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  • A61K35/744—Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs
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  • A61K35/744—Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs
  • A61K35/747—Lactobacilli, e.g. L. acidophilus or L. brevis
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  • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
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  • A61P1/14—Prodigestives, e.g. acids, enzymes, appetite stimulants, antidyspeptics, tonics, antiflatulents
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  • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
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  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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  • C12N1/00—Microorganisms; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/74—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
  • C12N15/746—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora for lactic acid bacteria (Streptococcus; Lactococcus; Lactobacillus; Pediococcus; Enterococcus; Leuconostoc; Propionibacterium; Bifidobacterium; Sporolactobacillus)
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  • C12N9/10—Transferases (2.)
  • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
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  • C12Y207/08—Transferases for other substituted phosphate groups (2.7.8)
  • C12Y207/0802—Phosphatidylglycerol--membrane-oligosaccharide glycerophosphotransferase (2.7.8.20)
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  • C12R2001/00—Microorganisms ; Processes using microorganisms
  • C12R2001/01—Bacteria or Actinomycetales ; using bacteria or Actinomycetales
  • C12R2001/225—Lactobacillus
  • C12R2001/23—Lactobacillus acidophilus

Definitions

• the present invention relates to methods and compositions for decreasing inflammation.
• sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 406734seqlist.txt, a creation date of June 16, 2011, and a size of 15.7 KB.
• ASCII American Standard Code for Information Interchange
• sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.
• intestinal immune homeostasis involves the balanced interaction of bacterial microflora, gut epithelium and host innate immune cells.
• IBD inflammatory bowl disease
• UC ulcerative colitis
• Crohn's disease a chronic intestinal inflammation induced by inflammatory cytokines (e.g. IL-12) plays a pivotal role.
• IL-12 inflammatory cytokines
• IL-12 secreted IL-23 from activated dendritic cells (DCs) that utilize the IL-12p40 subunit is also implicated in the development of various autoimmune diseases, including IBD.
• DCs activated dendritic cells
• IL-23 The inflammatory nature of IL-23 has been attributed to induction of Thl7. Furthermore, this cytokine also activates the production of inflammatory cytokines such as TNFa and IL-6 in DCs. Together, studies show that blocking the IL-12p40 subunit signaling significantly reduces inflammation, and indicate that both IL-12 and IL-23 participate in the inflammatory cascade causing IBD. In contrast to both of these cytokines, IL-10 exerts regulatory effects on the inflammatory signals, thereby modulating the immune response elicited by inflammatory cytokines.
• Probiotic microbes can interact with the host's immune cells and specific probiotic Lactobacillus species may stimulate DCs to produce inflammatory cytokines (i.e. IL-12) and regulatory IL-10.
• Lactobacilli are normal inhabitants of the human gastrointestinal tract and major components of the natural microbiota in the small bowel. These bacteria are considered beneficial commensals and some species and strains are generally recognized as safe due to a long history of human consumption.
• Methods comprise administering to a subject a recombinant bacterium modified to decrease the display of lipoteichoic acid on the cell surface.
• Administration of the recombinant bacterium promotes a desired therapeutic response.
• the recombinant bacterium may be administered in a single dose or series of doses. Methods find use in treating or preventing a variety of inflammatory disorders including, for example, treating or preventing inflammatory bowel disease, colitis, or Crohn's disease.
• Figure 1 shows the pathway and genes involved in LTA biosynthesis.
• C-D shows two noncontiguous fragments flanking an internal region of the target ORF amplified and joined using splicing by overlap extension (SOEing) PCR (Horton, RM (1995) Mol Biotechnol. Apr;3(2):93-9). The resulting fragments were cloned into pORI28 and transformed into L. acidophilus NCK1392 containing the temperature sensitive helper plasmid pTRK669. ERM-sensitive cells were screened for a deletion mutation using PCR with primers flanking the targeted region and confirmed by sequencing the region containing the deletion.
• Figure 2 (A) shows the phenotype of DCs treated with NCK56 (also designated as L.
• NCFM acidophilus NCFM
• NCK2025 Bone marrow derived DCs were co-cultured with NCK56 or NCK2025 for 24 hours. Cells were stained with corresponding antibodies, fixed and subsequently analyzed by a FACSCalibur.
• Panel B shows DCs cultured alone or 1 : 1 with either NCK56 or NCK2025 for 1 and 6 hours. R A was extracted, reverse transcribed and real-time PCR was performed using primers for TLRl and TLR2. Data shown represents the 1 hr DC alone, or co-cultures of these cells with NCK56 or NCK2025.
• Panel C shows cytokine analysis.
• Cytokines released in the supernatants of NCK56 or NCK2025 -treated and untreated DCs were assayed by ELISA.
• Panel D shows T cell proliferation.
• Groups of C57BL/6 mice (5/group) were orally treated with NCK56 or NCK2025 for four consecutive days.
• Mesenteric LN-T cells were derived and co-cultured with NCK56 or NCK2025-treated and untreated DCs for four days to assay T cell proliferation using [ HJthymidine incorporation.
• anti-IL-10 antibodies were added to supernatants derived from DCs that were co-cultured with NCK2025.
• Mesenteric LN-T cells derived from each group of mice were co-cultured with DCs that were treated or untreated with L. acidophilus strains to assay cytokines.
• Figure 3 shows the amelioration of DSS-induced colitis by NCK2025.
• mice were exposed to 3% DSS dissolved in the drinking water for 5 days followed by 7 days of plain water and assessed over time for colitis progression, including H&E staining, weight lost, diarrhea and hemoccult positivity.
• Panels B-E show colonic H&N staining.
• B shows untreated mice;
• C shows DSS-treated mice;
• D shows NCK56-DSS treated mice;
• E shows NCK2025-DSS treated mice.
• F represents the colitis score.
• FOB stands for fecal hemoccult blood positivity and DAI stands for disease activity index. Data are representative of at least three independent experiments.
• Panel G shows the colonic cytokine analysis. Colons of the mice (5/group) that were treated with NCK56 or NCK2025 or DSS were cleaned with cold PBS, cut into pieces and cultured for 18 h at 37°C. Cytokines were assayed by ELISA.
• Figure 4 shows mitigation of established colitis by NCK2025.
• Panels A-D show three groups of C57BL/6 mice (10/group) that first received a five-day cycle of 3% DSS dissolved in sterile water to initiate colitis, and two of the groups were subsequently treated orally with NCK56 or NCK2025 for four consecutive days. Disease progression was monitored to day 13 of the protocol when mice were sacrificed, and colons assessed.
• Panels B-D show colonic H&N staining.
• Panel B shows DSS-treated mice;
• Panel C shows DSS-NCK56 treated mice;
• Panel D shows DSS-NCK025 treated mice.
• Panel E represents the colitis score.
• FOB stands for fecal hemoccult blood positivity and DAI stands for disease activity index. Data are representative of at least three independent experiments.
• Panel F shows the colonic cytokine analysis. Colons of each group of mice were washed, cut into pieces and cultured for 18 h at 37°C. Cytokines
• Figure 5 shows induction of Treg cells by NCK2025.
