lauryl sulphate).
  • binding agents e.g., pregelatinised mai
  • the tablets may be coated by methods well known in the art.
  • a coating shell may be present, and common membranes include, but are not limited to, polylactide, polyglycolic acid, polyanhydride, other biodegradable polymers, alginate- polylysine-alginate (APA), alginate-polymethylene-co-guanidine-alginate (A-PMCG-A), hydroymethylacrylate-methyl methacrylate (HEMA-MMA), multilayered HEMA-MMA-MAA, polyacrylonitrilevinylchloride (PAN-PVC), acrylonitrile/sodium methallylsulfonate (AN-69), polyethylene glycol/poly pentamethylcyclopentasiloxane/polydimethylsiloxane (PEG/PD5/PDMS), poly N,N- dimethyl acrylamide (PDMAAm), siliceous encapsulates, cellulose sulphate/sodium alginate/polymethylene-co-
  • the genetically engineered microorganisms are enterically coated for release into the gut or a particular region of the gut, for example, the large intestine.
  • the typical pH profile from the stomach to the colon is about 1-4 (stomach), 5.5-6 (duodenum), 7.3-8.0 (ileum), and 5.5-6.5 (colon).
  • the pH profile may be modified.
  • the coating is degraded in specific pH environments in order to specify the site of release. In some embodiments, at least two coatings are used. In some embodiments, the outside coating and the inside coating are degraded at different pH levels.
  • enteric coating materials may be used, in one or more coating layers (e.g., outer, inner and/o intermediate coating layers). Enteric coated polymers remain unionised at low pH, and therefore remain insoluble. But as the pH increases in the gastrointestinal tract, the acidic functional groups are capable of ionisation, and the polymer swells or becomes soluble in the intestinal fluid.
  • Materials used for enteric coatings include Cellulose acetate phthalate (CAP), Poly(methacrylic acid-co -methyl methacrylate), Cellulose acetate trimellitate (CAT), Poly(vinyl acetate phthalate) (PVAP) and Hydroxypropyl methylcellulose phthalate (HPMCP), fatty acids, waxes, Shellac (esters of aleurtic acid), plastics and plant fibers. Additionally, Zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch and starch derivatives, and dextrins (e.g., maltodextrin) are also used.
  • CAP Cellulose acetate phthalate
  • CAT Cellulose acetate trimellitate
  • PVAP Poly(vinyl acetate phthalate)
  • HPCP Hydroxypropyl methylcellulose phthalate
  • Zein, Aqua-Zein an aqueous zein formulation containing no alcohol
  • enteric coatings include ethylcellulose, methylcellulose, hydroxypropyl methylcellulose, amylose acetate phthalate, cellulose acetate phthalate, hydroxyl propyl methyl cellulose phthalate, an ethylacrylate, and a methylmethacrylate.
  • Coating polymers also may comprise one or more of, phthalate derivatives, CAT, HPMCAS, polyacrylic acid derivatives, copolymers comprising acrylic acid and at least one acrylic acid ester, EudragitTM S (poly(methacrylic acid, methyl methacrylate) 1:2); Eudragit LI 00TM S (poly(methacrylic acid, methyl methacrylate) 1: 1); Eudragit L30DTM, (poly(methacrylic acid, ethyl acrylate) 1: 1); and (Eudragit L100-55) (poly(methacrylic acid, ethyl acrylate)l: 1) (EudragitTM L is an anionic polymer synthesized from methacrylic acid and methacrylic acid methyl ester), polymethyl methacrylate blended with acrylic acid and acrylic ester copolymers, alginic acid, ammonia alginate, sodium, potassium, magnesium or calcium alginate, vinyl acetate copolymers,
  • Coating layers may also include polymers which contain Hydroxypropylmethylcellulose (HPMC), Hydroxypropylethylcellulose (HPEC), Hydroxypropylcellulose (HPC), hydroxypropylethylcellulose (HPEC), hydroxymethylpropylcellulose (HMPC), ethylhydroxyethylcellulose (EHEC) (Ethulose), hydroxyethylmethylcellulose (HEMC), hydroxymethylethylcellulose (HMEC), propylhydroxyethylcellulose (PHEC), methylhydroxyethylcellulose (M H EC), hydrophobically modified hydroxyethylcellulose (NEXTON), carboxymethyl hydroxyethylcellulose (CMHEC), Methylcellulose, Ethylcellulose, water soluble vinyl acetate copolymers, gums, polysaccharides such as alginic acid and alginates such as ammonia alginate, sodium alginate, potassium alginate, acid phthalate of carbohydrates, amylose acetate phthalate
  • Liquid preparations for oral administration may take the form of solutions, syrups, suspensions, or a dry product for constitution with water or other suitable vehicle before use.
  • Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable agents such as suspending agents (e.g., sorbitol syrup, cellulose derivatives, or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g, almond oil, oily esters, ethyl alcohol, or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid).
  • the preparations may also contain buffer salts, flavoring, coloring, and sweetening agents as appropriate.
  • Preparations for oral administration may be suitably formulated for slow release, controlled release, or sustained release of the genetically engineered microorganisms described herein.
  • the genetically engineered microorganisms of the disclosure may be formulated in a composition suitable for administration to pediatric subjects.
  • a composition suitable for administration to pediatric subjects may include easy-to-swallow or dissolvable dosage forms, or more palatable compositions, such as compositions with added flavors, sweeteners, or taste blockers.
  • a composition suitable for administration to pediatric subjects may also be suitable for administration to adults.
  • the composition suitable for administration to pediatric subjects may include a solution, syrup, suspension, elixir, powder for reconstitution as suspension or solution, dispersible/effervescent tablet, chewable tablet, gummy candy, lollipop, freezer pop, troche, chewing gum, oral thin strip, orally disintegrating tablet, sachet, soft gelatin capsule, sprinkle oral powder, or granules.
  • the composition is a gummy candy, which is made from a gelatin base, giving the candy elasticity, desired chewy consistency, and longer shelf-life.
  • the gummy candy may also comprise sweeteners or flavors.
  • the composition suitable for administration to pediatric subjects may include a flavor.
  • flavor is a substance (liquid or solid) that provides a distinct taste and aroma to the formulation. Flavors also help to improve the palatability of the formulation. Flavors include, but are not limited to, strawberry, vanilla, lemon, grape, bubble gum, and cherry.