• Panels A-B show induction of Treg cells by NCK2025.
• mice C57BL/6 mice (5/group) orally inoculated with NCK56 or NCK2025 (5x 10 8 cfu/l 00 ⁇ /mouse) or PBS for 4 consecutive days. On day five, mice were sacrificed, and isolated colons were cleaned. Colonic single cell-suspensions were prepared from each group of mice and enriched by Percol gradient. Lymphocytes were stained with corresponding or isotype match antibodies and analyzed by FACSCalibur. Experiments were repeated at least 7 times.
• Figure 6 shows induction of Colitis in IL-10 ' " mice.
• A-B C57BL/6 IL-10 7" mouse groups (10/group) were housed conventionally for 1 week. Mice were inoculated with NCK56 or NCK2025 for four consecutive days and then fed low dose piroxicam for 1 week, followed by high dose piroxicam for 1 week to accelerate and induce the onset of colitis. Weight lost was determined and two weeks later mice were sacrificed, colon cross-sectional Swiss rolls and tissue sections were prepared for H&E staining.
• C shows Piroxicam alone treated mice; D shows NCK56-piroxicam treated mice; and E shows NCK2025 -piroxicam treated mice. The scores were blindly determined on a scale from 0 to 4.
• Figure 7 shows regulation of genes in DSS induced colitis in mice upon treatment with NCK56 or NCK2025 or no treatment.
• Panels A-B show mice (5/group) given NCK56, NCK2025, or left untreated, for four days before DSS induction of colitis. Proximal or distal colonic regions were isolated and RNA extracted.
• cDNA microarray analysis reveals differential gene expression patterns in pathways involving immune regulatory/stimulatory, signaling, proliferation, apoptosis, angiogenesis, and adhesion in the colon of mice. Values represent fold increase in expression (>1.0) or fold decrease in expression ( ⁇ 1.0) of genes exposed to experimental conditions compared to control mice.
• Figure 8 provides the sequences of SEQ ID NOS: 1-16.
• Methods and compositions for decreasing inflammation in a subject are provided, including methods and compositions for treating or preventing inflammatory disorders. Such methods and compositions can be employed to reduce inflammation in the gastrointestinal tract using recombinant bacteria modified to decrease the display of LTA on the bacterial cell surface. Overt inflammation of the gastrointestinal tract is representative of human IBD, including uncreative colitis and Crohn's disease. By decreasing the display of LTA on the cell surface, the recombinant bacteria of the present invention reduce the net inflammatory response significantly more than the corresponding wild-type bacterial cells.
• a decrease in the display of LTA on the surface of a cell comprises any statistically significant decrease in the level of LTA displayed on the surface of a cell, when compared to an appropriate control.
• Such decrease can include, for example, at least a 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% decrease in the amount of LTA displayed on the surface of a cell.
• Methods to assay for the amount of LTA on the surface of a cell include, for example, butanol and hydrophobic interaction chromatography (Morath S, Geyer A, & Hartung T (2001) J Exp Med 193(3):393-397) or enzyme-linked immunosorbent assay (ELISA) (Tadler et al. (2005) J Clin Lab Anal 1989;3(1):21).
• ELISA enzyme-linked immunosorbent assay
• surface refers to an area of the bacterial cell including and external to the plasma membrane.
• Gram positive bacteria contain a layer of peptidoglycan external to the plasma membrane with teichoic acids interspersed within.
• Gram negative bacteria further contain an outer membrane covering the peptidoglycan layer.
• display of the LTA on the surface according to the invention can be in or on the plasma membrane or peptidoglycan layer of Gram positive bacteria, or in or on the plasma membrane, peptidoglycan layer, or outer membrane of Gram negative bacteria.
• Recombinant bacterial cells are provided which have been genetically modified to decrease the display of LTA on the cell surface.
• recombinant bacterium or “recombinant bacterial cells” refer to a bacterium or plurality or bacterial cells in which at least one genetic alteration, has been effected as to a gene of interest, or a cell which is descended from a cell so altered and which comprises the genetic alteration.
• genetic alteration refers to a genetic alteration, such as a deletion, addition or substitution, which has been effected as to a gene or nucleic acid sequence of interest.
• the genetic alteration is an alteration caused by a recombinant technique at the hand of man.
• a genetic alteration comprises the introduction of a heterologous polynucleotide into the genome of the bacterial cell.
• heterologous in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
• a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the
• the same/analogous species one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide.
• the bacterium comprises a probiotic bacterium.
• probiotic refers to "live microorganisms, which when
• probiotic properties comprises enhanced gut function and stability; improved protection against infectious and non-infectious diseases; immune system modulation; alleviated lactose intolerance; improved digestion and nutrient absorption; reduced blood cholesterol; reduced allergy risk; and reduced risk of urinary tract infections.
• probiotic properties comprise an increase in anti-inflammatory cytokine production in the subject receiving the probiotic bacterium, a decrease in pro-inflammatory cytokine production in the subject receiving the probiotic bacterium, or an increase in the ratio of anti-inflammatory to proinflammatory cytokine production in the subject receiving the probiotic bacterium.
• the bacteria described herein have been modified to enhance one or more than one probiotic property.
• bacteria are provided having been modified to increase adhesion to the gastrointestinal epithelium and having been further modified to decrease the display of LTA on the cell surface.
• bacteria are provided having been modified to increase resistance to acid or bile and having further been modified to decrease the display of LTA on the cell surface.
• the bacteria are lactic acid bacteria.
• lactic acid bacteria is intended bacteria from a genus selected from the following: Aerococcus, Carnobacterium, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Oenococcus, Pediococcus, Streptococcus, Melissococcus, Alloiococcus, Dolosigranulum, Lactosphaera, Tetragenococcus, Vagococcus, and Weissella
• Lactobacillus is used.
• Lactobacillus any bacteria from the genus Lactobacillus, including but not limited to L. casei, L. paracasei, L. reuteri, L. rhamnosus, L. johnsonni, L. gasseri, L. acidophilus, L.
• the bacterium is L. acidophilus NCFM.
• the production of bacteria with a decreased display of LTA, the preparation of starter cultures of such bacteria, and methods of fermenting substrates, particularly food substrates such as milk, may be carried out in accordance with known techniques, including but not limited to those described in Mayra-Makinen and Bigret (1993) Lactic Acid Bacteria. Salminen and von Wright eds. Marcel Dekker, Inc. New York. 65-96.; Sandine (1996) Dairy Starter Cultures Cogan and Accolas eds. VCH
• Bacterial cells described herein can be cultured in suitable media, as described generally in Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York).
• bacterial strains described herein are biologically pure cultures of a bacterium comprising at least one genetic alteration resulting in decreased display of LTA on the cell surface as described herein.
• the bacterium comprises one or several nucleotide additions, deletions and/or substitutions. These strains may include but are not limited to: Lactobacillus acidophilus, L. gasseri, L. johnsonii, or L. plantarum. By “biologically pure” is intended 90%, 95%>, 96%>, 97%o, 98%o, 99%), or 100% free of other bacterial cells.