  • the genetically engineered microorganisms may be orally administered, for example, with an inert diluent or an assimilable edible carrier.
  • the compound may also be enclosed in a hard or soft shell gelatin capsule, compressed into tablets, or incorporated directly into the subject’s diet.
  • the compounds may be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like.
  • the pharmaceutical composition comprising the recombinant bacteria of the disclosure may be a comestible product, for example, a food product.
  • the food product is milk, concentrated milk, fermented milk (yogurt, sour milk, frozen yogurt, lactic acid bacteria-fermented beverages), milk powder, ice cream, cream cheeses, dry cheeses, soybean milk, fermented soybean milk, vegetable-fruit juices, fruit juices, sports drinks, confectionery, candies, infant foods (such as infant cakes), nutritional food products, animal feeds, or dietary supplements.
  • the food product is a fermented food, such as a fermented dairy product.
  • the fermented dairy product is yogurt.
  • the fermented dairy product is cheese, milk, cream, ice cream, milk shake, or kefir.
  • the recombinant bacteria of the disclosure are combined in a preparation containing other live bacterial cells intended to serve as probiotics.
  • the food product is a beverage.
  • the beverage is a fruit juice-based beverage or a beverage containing plant or herbal extracts.
  • the food product is a jelly or a pudding.
  • Other food products suitable for administration of the recombinant bacteria of the disclosure are well known in the art. For example, see U.S. 2015/0359894 and US 2015/0238545, the entire contents of each of which are expressly incorporated herein by reference.
  • the pharmaceutical composition of the disclosure is injected into, sprayed onto, or sprinkled onto a food product, such as bread, yogurt, or cheese.
  • the composition is formulated for intraintestinal administration, intrajejunal administration, intraduodenal administration, intraileal administration, gastric shunt administration, or intracolic administration, via nanoparticles, nanocapsules, microcapsules, or microtablets, which are enterically coated or uncoated.
  • the pharmaceutical compositions may also be formulated in rectal compositions such as suppositories or retention enemas, using, e.g., conventional suppository bases such as cocoa butter or other glycerides.
  • the compositions may be suspensions, solutions, or emulsions in oily or aqueous vehicles, and may contain suspending, stabilizing and/or dispersing agents.
  • the genetically engineered microorganisms described herein may be administered intranasally, formulated in an aerosol form, spray, mist, or in the form of drops, and conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant (e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas).
  • Pressurized aerosol dosage units may be determined by providing a valve to deliver a metered amount.
  • Capsules and cartridges (e.g., of gelatin) for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.
  • the genetically engineered microorganisms may be administered and formulated as depot preparations. Such long acting formulations may be administered by implantation or by injection, including intravenous injection, subcutaneous injection, local injection, direct injection, or infusion.
  • the compositions may be formulated with suitable polymeric or hydrophobic materials (e.g., as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives (e.g., as a sparingly soluble salt).
  • Single dosage forms may be in a liquid or a solid form.
  • Single dosage forms may be administered directly to a patient without modification or may be diluted or reconstituted prior to administration.
  • a single dosage form may be administered in bolus form, e.g., single injection, single oral dose, including an oral dose that comprises multiple tablets, capsule, pills, etc.
  • a single dosage form may be administered over a period of time, e.g., by infusion.
  • the disclosure provides pharmaceutically acceptable compositions that are not in the form of or incorporated into a food or edible product.
  • Single dosage forms of the pharmaceutical composition may be prepared by portioning the pharmaceutical composition into smaller aliquots, single dose containers, single dose liquid forms, or single dose solid forms, such as tablets, granulates, nanoparticles, nanocapsules, microcapsules, microtablets, pellets, or powders, which may be enterically coated or uncoated.
  • a single dose in a solid form may be reconstituted by adding liquid, typically sterile water or saline solution, prior to administration to a patient.
  • the composition can be delivered in a controlled release or sustained release system.
  • a pump may be used to achieve controlled or sustained release.
  • polymeric materials can be used to achieve controlled or sustained release of the therapies of the present disclosure (see e.g., U.S. Patent No. 5,989,463).
  • polymers used in sustained release formulations include, but are not limited to, poly(2 -hydroxy ethyl methacrylate), poly(methyl methacrylate), poly(acrylic acid), poly(ethylene-co-vinyl acetate), poly(methacrylic acid), polyglycolides (PLG), polyanhydrides, poly(N- vinyl pyrrolidone), poly(vinyl alcohol), polyacrylamide, poly(ethylene glycol), polylactides (PLA), poly(lactide-co-glycolides) (PLGA), and polyorthoesters.
  • the polymer used in a sustained release formulation may be inert, free of leachable impurities, stable on storage, sterile, and biodegradable.
  • a controlled or sustained release system can be placed in proximity of the prophylactic or therapeutic target, thus requiring only a fraction of the systemic dose. Any suitable technique known to one of skill in the art may be used.
  • Dosage regimens may be adjusted to provide a therapeutic response. Dosing can depend on several factors, including severity and responsiveness of the disease, route of administration, time course of treatment (days to months to years), and time to amelioration of the disease. For example, a single bolus may be administered at one time, several divided doses may be administered over a predetermined period of time, or the dose may be reduced or increased as indicated by the therapeutic situation. The specification for the dosage is dictated by the unique characteristics of the active compound and the particular therapeutic effect to be achieved.
  • Dosage values may vary with the type and severity of the condition to be alleviated. For any particular subject, specific dosage regimens may be adjusted over time according to the individual need and the professional judgment of the treating clinician. Toxicity and therapeutic efficacy of compounds provided herein can be determined by standard pharmaceutical procedures in cell culture or animal models. For example, LD50, ED50, EC50, and IC50 may be determined, and the dose ratio between toxic and therapeutic effects (LD50/ED50) may be calculated as the therapeutic index. Compositions that exhibit toxic side effects may be used, with careful modifications to minimize potential damage to reduce side effects. Dosing may be estimated initially from cell culture assays and animal models. The data obtained from in vitro and in vivo assays and animal studies can be used in formulating a range of dosage for use in humans.
  • the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria, about 2xlO n live recombinant bacteria, about 3xl0 n live recombinant bacteria, about 4xlO n live recombinant bacteria, about 4.5x 10" live recombinant bacteria, about 5xl0 n live recombinant bacteria, about 6xlO n live recombinant bacteria, about IxlO 12 live recombinant bacteria, or about 2xl0 12 live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about 6xlO n live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria. In one embodiment, the administering is about 4.5x 10" live recombinant bacteria. In one embodiment, the administering is about 5xl0 n live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about IxlO 12 live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about 2xl0 12 live recombinant bacteria. In one embodiment, the administering is about 5xl0 n live recombinant bacteria with meals three times per day.
  • the recombinant bacteria are administered at a dose of about 6xlO n live recombinant bacteria with meals three times per day. In one embodiment, the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria with meals three times per day. In one embodiment, the recombinant bacteria are administered at a dose of about IxlO 12 live recombinant bacteria with meals three times per day. In one embodiment, the recombinant bacteria are administered at a dose of about 2xl0 12 live recombinant bacteria with meals three times per day. In one embodiment, the recombinant bacteria are administered at a dose of about 4.5xl0 12 live recombinant bacteria with meals three times per day. [0439] In some embodiments, a subject may not tolerate twice daily or three times daily dosing, and the dosing frequency may be reduced.
  • the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water-free concentrate in a hermetically sealed container such as an ampoule or sachet indicating the quantity of active agent. If the mode of administration is by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
  • the pharmaceutical compositions may be packaged in a hermetically sealed container such as an ampoule or sachet indicating the quantity of the agent.
  • a hermetically sealed container such as an ampoule or sachet indicating the quantity of the agent.
  • one or more of the pharmaceutical compositions is supplied as a dry sterilized lyophilized powder or water-free concentrate in a hermetically sealed container and can be reconstituted (e.g., with water or saline) to the appropriate concentration for administration to a subject.
  • one or more of the prophylactic or therapeutic agents or pharmaceutical compositions is supplied as a dry sterile lyophilized powder in a hermetically sealed container stored between 2° C and 8° C and administered within 1 hour, within 3 hours, within 5 hours, within 6 hours, within 12 hours, within 24 hours, within 48 hours, within 72 hours, or within one week after being reconstituted.
  • Cryoprotectants can be included for a lyophilized dosage form, principally 0-10% sucrose (optimally 0.5-1.0%).
  • Other suitable cryoprotectants include trehalose and lactose.
  • Suitable bulking agents include glycine and arginine, either of which can be included at a concentration of 0-0.05%, and polysorbate-80 (optimally included at a concentration of 0.005-0.01%).
  • Additional surfactants include but are not limited to polysorbate 20 and BRIJ surfactants.
  • the pharmaceutical composition may be prepared as an injectable solution and can further comprise an agent useful as an adjuvant, such as those used to increase absorption or dispersion, e.g., hyaluronidase.
  • the genetically engineered viruses are prepared for delivery, taking into consideration the need for efficient delivery and for overcoming the host antiviral immune response.
  • Approaches to evade antiviral response include the administration of different viral serotypes as part of the treatment regimen (serotype switching), formulation, such as polymer coating to mask the virus from antibody recognition and the use of cells as delivery vehicles.
  • the composition can be delivered in a controlled release or sustained release system.
  • a pump may be used to achieve controlled or sustained release.
  • polymeric materials can be used to achieve controlled or sustained release of the therapies of the present disclosure (see e.g., U.S. Patent No. 5,989,463).
  • polymers used in sustained release formulations include, but are not limited to, poly(2 -hydroxy ethyl methacrylate), poly(methyl methacrylate), poly(acrylic acid), polyethylene -co -vinyl acetate), poly(methacrylic acid), polyglycolides (PLG), polyanhydrides, poly(N- vinyl pyrrolidone), poly(vinyl alcohol), polyacrylamide, poly(ethylene glycol), polylactides (PLA), poly(lactide-co-glycolides)
  • PLGA polyorthoesters
  • the polymer used in a sustained release formulation may be inert, free of leachable impurities, stable on storage, sterile, and biodegradable.
  • a controlled or sustained release system can be placed in proximity of the prophylactic or therapeutic target, thus requiring only a fraction of the systemic dose. Any suitable technique known to one of skill in the art may be used.
  • the genetically engineered bacteria of the disclosure may be administered and formulated as neutral or salt forms.
  • Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
  • the recombinant bacteria of the disclosure may be evaluated in vivo, e.g., in an animal model.
  • Any suitable animal model of a disease or condition in which oxalate is detrimental may be used.
  • an alanine glyoxylate aminotransferase-deficient (agxt -/-) mouse model of PHI as described by Salido et al. can be used (see, e.g., Salido et al., Proc. Natl. Acad. Set. 103: 18249-54 (2006)).
  • a glyoxylate reductase/hydroxypyruvate reductase knock-out (GRHPR -/-) mouse model of PHII can also be used (see, e.g., Knight et al., Am. J. Physiol. Renal. Physiol. 302: F688-93 (2012)).
  • Mice deficient in the oxalate transporter protein SLC26A6 (S!c26a6-m ⁇ mice) which develop hyperoxaluria can also be used (see, e.g., Jiang et al. Nature Gen. 38: 474-8 (2006)).
  • a rat model may be used.
  • Canales et al. describe a rat model of Roux-en-Y gastric bypass (RYGB) surgery, in which high fat feeding results in steatorrhea, hyperoxaluria, and low urine pH.
  • RYGB animals on normal fat and no oxalate diets excreted twice as much oxalate as age-matched, sham controls; hyperoxaluria was partially reversible by lowering dietary fat and oxalate content (Canales et al., Steatorrhea And Hyperoxaluria Occur After Gastric Bypass Surgery In Obese Rats Regardless Of Dietary Fat Or Oxalate; J Urol. 2013 Sep; 190(3): 1102— 1109).
  • the recombinant bacterial cells of the disclosure may be administered to the animal, e.g., by oral gavage, and treatment efficacy is determined, e.g., by measuring urine levels of oxalic acid before and after treatment.
  • the animal may be sacrificed, and tissue samples may be collected and analyzed.
  • Table 14 includes additional rat models which can be used to assess in vivo activity of the genetically engineered bacteria.