• bacterial strains described herein are found in combination with other bacterial strains to produce mixed cultures.
• a “control” or “control cell” or “control bacteria” provides a reference point for measuring changes in phenotype of the recombinant bacterial cells.
• a control bacteria may comprise, for example: (a) a wild-type bacterium, i.e., of the same genotype as the starting material for the genetic alteration which resulted in the subject bacterium; or (b) a bacterium of the same genotype as the starting material but which has been transformed with a null construct (i.e. with a construct which has no known effect on the trait of interest, such as a construct comprising a marker gene).
• the recombinant bacteria having a decreased display of LTA on the cell surface have been altered such that the level of activity of at least one LTA-related
• LTA refers to lipoteichoic acid, a macroamphiphilic molecule with a glycolipid anchored in the membrane and poly(glycerophosphate) (Gro-P) chain extending into the wall.
• LTA or “lipoteichoic acid” includes wall teichoic acids (WTA), a teichoic acid covalently linked to the
• LTA-related polynucleotides and polypeptides of the invention are understood to encompass those polynucleotides and polypeptides involved with the production, composition, transport, assembly, and display of LTA on the cell surface.
• the display of LTA on the bacterial surface is decreased in order to modulate the inflammatory response in a subject administered the bacterium.
• LTA-related polynucleotides and polypeptides comprise SEQ ID NOS: 1 and 2, or an active fragment or variant thereof.
• the LTA-related polynucleotides and polypeptides comprise SEQ ID NOS: 3-16 or active fragments or variants thereof.
• An LTA-related polynucleotide comprises both the coding sequence encoding the LTA-related protein, but also regulatory sequences such as the promoter.
• An LTA- related polynucleotide can further comprise sites essential for correct translation of LTA-related mRNA, such as the ribosomal binding site.
• polypeptide are used interchangeably.
• expression refers to the transcription of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide.
• a target sequence comprises any sequence that one desires to modulate the level of expression.
• the target sequence includes sequences which both encode and do not encode polypeptides.
• a functional LTA-related polynucleotide or polypeptide is understood to encode proteins, sequences, or RNA responsible for the production, assembly, transport, or display of LTA on the surface of a bacterium.
• a LTA- related polynucleotide or polypeptide whose expression has been decreased would result in a bacterium having a decreased surface display of LTA when compared to its wild-type counterpart.
• a bacterium with decreased surface display of LTA can reduce or prevent the inflammatory response of a subject suffering from an IBD, such as colitis.
• the polynucleotide or polypeptide level of the target sequence is statistically lower than the polynucleotide level or polypeptide level of the same target sequence in an appropriate control.
• reducing the polynucleotide level and/or the polypeptide level of the target sequence results in at least a 95% decrease, at least a 90%> decrease, at least a 80%> decrease, at least a 70%> decrease, at least a 60%> decrease, at least a 50%> decrease, at least a 40%> decrease, at least a 30%> decrease, at least a 20%> decrease, at least a 10%> decrease, or at least a 5% decrease of the polynucleotide level, or the level of the polypeptide encoded thereby, of the same target sequence in an appropriate control.
• reducing the polynucleotide level and/or the polypeptide level of the target sequence results in a decrease of about 3%-15%, 10%-25%, 20% to 35%, 30% to 45%, 40%-55%, 50%- 65%, 60%-75%, 70%-90%, 70% to 80%, 70%-85%, 80%-95%, 90%-100% in the polynucleotide level, or the level of the polypeptide encoded thereby, when compared to an appropriate control.
• Methods to assay for the level of the RNA transcript, the level of the encoded polypeptide, or the activity of the polynucleotide or polypeptide are discussed elsewhere herein.
• increasing the level of a polynucleotide or polypeptide of interest can decrease the display of LTA on the cell surface.
• increasing the expression level of a polynucleotide or a polypeptide encoded thereby is intended to mean, the polynucleotide or polypeptide level of the target sequence is statistically greater than the polynucleotide level or polypeptide level of the same target sequence in an appropriate control.
• increasing the polynucleotide level and/or the polypeptide level of the target sequence results in at least a 95% increase, at least a 90%> increase, at least a 80% increase, at least a 70% increase, at least a 60% increase, at least a 50% increase, at least a 40% increase, at least a 30% increase, at least a 20% increase, at least a 10% increase, or at least a 5% increase of the polynucleotide level, or the level of the polypeptide encoded thereby, of the same target sequence in an appropriate control.
• increasing the polynucleotide level and/or the polypeptide level of the target sequence results in an increase of about 3%-15%, 10%-25%, 20% to 35%, 30% to 45%, 40%-55%, 50%-65%, 60%-75%, 70%-90%, 70% to 80%, 70%-85%, 80%-95%, 90%- 100% in the polynucleotide level, or the level of the polypeptide encoded thereby, when compared to an appropriate control.
• Methods to assay for the level of the RNA transcript, the level of the encoded polypeptide, or the activity of the polynucleotide or polypeptide are discussed elsewhere herein.
• Recombinant organisms having a decrease in the display of LTA on the surface may be constructed using a variety of techniques.
• the expression of polynucleotides or polypeptides encoding at least one of the enzymes of one of the LTA assembly pathways, for example, phosphoglycerol transferase or glycosyltransferase may be decreased, as described herein.
• the level of an LTA-related polypeptide comprising a phosphoglycerol transferase is decreased.
• the expression of the phosphoglycerol transferase set forth in SEQ ID NO: 2, or an active fragment or variant thereof, is decreased.
• Phosphoglycerol transferase is a polypeptide involved the transfer of Gro-P units to a glycolipid, thereby extending the LTA chain.
• Various phosphoglycerol transferase polypeptides and genes encoding the polypeptides are known.
• phosphoglycerol transferase encompasses LTA synthase (LtaS), glycerol phosphotransferase, glycerophosphotransferase, and any other polypeptide that catalyzes the transfer of Gro-P units for the formation of the polyglycerolphosphate backbone of LTA.
• LTA synthase LTA synthase
• glycerol phosphotransferase glycerophosphotransferase
• any other polypeptide that catalyzes the transfer of Gro-P units for the formation of the polyglycerolphosphate backbone of LTA.
• Phosphoglycerol transferase is a member of the alkaline phosphatase superfamily (MdoB [COG1368] Phosphoglycerol transferase). See, for example, NCBI Accession No. NZ ACGXO 1000068.1 and NC 010609.1. Each of these references is herein incorporated by reference.
• the LTA-related polypeptide can comprise a
• glycosyltransferase In this embodiment, the level of glycosyltransferase is decreased using any of the methods to decrease the level of a polynucleotide or polypeptide described elsewhere herein. In one embodiment, the expression of the
• glycosyltransferase set forth in SEQ ID NO: 4 or 6, or an active fragment or variant thereof, is decreased.
• Glycosyltransferase is a polypeptide involved in the synthesis of glycolipids and lipid anchors for LTA.
• the glycosyltransferase polypeptides and genes encoding the polypeptides are known.