  • the efficacy or activity of any of the importers, exporters, antiporters, and oxalate catabolism enzymes can be improved through mutations in any of these genes.
  • Methods for directed mutation and screening are known in the art. Methods of Treatment
  • One aspect of the disclosure provides methods of treating a disorder in which oxalate is detrimental in a subject, or symptom(s) associated with the disorder in which oxalate is detrimental in a subject.
  • the disorder in which oxalate is detrimental is a disorder associated with increased levels of oxalate.
  • a disorder associated with increased levels of oxalate is a disorder in which daily urinary oxalate excretion is 40 mg or higher per 24 hours.
  • Disorders associated with increased levels of oxalate include PHI, PHII, PHIII, secondary hyperoxaluria, enteric hyperoxaluria, dietary hyperoxaluria, idiopathic hyperoxaluria, syndrome of bacterial overgrowth, Crohn’s disease, inflammatory bowel disease, hyperoxaluria following renal transplantation, hyperoxaluria after a jejunoileal bypass for obesity, hyperoxaluria after gastric ulcer surgery, chronic mesenteric ischemia, gastric bypass, cystic fibrosis, short bowel syndrome, biliary/pancreatic diseases (e.g., chronic pancreatitis), hyperoxaluria with recurrent kidney stones with relatively preserved renal function, and hyperoxaluria with recurrent kidney stones with severe renal dysfunction (e.g., including patients on hemodialysis).
  • PHI PHII
  • PHIII secondary hyperoxaluria
  • enteric hyperoxaluria enteric hyperoxaluria
  • dietary hyperoxaluria id
  • the disorder in which oxalate is detrimental is PHI. In one embodiment, the disorder in which oxalate is detrimental is PHII. In another embodiment, the disorder in which oxalate is detrimental is PHIII. In one embodiment, the disorder in which oxalate is detrimental is secondary hyperoxaluria. In another embodiment, the disorder in which oxalate is detrimental is dietary hyperoxaluria. In one embodiment, the disorder in which oxalate is detrimental is idiopathic hyperoxaluria. In another embodiment, the disorder in which oxalate is detrimental is enteric hyperoxaluria. In one embodiment, the disorder in which oxalate is detrimental is the syndrome of bacterial overgrowth.
  • the disorder in which oxalate is detrimental is Crohn’s disease. In one embodiment, the disorder in which oxalate is detrimental is inflammatory bowel disease. In another embodiment, the disorder in which oxalate is detrimental is hyperoxaluria following renal transplantation. In one embodiment, the disorder in which oxalate is detrimental is hyperoxaluria after a jejunoileal bypass for obesity. In another embodiment, the disorder in which oxalate is detrimental is hyperoxaluria after gastric ulcer surgery. In one embodiment, the disorder in which oxalate is detrimental is chronic mesenteric ischemia. In another embodiment, the disorder in which oxalate is detrimental is gastric bypass, e.g., Roux-enY gastric bypass.
  • gastric bypass e.g., Roux-enY gastric bypass.
  • the disorder in which oxalate is detrimental is cystic fibrosis. In another embodiment, the disorder in which oxalate is detrimental is short bowel syndrome. In another embodiment, the disorder in which oxalate is detrimental are biliary/pancreatic diseases. In another embodiment, the disorder in which oxalate is detrimental is chronic pancreatitis. In another embodiment, the disorder in which oxalate is detrimental is hyperoxaluria with recurrent kidney stones with relatively preserved renal function. In another embodiment, the disorder in which oxalate is detrimental is hyperoxaluria with recurrent kidney stones with severe renal dysfunction (e.g., including patients on hemodialysis). [0451] The present disclosure surprisingly demonstrates that pharmaceutical compositions comprising the recombinant bacterial cells disclosed herein may be used to treat disorders in which oxalate is detrimental, such as PHI and PHI.
  • the subject having PHI has a mutation in a A GXT gene.
  • the subject having PHII has a mutation in a GRHPR gene.
  • the subject having PHIII has a mutation in a HOGA1 gene.
  • the disclosure provides methods for decreasing the plasma level of oxalate and/or oxalic acid in a subject by administering a pharmaceutical composition comprising a bacterial cell of the disclosure to the subject, thereby decreasing the plasma level of the oxalate and/or oxalic acid in the subject.
  • the subject has a disease or disorder in which oxalate is detrimental.
  • the disorder in which oxalate is detrimental is PHI.
  • the disorder in which oxalate is detrimental is PHII. In another embodiment, the disorder in which oxalate is detrimental is PHIII. In one embodiment, the disorder in which oxalate is detrimental is secondary hyperoxaluria. In another embodiment, the disorder in which oxalate is detrimental is dietary hyperoxaluria. In one embodiment, the disorder in which oxalate is detrimental is idiopathic hyperoxaluria. In another embodiment, the disorder in which oxalate is detrimental is enteric hyperoxaluria. In one embodiment, the disorder in which oxalate is detrimental is the syndrome of bacterial overgrowth. In another embodiment, the disorder in which oxalate is detrimental is Crohn’s disease.
  • the disorder in which oxalate is detrimental is inflammatory bowel disease. In another embodiment, the disorder in which oxalate is detrimental is hyperoxaluria following renal transplantation. In one embodiment, the disorder in which oxalate is detrimental is hyperoxaluria after a jejunoileal bypass for obesity. In another embodiment, the disorder in which oxalate is detrimental is hyperoxaluria after gastric ulcer surgery. In one embodiment, the disorder in which oxalate is detrimental is chronic mesenteric ischemia. In another embodiment, the disorder in which oxalate is detrimental is gastric bypass. In another embodiment, the disorder in which oxalate is detrimental is cystic fibrosis.
  • the disorder in which oxalate is detrimental is short bowel syndrome. In another embodiment, the disorder in which oxalate is detrimental are biliary/pancreatic diseases. In another embodiment, the disorder in which oxalate is detrimental is chronic pancreatitis.
  • the disclosure provides methods for reducing, ameliorating, or eliminating one or more symptom(s) associated with these diseases, including but not limited to fever, vomiting, nausea, diarrhea, kidney stones, oxalosis, bone disease, erythropoietin refractory anemia, skin ulcers, digital gangrene, cardiac arrhythmias, and cardiomyopathy.