• the term glycosyltransferase refers to any polypeptide that catalyzes the synthesis of glycolipids or lipid anchors for LTA including, for example, YgpP, Ugt, BgsA, IagA, LafA, or LafB.
• Glycosyltransferase is a member of the Glycosyltransferase GTB type super family[cll0013].
• Various glycosyltransferases are known. See, for example, NCBI Accession No. NC 010609.1 and EF138835.1. Each of these references is herein incorporated by reference.
• the quality and level of D-Ala substitution on teichoic acids can decrease the display of LTA on the cell surface.
• the synthesis of D-alanyl-LTA requires four proteins that are encoded by the dlt operon, DltA, DltB, DltC, or DltD.
• the LTA-related polynucleotide or polypeptide can comprise the polynucleotide or polypeptide set forth in the Dlt operon, including SEQ ID NOS: 9-16.
• the level of DltA, DltB, DltC, or DltD is decreased using any of the methods to decrease the level of a LTA-related polynucleotide or
• LTA LTA can be measured by NMR and MS using known techniques. See, for example, Morath S, Geyer A, & Hartung T (2001) J Exp Med 193(3):393-397.
• a decrease in the expression of LTA-related polynucleotides or polypeptides can be achieved by a variety of techniques well known in the art.
• gene expression can be decreased by a mutation.
• the mutation can be an insertion, a deletion, a substitution or a combination thereof, provided that the mutation leads to a decrease in the expression of a functional LTA-related protein or results in a decrease in expression of an LTA-related polynucleotide such that the display of LTA on the surface of the cell is decreased.
• Bacteria with decreased display of LTA can be used to reduce the inflammatory response of a subject, thereby treating or preventing inflammatory bowel diseases, such as colitis.
• Recombinant DNA technology can be used to introduce a mutation into a specific site on the chromosome.
• a mutation may be an insertion, a deletion, a replacement of one nucleotide by another one or a combination thereof, as long as the mutated gene leads to a decrease in the expression of a functional LTA-related protein or results in a decrease in express of an LTA-related gene such that the display of LTA on the surface of the cell is decreased.
• Such a mutation can be made by deletion of a number of base pairs.
• the deletion of one single base pair could render a LTA related protein non- functional, thereby decreasing the display of LTA on the bacterial surface, since as a result of such a mutation, the other base pairs are no longer in the correct reading frame.
• multiple base pairs are removed e.g. 100 base pairs.
• the length of the entire LTA- related gene is deleted. Mutations introducing a stop-codon in the open reading frame, or mutations causing a frame-shift in the open reading frame could be used to reduce the expression of a LTA-related gene.
• LTA-related gene in order to decrease the display of LTA are well-known in the art.
• techniques may include modification of the gene sequence by site-directed mutagenesis, restriction enzyme digestion followed by re-ligation, PCR-based mutagenesis techniques, allelic exchange, allelic replacement, RNA interference, or post-translational modification.
• Standard recombinant DNA techniques such as cloning the LTA-related gene into a plasmid, digestion of the gene with a restriction enzyme, followed by endonuclease treatment, re-ligation, and homologous recombination are all known in the art and described in Maniatis/Sambrook (Sambrook, J. et al.
• the recombinant bacterium is modified by site-directed mutagenesis to have decreased display of LTA on the surface.
• the bacterium having decreased display of LTA is isolated from a bacterial population.
• isolated as used herein refers to a bacterium which is separated from its natural environment. This may be, for example, by purification from a mixed bacterial population or an environmental sample.
• An isolated bacterium is substantially free of other bacterial species and components of the natural environment of the bacterium.
• a bacterium that is substantially free of other bacterial species and components of the natural environment includes bacterial preparations having less than about 30%, 20%, 10%>, 5%, or 1% of contaminating bacterial species or components of the natural environment.
• Assays to detect expression of the disclosed polypeptides and/or nucleic acid molecules can include the detection and/or quantitation of LTA. Methods for the detection of LTA are described elsewhere herein. A decrease in the display of LTA on the surface of a bacterial cell can result in an increase in the anti-inflammatory response or a decrease in the pro-inflammatory response of host cells exposed to the bacterium. Assays to measure anti-inflammatory or pro-inflammatory response, for example, can also be used to evaluate the expression of LTA-related polypeptides of the present invention. Methods to measure inflammatory response are also described elsewhere herein.
• fragment refers to a portion of the amino acid sequence of a polypeptide or protein, or polynucleotide encoding a portion of the amino acid sequence of a polypeptide or protein. Fragments may retain the activity of the original protein and hence, such "active" fragments include, for example, fragments of an LTA-related protein, such as a fragment of SEQ ID NO: 2 that retains
• a fragment of a LTA-related nucleotide sequence such as a fragment of SEQ ID NO: 1 that encodes an active phosphoglycerol transferase, may encode a protein fragment that is biologically active. Additionally, fragments of LTA-related proteins include fragments of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14 and 16.
• a biologically active nucleotide fragment can be prepared by isolating a portion of an LTA-related polynucleotide or polypeptide, expressing the encoded portion of the LTA-related protein, and assessing the activity of the encoded portion of the LTA-related protein.
• a fragment of nucleotide sequence of a LTA-related protein need not encode a biologically active polypeptide, but rather could comprise a polynucleotide which, when expressed, suppresses the expression of the target LTA-related polypeptide (i.e. sense, antisense, miRNA, or siRNA
• Fragments of LTA-related polynucleotides include fragments of SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13 and 15. Fragments of LTA-related nucleic acid molecules comprise at least about 15, 20, 50, 75, 100, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 nucleotides or up to the total number of nucleotides present in a full-length LTA-related nucleotide sequence as disclosed herein.
• Fragments of amino acid sequences include peptides comprising amino acid sequences sufficiently identical to or derived from the amino acid sequence of a LTA- related protein, or a partial-length protein and exhibiting at least one activity of a LTA- related protein (i.e. modulate the level of LTA displayed on the cell surface), but which include fewer amino acids than the full-length LTA-related proteins disclosed herein.
• a biologically active portion of a LTA-related protein can be a polypeptide that is, for example, 10, 25, 50, 100, 150, 200 contiguous amino acids in length, or up to the total number of amino acids present in a full-length LTA-related protein of the current invention (i.e., of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14 or 16).
• Such biologically active portions can be prepared by recombinant techniques and evaluated for one or more of the functional activities of a native LTA-related protein, such as phosphoglycerol transferase activity.
• a fragment comprises at least 5 contiguous amino acids of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14 or 16.
• the invention encompasses other fragments, however, such as any fragment in the protein greater than 6, 7, 8, or 9 amino acids.
• recombinant bacteria are provided which have been modified to reduce the expression of variants of the nucleotide and amino acid sequences provided elsewhere herein.
• variant is intended a sufficiently identical sequence.
• the invention encompasses bacteria, modified to reduce the expression of nucleic acid molecules that are sufficiently identical to the nucleotide sequences encoding LTA-related proteins in SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14 or 16, or nucleic acid molecules that comprise the nucleotide sequence of SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13 or 15, or a complement thereof.
• Variant polynucleotides further include sequences comprising one or several additions, deletions, or substitutions.
• Variants also include variant polypeptides encoded by the nucleotide sequences of the present invention.
• polypeptides of the current invention have an amino acid sequence that is sufficiently identical to an amino acid sequence put forth in SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14 or 16.
• amino acid sequence put forth in SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14 or 16.
• amino acid sequence or nucleotide sequence contains a sufficient or minimal number of equivalent or identical amino acid residues or nucleotides as compared to a second amino acid sequence or nucleotide sequence, thus providing a common structural domain and/or indicating a common functional activity, such as LTA-related biological activity.
• Conservative variants include those nucleotide sequences that differ due to the degeneracy of the genetic code.
• amino acid sequences or nucleotide sequences that have at least about 45%, 55%), or 65%> identity, preferably at least about 70%> or 75% identity, more preferably at least about 80%>, 85% or 90%>, most preferably at least about 91 >, 92%, 93%, 94%, 95%, 95%, 96%, 97%, 98%, 99%, or 99.5% sequence identity to any of the amino acid sequences of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14 or 16 or any of the nucleotide sequences of SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13 or 15, respectively, are defined herein as sufficiently identical.
• Variant proteins encompassed by the present invention are biologically active, that is they retain the desired LTA-related biological activity of the native protein, such as phosphoglycerol transferase activity of SEQ ID NO: 2. See, for example, Varcamonti et al. (2003) Appl. Environ. Microbiol. 69: 1287— 1289.
• a biologically active variant of a protein may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
• LTA-related polypeptides may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions.
• a "native sequence" polypeptide comprises a polypeptide having the same amino acid sequence as the corresponding polypeptide derived from nature. Such native sequence polypeptides can be isolated from nature or can be produced by recombinant and/or synthetic means.
• the term "native sequence” specifically encompasses naturally-occurring truncated, soluble or secreted forms, naturally-occurring variant forms, and naturally-occurring allelic variants of the polypeptide.
• sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
• sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
• percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule.
• sequences differ in conservative substitutions the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution.
• Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE
• percentage of sequence identity means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
• sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof.
• equivalent program is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
• Methods are provided for decreasing inflammation in a subject comprising administration of a recombinant bacterium described elsewhere herein.
• administration of a recombinant bacterium with a decreased display of LTA can ameliorate the symptoms of IBD, such as colitis, in a subject.
• administration of a recombinant bacterium with decreased display of LTA can prevent the onset of IBD, such as colitis, in a subject.
• a recombinant bacterium with decreased expression of an LTA-related protein including, for example, phosphoglycerol transferase, including, for example, decrease in expression of SEQ ID NO: 1 or active fragments or variants thereof, has a decreased display of LTA on the cell surface and can ameliorate the symptoms of established colitis and prevent the onset of colitis. See Example 1 below.
• methods for treating and/or preventing inflammation locally in the gastrointestinal tract, treating and/or preventing inflammatory disorders of the gastrointestinal tract, as well as treating pain locally in the intestines, in a subject are provided.
• Treatment is herein defined as curing, healing, alleviating, relieving, altering, remedying, ameliorating, improving, or affecting the condition or the symptoms of a subject with a gastrointestinal disorder.
• the subject to be treated can be suffering from or at risk of developing a gastrointestinal disorder, including, for example, be suffering from an inflammatory bowel disease or be at risk of developing an inflammatory bowel disease.
• Administration of the recombinant bacterium can be for either a prophylactic or therapeutic purpose.
• preventing is intended that the recombinant bacterium is provided prophylactically, i.e., the bacterium is provided in advance of any symptom.
• the prophylactic administration of the recombinant bacterium serves to prevent or attenuate any subsequent symptom.
• the bacterium is provided at (or shortly after) the onset of a symptom.
• the therapeutic administration of the substance serves to attenuate any actual symptom.
• subjects are mammals, e.g., primates or humans.
• subjects include domestic animals, such as a feline or canine, or agricultural animals, such as a ruminant, horse, swine, poultry, or sheep.
• the subject undergoing treatment with the pharmaceutical formulations of the invention is a human.
• the human undergoing treatment can be a newborn, infant, toddler, preadolescent, adolescent or adult.
• the subjects of the invention may be suffering from the symptoms of a gastrointestinal disorder or may be at risk for a gastrointestinal disorder (e.g. a subject that has undergone antibiotic treatment).
• inflammatory gastrointestinal disorder or "gastrointestinal disorder” or “inflammatory disorder of the gastrointestinal tract” refers to a disease of the gastrointestinal tract or bowel that is mediated by the immune system or cells of the immune system.
• Inflammatory gastrointestinal disorders include, for example, inflammatory bowel diseases (IBD) such as Crohn's disease and ulcerative colitis, lymphocytic colitis, microscopic colitis, collagenous colitis, autoimmune enteropathy, allergic gastrointestinal disease and eosinophilic gastrointestinal disease, as well as diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, or constipation.
• IBD inflammatory bowel diseases
• the methods of the invention relate to the treatment or prevention of obesity, or the symptoms of obesity including, IBD, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, or constipation. See, for example, Kadooka Y, et. al. (2010) Eur J Clin Nutr. 64(6):636-43, herein incorporated by reference.
• the decrease in inflammation may include stimulation of intestinal integrity; reduction of intestinal permeability; improvement of mucin synthesis, secretion, and/or quality; improvement of the maturation and differentiation of the intestinal epithelium; improvement of nutrient absorption; increase of the production of soluble factors that transfer antimicrobial activity; stimulation of, improvement of, or support of resistance to infection; support of cellular or humoral responses against viral or bacterial infection; increased cytotoxicity (both anti-viral and anti-tumor); support of systemic and/or mucosal vaccination responses; increase or support of cellular and/or humoral immunity; increase or support of natural immunity (including neutrophils, phagocytes, macrophages, and natural killer cell activity);
• helper T cell 1 helper T cell 1
• Thl helper T cell 1
• IFN-gamma increase or support of adaptive T and B cell immunity
• HLA-Dr helper T cell 1
• suppression of inflammation or production of systemic and mucosal inflammatory mediators including cytokines and/or chemokines
• reduction of sensitization by reducing total and/or allergen- specific IgE reduction of the production of allergic cytokines; reduction of a Th2 supporting immunoglobulin profile; and combinations thereof.
• anti-inflammatory cytokine refers to a naturally occurring or recombinant protein, analog thereof or fragment thereof that elicits an antiinflammatory response in a cell that has a receptor for that cytokine.
• Antiinflammatory cytokines of the invention can be immunoregulatory molecules that control the proinflammatory cytokine response.
• Anti-inflammatory cytokines of the invention include interleukin (IL)-l receptor antagonist, IL-4, IL-10, IL-11, and IL-13, IL-16, IFN-alpha, TGF-beta, G-CSF.
• IL interleukin
• proinflammatory cytokine refers to an
• Proinflammatory cytokines of the invention include IL1 -alpha, ILl-beta, TNF-alpha, IL-2, IL-3, IL-6, IL-7, IL-9, IL- 12, IL-17, IL-18, TNF-alpha, LT, LIF, Oncostatin, or IFN-alpha, IFN-beta, IFN- gamma.