  • the disease is secondary to other conditions, e.g., liver disease.
  • the human patient to be treated by the methods disclosed herein may meet one or more of the inclusion and exclusion criteria disclosed in the Examples below.
  • the human patient may of age > 18 to ⁇ 74 years.
  • the human patient has a history of gastric bypass surgery (at least 12 months prior to Day 1) or of short-bowel syndrome.
  • the human patient subject to any treatment disclosed herein may be free of or does not have one or more of (1) Acute or chronic medical (including COVID-19 infection), (3) Estimated glomerular filtration rate ⁇ 45 mL/min/1.73 m2 (4) History of kidney stones (5) Inability to discontinue vitamin C supplementation; (6) known primary hyperoxaluria (7) Administration or ingestion of any type of systemic (e.g., oral or intravenous) antibiotic within 5 halflives of the agent prior to Day 1 (8) Intolerance of, or allergic reaction to, EcN, all PPIs, or any of the ingredients in SYNB8802 or placebo formulations (9) Dependence on alcohol or drugs of abuse (10) Current, immunodeficiency disorder including autoimmune disorders and uncontrolled human immunodeficiency virus (HIV).
  • Acute or chronic medical including COVID-19 infection
  • Estimated glomerular filtration rate ⁇ 45 mL/min/1.73 m2
  • History of kidney stones (5) Inability to discontinue vitamin C supplementation;
  • the bacterial cells disclosed herein are capable of catabolizing oxalate and/or oxalic acid in a subject in order to treat a disorder in which oxalate is detrimental.
  • a patient suffering from a disorder in which oxalate is detrimental e.g., PHI or PHII
  • the bacterial cells may be capable of catabolizing oxalate and/or oxalic acid, from additional sources, e.g., the blood, in order to treat a disorder in which oxalate is detrimental.
  • dietary uptake of oxalate is suppressed by providing the genetically engineered bacteria described herein.
  • oxalate generated through metabolic pathways, e.g., in a mammal is reduced.
  • the method may comprise preparing a pharmaceutical composition with at least one genetically engineered species, strain, or subtype of bacteria described herein, and administering the pharmaceutical composition to a subject in a therapeutically effective amount.
  • the method of treating a disease or disorder associated with elevated oxalate comprises administering to a subject in need thereof an engineered bacterium comprising gene sequence(s) encoding one or more oxalate catabolism enzyme(s) or a pharmaceutical composition thereof.
  • the method of treating a disease or disorder associated with elevated oxalate comprises administering to a subject in need thereof an engineered bacterium comprising gene sequence(s) encoding one or more oxalate transporter(s) or a pharmaceutical composition thereof.
  • the method of treating a disease or disorder associated with elevated oxalate comprises administering to a subject in need thereof an engineered bacterium comprising gene sequence(s) encoding one or more formate importers(s) or a pharmaceutical composition thereof. In some embodiments, the method of treating a disease or disorder associated with elevated oxalate comprises administering to a subject in need thereof an engineered bacterium comprising gene sequence(s) encoding one or more oxalate: formate antiporter(s) or a pharmaceutical composition thereof.
  • the method of treating a disease or disorder associated with elevated oxalate comprises administering to a subject in need thereof an engineered bacterium comprising gene sequence(s) encoding one or more oxalate catabolism enzyme(s) and gene sequence(s) encoding one or more of the following: (i) one or more oxalate transporter(s); (ii) one or more formate exporter(s); (iii) one or more oxalate: formate antiporter(s); and (iv) combinations thereof or a pharmaceutical composition thereof.
  • the method of treating a disease or disorder associated with elevated oxalate comprises administering to a subject in need thereof an engineered bacterium SYNB8802.
  • the bacterial cells disclosed herein are administered orally, e.g., in a liquid suspension. In some embodiments, the bacterial cells disclosed herein are lyophilized in a gel cap and administered orally. In some embodiments, the bacterial cells disclosed herein are administered via a feeding tube or gastric shunt. In some embodiments, the bacterial cells disclosed herein are administered rectally, e.g., by enema. In some embodiments, the genetically engineered bacteria are administered topically, intraintestinally, intrajej unally, intraduodenally, intraileally, and/or intracolically.
  • the administering the pharmaceutical composition described herein is administered to reduce oxalate and/or oxalic acid levels in a subject.
  • the methods of the present disclosure reduce the oxalate and/or oxalic acid levels in a subject by at least about 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or more.
  • the methods of the present disclosure reduce the oxalate and/or oxalic acid levels in a subject by at least two-fold, three-fold, four-fold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, or ten-fold.
  • the methods of the present disclosure reduce the daily urinary oxalate excretion of a subject to less than 40 mg per 24 hours. In some embodiments, reduction is measured by comparing the oxalate and/or oxalic acid level in a subject before and after administration of the pharmaceutical composition. In one embodiment, the oxalate and/or oxalic acid level is reduced in the gut of the subject. In one embodiment, the oxalate and/or oxalic acid level is reduced in the urine of the subject. In another embodiment, the oxalate and/or oxalic acid level is reduced in the blood of the subject. In another embodiment, the oxalate and/or oxalic acid level is reduced in the plasma of the subject.
  • the oxalate and/or oxalic acid level is reduced in the fecal matter of the subject. In another embodiment, the oxalate and/or oxalic acid level is reduced in the brain of the subject. Creatinine is measured is used to correct for urine concentration, i. e. , in some embodiments, the Uox: Creatinine ratio is measured to assess reduction in urinary oxalate levels.
  • the pharmaceutical composition described herein is administered to reduce oxalate and/or oxalic acid levels in a subject to normal levels. In another embodiment, the pharmaceutical composition described herein is administered to reduce oxalate and/or oxalic acid levels in a subject to below a normal level. In another embodiment, the pharmaceutical composition described herein is administered to reduce the daily urinary oxalate excretion of a subject to less than 40 mg per 24 hours. [0462] In certain embodiments, the pharmaceutical composition described herein is administered to reduce oxalate levels in a subject.
  • the methods of the present disclosure reduce the oxalate levels, in a subject by at least about 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or more as compared to levels in an untreated or control subject.