• administering results in an increase in anti-inflammatory cytokine production.
• an "increase in” or “increasing" anti-inflammatory cytokine production comprises any statistically significant increase the anti-inflammatory cytokine level when compared to an appropriate control.
• Such increases can include, for example, at least a 5%, 10%, 20%>, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200% or greater increase in the anti-inflammatory cytokine level.
• Such increases can also include, for example, at least about a 3%- 15%, 10%-25%, 20% to 35%, 30% to 45%, 40%-55%, 50%-65%,
• Methods and compositions also include those which decrease proinflammatory cytokine production, which may decrease or prevent an inflammatory response.
• a decrease in the level of pro-inflammatory cytokine production comprises any statistically significant decrease in the level of pro-inflammatory cytokine production in a subject when compared to an appropriate control. Such decreases can include, for example, at least a 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% decrease in the level of proinflammatory cytokines.
• Methods to assay for cytokine levels are known and include, for example Leng S., et al. (2008) J Gerontol A Biol Sci Med Sci 63(8): 879-884.
• Methods to assay for the production of proinflammatory cytokines include multiplex bead assay, ELISPOT and flow cytometry. See, for example, Maecker et al. (2005) BMC Immunology 6:13.
• Inflammatory cytokine production can also be measured by assaying the ratio of anti-inflammatory cytokine production to proinflammatory cytokine production.
• the ratio of anti-inflammatory cytokine production to proinflammatory cytokine production is increased by about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 300, 600, 900, 1000 fold or greater when compared to an appropriate control.
• the ratio of anti-inflammatory cytokine production to proinflammatory cytokine production is increased by about 1 to 5 fold, about 5 to 10 fold, about 10 to 20 fold, about 20 to 30 fold, about 30 to 40 fold, about 40 fold to 60 fold, about 60 fold to 80 fold, about 80 fold to about 100 fold, about 100 to 200 fold, about 200 fold to 300 fold, about 300 to 400 fold, about 400 to about 500 fold, about 500 to about 500 fold, about 500 fold to about 700 fold, about 700 fold to 800 fold, about 800 fold to about 1000 fold or greater when compared to an appropriate control.
• Methods to determine the ratio of anti-inflammatory cytokine production to pro-inflammatory cytokine production can be found, for example, Leng S., et al.
• cytokines include multiplex bead assay, ELISPOT and flow cytometry. See, for example, Maecker et al. (2005) BMC Immunology 6: 13.
• immune and inflammatory disorders can be treated or prevented.
• disorders that could be treated or prevented by the methods and compositions described herein include, but are not limited to: arthritis (rheumatoid arthritis, juvenile rheumatoid arthritis, osteoarthritis, psoriatic arthritis), psoriasis, dermatitis including atopic dermatitis; chronic autoimmune urticaria, polymyositis/dermatomyositis, toxic epidermal necrolysis, systemic scleroderma and sclerosis, respiratory distress syndrome, adult respiratory distress syndrome (ARDS), meningitis, allergic rhinitis, encephalitis, uveitis, colitis, glomerulonephritis, allergic conditions, eczema, asthma, conditions involving infiltration of T cells and chronic inflammatory responses, atherosclerosis, autoimmune myocarditis, leukocyte adhesion deficiency,
• polyendocrinopathies Reiter's disease, stiff-man syndrome, giant cell arteritis, immune complex nephritis, IgA nephropathy, IgM polyneuropathies or IgM mediated neuropathy, idiopathic thrombocytopenic purpura (ITP), thrombotic throbocytopenic purpura(TTP), autoimmune thrombocytopenia, autoimmune disease of the testis and ovary including autoimune orchitis and oophoritis, primary hypothyroidism;
• autoimmune endocrine diseases including autoimmune thyroiditis, chronic thyroiditis (Hashimoto's Thyroiditis), subacute thyroiditis, idiopathic hypothyroidism, Addison's disease, Grave's disease, autoimmune polyglandular syndromes (or polyglandular endocrinopathy syndromes), Type I diabetes also referred to as insulin-dependent diabetes mellitus (IDDM) and Sheehan's syndrome; autoimmune hepatitis, Lymphoid interstitial pneumonitis (HIV), bronchiolitis obliterans (non- transplant) vs
• a disorder of the heart includes but is not limited to: heart failure, including but not limited to, cardiac hypertrophy, left-sided heart failure, and right-sided heart failure; ischemic heart disease, including but not limited to angina pectoris, myocardial infarction, chronic ischemic heart disease, and sudden cardiac death; hypertensive heart disease, including but not limited to, systemic (left-sided) hypertensive heart disease and pulmonary (right-sided) hypertensive heart disease; valvular heart disease, including but not limited to, valvular degeneration caused.by calcification, such as calcific aortic stenosis, calcification of a congenitally bicuspid aortic valve, and mitral annular calcification, and myxomatous degeneration of the mitral valve (mitral valve prol apse), rheumatic fever and rheumatic heart disease,
• bacterial strains having a decrease in the display of LTA are administered to a subject in the form of a nutraceutical composition such as a nutritional supplement and/or food additive.
• a nutraceutical composition such as a nutritional supplement and/or food additive.
• composition comprises a recombinant bacterium that has been modified to decrease the expression of a polynucleotide or polypeptide encoding a
• the extracts are administered to a subject in the form of a pharmaceutical composition.
• the administration may comprise a single dose or multiple dose administration, as described elsewhere herein.
• the pharmaceutical composition may be a liquid formulation or a solid formulation.
• the pharmaceutical composition may be formulated as a tablet, a sucking tablet, a chewing tablet, a chewing gum, a capsule, a sachet, a powder, a granule, a coated particle, a coated tablet, an enterocoated tablet, an enterocoated capsule, a melting strip or a film.
• composition When the pharmaceutical composition is a liquid formulation it may be formulated as an oral solution, a suspension, an emulsion or syrup. Said composition may further comprise a carrier material independently selected from, but not limited to, the group consisting of lactic acid fermented foods, fermented dairy products, resistant starch, dietary fibers,
• the term "pharmaceutical composition” could be formulated as a food composition, a dietary supplement, a functional food, a medical food or a nutritional product as long as the required effect is achieved, i.e. treatment or prevention of an inflammatory disorder of the gastrointestinal tract.
• Said food composition may be chosen from the group consisting of beverages, yogurts, juices, ice creams, breads, biscuits, crackers, cereals, health bars, spreads and nutritional products.
• the food composition may further comprise a carrier material, wherein said carrier material is chosen from the group consisting of lactic acid fermented foods, fermented dairy products, resistant starch, dietary fibers, carbohydrates, proteins and glycosylated proteins.
• composition according to the invention used according to the invention or produced according to the invention may also comprise other substances, such as an inert vehicle, or pharmaceutical acceptable adjuvants, carriers, preservatives etc., which are well known.
• bacteria of the invention may be administered in combination with effective doses of conventional anti-inflammatory agents for treatment of inflammatory disorders of the gastrointestinal tract, such as prednisone, mesalamine, azathioprine, TNF inhibitors, methotrexate, or 6- mercaptopurine.
• conventional anti-inflammatory agents for treatment of inflammatory disorders of the gastrointestinal tract, such as prednisone, mesalamine, azathioprine, TNF inhibitors, methotrexate, or 6- mercaptopurine.
• administration in combination refers to both concurrent and sequential administration of the active agents.
• the combination therapies are of course not limited to the agents provided herein, but include any composition for the treatment of inflammatory disorders. Therapeutically effective amount
• terapéuticaally effective dose By “therapeutically effective dose,” “therapeutically effective amount,” or “effective amount” is intended an amount of the recombinant bacterium having a decreased display of LTA that, when administered to a subject, decreases the inflammatory response, or prevents an inflammatory response from increasing.
• “Positive therapeutic response” refers to, for example, improving the condition of at least one of the symptoms of an inflammatory gastrointestinal disorder.
• unit dose refers to a physically discrete unit suitable for use in a subject, each unit containing a predetermined quantity of the therapeutic composition calculated to produce the desired response in association with its administration, i.e., the appropriate route and treatment regimen.
• the quantity to be administered depends on the subject to be treated, the state of the subject and the protection desired. Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual.
• the dosage of recombinant bacteria will vary depending upon such factors as the patient's age, weight, height, sex, general medical condition and previous medical history. In specific embodiments, it may be desirable to administer the bacterium in the range of about 10 4 to about 10 12 CFU, 10 5 to 10 11 CFU, 10 6 to 10 10 CFU, 10 8 to 10 10 CFU or 10 8 to 10 12 CFU .
• the method comprises administration of multiple doses of the bacterium.
• the method may comprise administration of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, or more therapeutically effective doses of a composition comprising the bacterium as described herein.
• doses are administered over the course of 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 14 days, 21 days, 30 days, or more than 30 days.
• the frequency and duration of administration of multiple doses of the compositions is such as to reduce or prevent an inflammatory response and thereby treat or prevent a gastrointestinal disorder.
• treatment of a subject with a therapeutically effective amount of the recombinant bacterium of the invention can include a single treatment or can include a series of treatments. It will also be appreciated that the effective dosage of a bacterium used for treatment may increase or decrease over the course of a particular treatment. Changes in dosage may result and become apparent from the results of diagnostic assays for detecting inflammation known in the art and described herein.
• Applicant made a deposit of Lactobacillus acidophilus NCK2025 with the American Type Culture Collection (ATCC), Manassas, VA 20110 USA, ATCC Deposit No. PTA-11587 on January 10, 2011.
• ATCC American Type Culture Collection
• the bacterial culture deposited with the ATCC on January 10, 2011 was taken from the deposit maintained by North Carolina State University, 100 Schaub Hall, Campus Box 7624, Raleigh, North Carolina, 27695 since prior to the filing date of this application. Access to this deposit will be available during the pendency of the application to the Commissioner of Patents and Trademarks and persons determined by the Commissioner to be entitled thereto upon request.
• the Applicant will make the deposit available to the public pursuant to 37 C.F.R. ⁇ 1.808.
• Lactobacillus acidophilus NCK2025 will be maintained in the ATCC depository, which is a public depository, for a period of 30 years, or 5 years after the most recent request, or for the enforceable life of the patent, whichever is longer, and will be replaced if it becomes nonviable during that period. Additionally, Applicant has or will satisfy all of the requirements of 37 C.F.R. ⁇ 1.801 - 1.809, including providing an indication of the viability of the sample upon deposit. Applicant has no authority to waive any restrictions imposed by law on the transfer of biological material or its transportation in commerce
• a recombinant or isolated bacterium having been genetically modified to decrease the display of lipoteichoic acid (LTA) on the surface of said bacterium.
• LTA lipoteichoic acid
• Lactobacillus is Lactobacillus acidophilus.
• Lactobacillus acidophilus is Lactobacillus acidophilus NCK2025, deposited under ATCC accession number PTA-11587.
• a method of making a recombinant or isolated bacterium comprising genetically modifying a bacterium to decrease the display of lipoteichoic acid (LTA) on the surface of said bacterium.
• LTA lipoteichoic acid
• recombinant bacterium is a probiotic bacterium.
• Lactobacillus acidophilus Lactobacillus acidophilus.
• Lactobacillus acidophilus is Lactobacillus acidophilus NCK2025, deposited under ATCC accession number PTA-11587.
• Lactobacillus acidophilus has been modified to decrease the expression of a polynucleotide comprising the nucleotide sequence as set forth in SEQ ID NO: 1.
• a method of decreasing inflammation in a subject comprising, administering to said subject a therapeutically effective amount of the recombinant or isolated bacterium of any one of embodiments 1-10.
• a method of treating or preventing an inflammatory disorder of the gastrointestinal tract of a subject comprising, administering to a subject a
• pro-inflammatory cytokine is selected from the group consisting of: IL-12, IL-6, IFNy,TNFa, and any combination thereof.
• therapeutically effective amount of the bacterium is about 10 8 to 1012 CFU/day.
• a pharmaceutical composition comprising the recombinant or isolated bacterium according to any one of embodiments 1-10.
• the recombinant or isolated bacterium for use according to embodiment 40 wherein said pro-inflammatory cytokine is selected from the group consisting of: IL-12, IL-6, IFNy, TNFa, and any combination thereof.
• said recombinant or isolated bacterium for use according to any one of embodiments 36-41 wherein said bacterium is formulated to be administered to a subject in a therapeutically effective amount, wherein the therapeutically effective amount of the bacterium is about 10 8 to 1012 CFU/day.
• gastrointestinal disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• a bacterium according to 44 in the manufacture of a medicament for treatment or prevention of a disorder of the gastrointestinal tract of a subject, for example a subject according to any one of embodiments 23-27.
• a bacterium according to embodiment 46 wherein said disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• a bacterium according to embodiment 50 wherein said gastrointestinal disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• gastrointestinal disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• a recombinant or isolated bacterium genetically modified to decrease the display of lipoteichoic acid (LTA) on the surface of said bacterium.
• LTA lipoteichoic acid
• the recombinant or isolated bacterium has been genetically modified to decrease the expression of a phosphoglycerol transferase.
• the recombinant or isolated bacterium has been genetically modified to decrease the expression of a phosphoglycerol transferase by about 3%-15%, 10%-25%, 20% to 35%, 30% to 45%, 40%-55%, 50%-65%, 60%-75%, 70%-90%, 70% to 80%, 70%-85%, 80%-95%, 90%- 100% when compared to an unmodified control.
• the recombinant or isolated bacterium has been genetically modified to decrease the expression of a polynucleotide comprising a nucleotide sequence having at least 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%), 98%o, 99%), or 100% sequence identity to the nucleic acid sequence as set forth in any of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13 or 15 or a fragment or variant thereof.