  • the methods of the present disclosure reduce the oxalate levels, in a subject by at least two-fold, three-fold, four-fold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, or ten-fold.
  • reduction is measured by comparing the oxalate levels in a subject before and after administration of the pharmaceutical composition.
  • the oxalate level is reduced in the gut of the subject.
  • the oxalate level is reduced in the blood of the subject. In another embodiment, the oxalate level is reduced in the plasma of the subject. In another embodiment, the oxalate level is reduced in the liver of the subject. In another embodiment, the oxalate level is reduced in the kidney of the subject.
  • the pharmaceutical composition described herein is administered to reduce oxalate in a subject to a normal level.
  • the methods provided herein include monitoring of and/or result in changes in one or more endpoints described in Example 10 or other Examples below.
  • the methods described herein include measurement and recordal of change from baseline in biomarkers associated with increased risk of kidney stones, such as urine supersaturation scores.
  • the methods provided herein include monitoring for the presence of kidney stones on screening, degree of malabsorption, tolerability profile, and other patient factors. In some embodiments, the methods described herein promote a change in these factors.
  • the method of treating the disorder in which oxalate is detrimental allows one or more symptoms of the condition or disorder to improve by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more.
  • the method of treating the disorder in which oxalate is detrimental e.g., PHI or PHII, allows one or more symptoms of the condition or disorder to improve by at least about two-fold, three-fold, four-fold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, or ten-fold.
  • oxalate and/or oxalic acid levels in the subject may be measured in a biological sample, such as blood, serum, plasma, urine, peritoneal fluid, cerebrospinal fluid, fecal matter, intestinal mucosal scrapings, a sample collected from a tissue, and/or a sample collected from the contents of one or more of the following: the stomach, kidney, liver, duodenumjejunum, ileum, cecum, colon, rectum, and anal canal.
  • the methods may include administration of the compositions disclosed herein to reduce levels of the oxalate and/or oxalic acid.
  • the methods may include administration of the compositions of the disclosure to reduce the oxalate and/or oxalic acid to undetectable levels in a subject. In some embodiments, the methods may include administration of the compositions of the disclosure to reduce the oxalate and/or oxalic acid concentrations to undetectable levels, or to less than about 1%, 2%, 5%, 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, or 95% of the subject’s oxalate and/or oxalic acid levels prior to treatment.
  • the recombinant bacterial cells disclosed herein produce an oxalate catabolism enzyme under exogenous environmental conditions, such as the low-oxygen environment of the mammalian gut, to reduce levels of oxalate and/or oxalic acid in the urine, blood or plasma by at least about 1.5 -fold, at least about 2-fold, at least about 3 -fold, at least about 4-fold, at least about 5- fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15 -fold, at least about 20-fold, at least about 30-fold, at least about 40- fold, or at least about 50-fold as compared to unmodified bacteria of the same subtype under the same conditions.
  • exogenous environmental conditions such as the low-oxygen environment of the mammalian gut
  • the bacteria disclosed herein reduce plasma levels of oxalate will be reduced to less than 4 mg/dL. In one embodiment, the bacteria disclosed herein reduce plasma levels of oxalate will be reduced to less than 3.9 mg/dL.
  • the bacteria disclosed herein reduce plasma levels of oxalate, to less than 3.8 mg/dL, 3.7 mg/dL, 3.6 mg/dL, 3.5 mg/dL, 3.4 mg/dL, 3.3 mg/dL, 3.2 mg/dL, 3.1 mg/dL, 3.0 mg/dL, 2.9 mg/dL, 2.8 mg/dL, 2.7 mg/dL, 2.6 mg/dL, 2.5 mg/dL, 2.0 mg/dL, 1.75 mg/dL, 1.5 mg/dL, 1.0 mg/dL, or 0.5 mg/dL.
  • the subject has plasma levels of at least 4 mg/dL oxalate prior to administration of the pharmaceutical composition disclosed herein.
  • the subject has plasma levels of at least 4. 1 mg/dL, 4.2 mg/dL, 4.3 mg/dL, 4.4 mg/dL, 4.5 mg/dL, 4.75 mg/dL, 5.0 mg/dL, 5.5 mg/dL, 6 mg/dL, 7 mg/dL, 8 mg/dL, 9 mg/dL, or 10 mg/dL prior to administration of the pharmaceutical composition disclosed herein.
  • Certain unmodified bacteria will not have appreciable levels of oxalate or oxalyl-CoA processing.
  • processing of oxalate and/or oxalyl -CoA will be appreciable under exogenous environmental conditions.
  • Oxalate and/or oxalic acid levels may be measured by methods known in the art.
  • plasma oxalate levels can be measured using the spectrophotometric plasma oxalate assay described by Ladwig et al. (Ladwig et. al. , Clin. Chem. 51 : 2377-80 (2005)).
  • urine oxalate levels can be measured for example, by using a oxalate oxidase colorimetric enzymatic assay (Kasidas and Rose, Ann. Clin. Biochem. . 412-9 (1985)).
  • oxalate catabolism enzyme e.g., Frc
  • expression is measured by methods known in the art.
  • oxalate catabolism enzyme activity is measured by methods known in the art to assess Frc activity (see oxalate catabolism enzyme sections, supra).
  • the recombinant bacteria are A. coli Nissle.
  • the recombinant bacteria may be destroyed, e.g., by defense factors in the gut or blood serum (Sonnenbom et al. , 2009) or by activation of a kill switch, several hours or days after administration.
  • the pharmaceutical composition comprising the recombinant bacteria may be re-administered at a therapeutically effective dose and frequency.
  • the recombinant bacteria are not destroyed within hours or days after administration and may propagate and colonize the gut.
  • the bacterial cells disclosed herein are administered to a subject once daily. In another embodiment, the bacterial cells disclosed herein are administered to a subject twice daily. In another embodiment, the bacterial cells disclosed herein are administered to a subject three times daily. In another embodiment, the bacterial cells disclosed herein are administered to a subject in combination with a meal. In another embodiment, the bacterial cells disclosed herein are administered to a subject prior to a meal. In another embodiment, the bacterial cells disclosed herein are administered to a subject after a meal. In another embodiment, the bacterial cells of the disclosure are not administered in the form of a food or edible product or incorporated into a food or edible product.
  • the dosage of the pharmaceutical composition and the frequency of administration may be selected based on the severity of the symptoms and the progression of the disease. The appropriate therapeutically effective dose and/or frequency of administration can be selected by a treating clinician.
  • the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria, about 2xlO n live recombinant bacteria, about 3xl0 n live recombinant bacteria, about 4xlO n live recombinant bacteria, about 4.5x 10" live recombinant bacteria, about 5xl0 n live recombinant bacteria, about 6xlO n live recombinant bacteria, about IxlO 12 live recombinant bacteria, or about 2xl0 12 live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about 6xlO n live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about 3x10 11 live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria. In one embodiment, the administering is about 4.5x 10" live recombinant bacteria. In one embodiment, the administering is about 5x10 11 live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about IxlO 12 live recombinant bacteria. In one embodiment, the recombinant bacteria are administered at a dose of about 2xl0 12 live recombinant bacteria.
  • the administering are about 5xl0 n live recombinant bacteria with meals three times per day.
  • the recombinant bacteria are administered at a dose of about IxlO 11 live recombinant bacteria to about 2xl0 12 live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about IxlO 12 live recombinant bacteria to about 2xl0 12 live recombinant bacteria.
  • the recombinant bacteria are administered at a dose of about 5xl0 n live recombinant bacteria to about 2xl0 12 live recombinant bacteria.
  • a proton pump inhibitor is administered to the subject.
  • the PPI is esomeprazole.
  • esomeprazole is administered at 40 mg once daily.
  • suitable PPIs include lansoprazole, pantoprazole, rabeprazole, esomeprazole, and dexlansoprazole.
  • the administering of the PPI is once a day.
  • the methods disclosed herein may comprise administration of a composition disclosed herein alone or in combination with one or more additional therapies, e.g., pyridoxine, citrate, orthophosphate, and magnesium, oral calcium supplementation, and bile acid sequestrants, or a low fat and /or low oxalate diet.
  • additional therapies e.g., pyridoxine, citrate, orthophosphate, and magnesium, oral calcium supplementation, and bile acid sequestrants, or a low fat and /or low oxalate diet.
  • additional therapies e.g., pyridoxine, citrate, orthophosphate, and magnesium, oral calcium supplementation, and bile acid sequestrants, or a low fat and /or low oxalate diet.
  • the agent(s) should be compatible with the bacteria disclosed herein, e.g., the agent(s) must not interfere with or kill the bacteria.
  • the genetically engineered bacteria are administered in combination with a low fat and/or low
  • the methods disclosed herein may further comprise isolating a plasma sample from the subject prior to administration of a composition disclosed herein and determining the level of the oxalate and/or oxalic acid in the sample. In some embodiments, the methods disclosed herein may further comprise isolating a plasma sample from the subject after to administration of a composition disclosed herein and determining the level of oxalate and/or oxalic acid in the sample.
  • the methods of the disclosure may further comprise isolating a urine sample from the subject prior to administration of a composition of the disclosure and determining the level of the oxalate and/or oxalic acid in the sample.
  • the methods of the disclosure may further comprise isolating a urine sample from the subject after to administration of a composition of the disclosure and determining the level of oxalate and/or oxalic acid in the sample.
  • the methods disclosed herein further comprise comparing the level of the oxalate and/or oxalic acid in the plasma sample from the subject after administration of a composition disclosed herein to the subject to the plasma sample from the subject before administration of a composition disclosed herein to the subject.
  • a reduced level of the oxalate and/or oxalic acid in the plasma sample from the subject after administration of a composition disclosed herein indicates that the plasma levels of the oxalate and/or oxalic acid are decreased, thereby treating the disorder in which oxalate is detrimental in the subject.
  • the plasma level of oxalate and/or oxalic acid is decreased at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% in the sample after administration of the pharmaceutical composition as compared to the plasma level in the sample before administration of the pharmaceutical composition.
  • the plasma level of the oxalate and/or oxalic acid is decreased at least two-fold, three-fold, four-fold, or five-fold in the sample after administration of the pharmaceutical composition as compared to the plasma level in the sample before administration of the pharmaceutical composition.
  • the methods of the disclosure further comprise comparing the level of the oxalate and/or oxalic acid in the urine sample from the subject after administration of a composition of the disclosure to the subject to the urine sample from the subject before administration of a composition of the disclosure to the subject.
  • a reduced level of the oxalate and/or oxalic acid in the urine sample from the subject after administration of a composition of the disclosure indicates that the urine levels of the oxalate and/or oxalic acid are decreased, thereby treating the disorder in which oxalate is detrimental in the subject.
  • the urine level of oxalate and/or oxalic acid is decreased at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% in the sample after administration of the pharmaceutical composition as compared to the plasma level in the sample before administration of the pharmaceutical composition.
  • the urine level of the oxalate and/or oxalic acid is decreased at least two-fold, three-fold, four-fold, or five-fold in the sample after administration of the pharmaceutical composition as compared to the urine level in the sample before administration of the pharmaceutical composition.
  • the methods disclosed herein further comprise comparing the level of the oxalate/oxalic acid in the plasma sample from the subject after administration of a composition disclosed herein to a control level of oxalate and/or oxalic acid.
  • the methods of the disclosure further comprise comparing the level of the oxalate/oxalic acid in the urine sample from the subject after administration of a composition of the disclosure to a control level of oxalate and/or oxalic acid.
  • SYNB8802 was developed by engineering a pathway for oxalate degradation in a probiotic strain of Escherichia coli Nissle 1917 (EcN). It is intended to act within the GI tract to reduce the oxalate levels in patients with EH by converting oxalate to formate and CO2, two naturally occurring GI metabolites.
  • EcN Escherichia coli Nissle 1917
  • scaaE3 from yeast, were chromosomally integrated under the control of an anaerobic-inducible promoter (PfhrS) and the anaerobic-responsive transcriptional activator, fumarate and nitrate reductase (FNR). These regulatory components are meant to ensure that the oxalate degrading gene products are produced in the anoxic environment of the human gut.
  • SYNB8802 uses OxlT to import oxalate and export formate. Once oxalate enters the cell, ScaaE3 catalyzes the conversion of oxalate to oxalyl-CoA.
  • OxdC is responsible for decarboxylation of oxalyl-CoA to formyl-CoA and CO2.
  • FRC can transfer the CoA from formyl-CoA to a new incoming oxalate, thereby releasing formate.
  • SYNB8802 was engineered to be an auxotrophic strain through deletion of the thyA gene that encodes for thymidylate synthetase, which is essential for replication.
  • SYNB8802(/l/A.s) is identical to SYNB8802 but has the genes encoding colibactin deleted by removal of the pks island from the EcN genome (Apks) as an additional safety measure.
  • SYNB8802 has been designed to treat Enteric hyperoxaluria (EH) by consuming oxalate in the GI tract. Inoculation of SYNB8802 into oxalate -containing minimal media resulted in the disappearance of oxalate overtime as compared to EcN, suggesting in vitro consumption of the metabolite by engineered bacteria in those conditions.
  • EH Enteric hyperoxaluria
  • Table 15 provides constructs comprising oxalate catabolism cassettes drive by a Tet responsive promoter.
  • Table 16 lists the construct for the chromosomally integrated OxlT at the lacZ locus.
  • the dosing period included a dose escalation plan with the first six days at the lower dose of 1 x 10 11 live cells, followed by six days at the 3 x 10 11 live cell dose. Each six-day treatment period included a stepwise increase in dose frequency.
  • patients consumed a controlled diet for the duration of the inpatient stay. Urine was also collected for a 24-hour sample for each patient, each day. Study design is summarized in FIG. 7. [0488] Overall, SYNB8802 demonstrated a dose-dependent reduction in urinary oxalate.
  • Dosing with SYNB8802 was associated with a dose dependent reduction in urinary oxalate.
  • dose level and dose frequency there was a -28% (-37.2, -18.2) change from baseline in urinary oxalate vs. that of placebo at the IxlO 11 TID dose and a -38% (-46.4, -28.7) change from baseline in urinary oxalate vs. placebo at the at the 3x10" TID dose (FIG. 8 and FIGs. 9A and 9B).
  • Example 3 A Double-Blind, Randomized, Placebo-controlled Study to Assess the Safety, Tolerability, and Pharmacodynamics of SYNB8802 in Subjects with History of Gastric Bypass Surgery or Short-bowel Syndrome Table 25A. Study Objectives and Endpoints
  • Dietary oxalate and calcium were distributed across 3 meals per day. Subjects maintained this diet until the end of the period. Open-label placebo was administered 3 times daily (TID) during the run-in period.
  • a proton pump inhibitor was administered once daily (QD), 60-90 minutes before breakfast, from the start of the run-in period (Day -3) until the end of the randomized period (Day 12); if a subject was already regularly taking a different PPI, that agent may have been continued, or a different PPI was given if needed due to allergy or drug interaction.
  • the dosing frequency may have been reduced by the Investigator.
  • the dose level i.e., 1 x 10 11 or 3 x 10 11 live cells SYNB8802
  • Table 26 summarizes the disposition and analysis groups for this study. Seven subjects were treated with SYNB8802 and 4 subjects were in the placebo group. All 11 treated subjects were included in the analysis of safety. One placebo subject was discontinued early when the Sponsor was informed that the subject did not meet inclusion criteria.
  • Percentages are based on the number of subjects in each group in the Randomized Population.
  • the Enrolled Population includes all subjects who signed the informed consent form and were enrolled.
  • Safety population includes all subjects who received at least 1 dose of IMP.
  • Efficacy/PD population includes all subjects in the safety population who had at least one postbaseline PD measurement, tolerated TID administration (regardless of dose level; any deviation from TID administration at any dose level was considered as the subject not tolerating), and had not missed >3 doses of SYNB8802 during the steady-state period at that dose level and had not missed more than 3 administrations of placebo during the corresponding steady-state period, respectively.
  • Per Protocol population includes all subjects who completed the randomized period and did not have any major protocol deviations, (or other factors as determined by the blinded medical monitor prior to database lock) that potentially impacted key endpoints, regardless of final dosing frequency or final dose level.
  • a pharmacometrics analysis including data from 7 patients receiving SYNB8802 at both the IxlO 11 and 3xl0 n dose levels and 4 patients receiving placebo is shown in FIG. 8.
  • Urinary oxalate levels at screening were consistent with diet and patient population (at ⁇ 30), and generally remained consistent with baseline values during the treatment period for placebo patients.
  • dose-related reduction in urinary oxalate levels in response to SYNB8802 were observed.
  • FIG. 10 depicts the mean absolute amount of UOx based on 24-hour urine collections.
  • the mean absolute UOx values were 32.5 mg for the SYNB8802 group and 29.4 mg for the placebo group.
  • the mean absolute UOx values were 24.8 (a decrease of 7.6 mg) for the SYNB8802 group and 24.4 mg (a decrease of 5.0 mg) for the placebo group.
  • the mean UOx values were lower for the SYNB8802 group (range: 17.9 on Day 11 to 23.8 on Day 8) compared with the placebo group (range: 23.5 on Day 11 to 32.4 on Day 8).
  • FIG. 11 depicts the effect of SYNB8802 on change from baseline (absolute values) in UOx:creatinine ratio overtime.
  • the median absolute UOx:creatinine ratios were 3.8 mg/mmol for the SYNB8802 group and 2.2 mg/mmol for the placebo group.
  • the decrease from baseline in UOx:creatinine ratio was more pronounced for subjects treated with SYNB8802 compared to those treated with placebo.

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Abstract

La présente invention concerne des cellules bactériennes recombinées comprenant au moins un gène hétérologue codant pour au moins une enzyme de catabolisme d'oxalate. Selon un autre aspect, les cellules bactériennes recombinées comprennent en outre au moins un gène hétérologue codant pour un importateur d'oxalate. L'invention concerne en outre des compositions pharmaceutiques comprenant les bactéries recombinantes, et des méthodes de traitement de troubles dans lesquels l'oxalate est préjudiciable, tel que l'hyperoxalurie, à l'aide des compositions pharmaceutiques de l'invention.
PCT/US2023/084033 2022-12-14 2023-12-14 Bactéries recombinantes destinées à être utilisées pour le traitement de troubles dans lesquels l'oxalate est préjudiciable WO2024129974A1 (fr)

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