• the recombinant or isolated bacterium of has been genetically modified to decrease the expression of a polynucleotide comprising the nucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13 or 15 or a fragment or variant thereof.
• a method of making a recombinant or isolated bacterium comprising genetically modifying a bacterium to decrease the display of lipoteichoic acid on the surface of the bacterium.
• the bacterium is modified by site-directed mutagenesis.
• said recombinant or isolated bacterium has been modified to decrease the expression of a phosphoglycerol transferase.
• the decrease in expression of the phosphoglycerol transferase may be as a result of disruption at the DNA, RNA or post translational level, suitable methods for achieving such a decrease in expression are known in the art and are discussed in further detail herein.
• said recombinant or isolated bacterium has been genetically modified to decrease the expression of a polynucleotide comprising the nucleotide sequence having at least 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%), 98%o, 99%), or 100% sequence identity to the nucleic acid sequence as set forth in any of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13 or 15 or a fragment or variant thereof.
• the Lactobacillus acidophilus has been modified to decrease the expression of a polynucleotide comprising the nucleotide sequence set forth in SEQ ID NO: 1, 3, 5, 7, 9, 11, 13 or 15 or a fragment or variant thereof.
• the recombinant or isolated bacterium is a probiotic bacterium. Specifically, a lactic acid bacterium. More specifically, Lactobacillus particularly Lactobacillus acidophilus. Even more specifically the genetic modification is performed on L. acidophilus NCFM.
• the recombinant or isolated bacterium is
• Lactobacillus acidophilus NCK2025 deposited under ATCC accession number PTA- 11587.
• a method of decreasing inflammation in a subject comprising, administering to said subject a therapeutically effective amount of the recombinant or isolated bacterium described elsewhere herein.
• the decrease in inflammation treats or prevents a disease of the heart such as coronary artery disease or heart failure.
• a method of treating or preventing an inflammatory disorder of the gastrointestinal tract comprising, administering to a subject a therapeutically effective amount of the recombinant or isolated bacterium described elsewhere herein.
• the subject is an animal, more specifically a mammal.
• the subject is a human.
• the subject is a domestic animal.
• the subject is an agricultural animal.
• the subject has a gastrointestinal disorder.
• the gastrointestinal disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• the bacterium may increase the production of one or more anti-inflammatory cytokines in the subject.
• the anti-inflammatory cytokine is IL-10.
• the bacterium decreases production of one or more proinflammatory cytokines in the subject.
• the pro-inflammatory cytokine is selected from the group consisting of: IL-12, IL-6, IFNy, TNFa, or any combination thereof.
• the bacterium is administered in a therapeutically effective amount, wherein the therapeutically effective amount of the bacterium is about 10 8 to 10 12 CFU/day.
• a pharmaceutical composition comprising the recombinant or isolated bacterium described herein.
• a recombinant or isolated bacterium described herein for use in treating or preventing a disorder of the gastrointestinal tract of a subject.
• the disorder is an inflammatory disorder.
• the gastrointestinal disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• the recombinant or isolated bacterium for use according to the methods described herein increases the anti-inflammatory cytokine production in the subject.
• the anti-inflammatory cytokine is IL-10.
• the recombinant or isolated bacterium for use according to the methods described herein decreases production of one or more pro-inflammatory cytokines in the subject.
• the pro-inflammatory cytokine is selected from the group consisting of: IL-12, IL-6, IFNy, TNFa, or any combination thereof.
• the bacterium is provided in a therapeutically effective amount, wherein the therapeutically effective amount of the bacterium is about 10 to 10 12 CFU/day.
• the medicament is for treating or preventing a disorder of the gastrointestinal tract of a subject.
• the disorder is an inflammatory disorder.
• the gastrointestinal disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• a bacterium described herein as a medicament.
• the medicament is for treating or preventing a disorder of the gastrointestinal tract of a subject.
• the disorder is an inflammatory disorder.
• the disorder is selected from the group consisting of: inflammatory bowel disease, Crohn's disease, irritable bowel syndrome, ulcerative colitis, obesity, diarrhea, bloating, flatulence, abdominal cramping, abdominal pain, constipation, and any combination thereof.
• LBA0448 are flanked by putative rho-independent terminators ( Kingsford C,
• LBA0444-LBA0447 genes have a putative role in LTA biosynthesis
• LBA0448 is a hypothetical protein that does not appear to play a role in this cascade.
• Lactobacillus species can effectively activate various signals in DCs that, in turn induce T cell immune responses ( Mohamadzadeh M, et al. (2005) Proc Natl Acad Sci USA 102(8):2880-2885; Konstantinov SR, et al. (2008) Proc Natl Acad Sci USA 105(49): 19474-19479).
• LBA0447 phosphoglycerol transferase gene
• PCR analysis of this genomic region showed that the deletion mutant, NCK2025, lost 2 kbp ( Figure 1C-D). Sequencing over this region confirmed the elimination of LBA0447.
• Chromatographic analysis of cell wall extracts of the parent NCK56 and mutant NCK2025 demonstrated the absence of LTA in the mutant where the phosphoglycerol transferase gene had been deleted
• NCK2025 treated-DCs Co-culturing DCs with NCK56 or LTA-negative mutant (NCK2025) showed that NCK2025 down-regulated MHC II, CD40, CD80 and CD86 on the surface of DCs (Fig. 2A). Moreover, treatment of DCs with NCK56 induced the transcription of TLR1 and 2 while these two pattern recognition receptors (PRRs) were not activated in NCK2025 treated-DCs (Fig. 2B). Both strains induced IL-10 production in DCs; however, the production of this cytokine was significantly increased in DCs co-cultured with NCK2025 (Fig. 2C). Concomitantly, IL-12 and TNFa were significantly reduced in NCK2025 treated-DCs (Fig. 2C).
• T cell proliferation was determined by co-culturing mesenteric LN derived T cells with bone marrow derived DCs treated with NCK56 or NCK2025. T cell proliferation was significantly abrogated in NCK2025 treated-DCs co-cultured with T cells relative to NCK56 (Fig. 2D).
• IL-10 may be a pivotal factor that regulates T cell proliferation in the DC:T cell co-cultures.
• Analysis of harvested supernatants from DC:T cell co-cultures showed that IL-10 was highly induced in T cells while IFNy, IL-2, and TNFa were minimally released from T cells of mice that were treated with NCK2025 (Fig. 2E).
• DSS-induced colitis was analyzed in mice that were treated with NCK56 or NCK2025 for four consecutive days before (preventative) or after (therapy) exposure to 3% DSS.
• Data show that DSS induced clinical and histological colitis in untreated C57BL/6 mice ( Figure 3A, C) relative to baseline ( Figure 3B).
• mice began to lose weight after day 9 with approximately 10% overall weight loss by day 13 and developed severe bloody diarrhea around day 10 to 11 ( Figure 3 A).
• oral inoculation of the mice with NCK2025 significantly prevented weight loss, reduced diarrhea and hemoccult positivity (Figure 3A).
• DAI Disease Activity Index
• Colonic cytokine analysis shows the levels of IL-6, IL-12, TNFa and IFNy were higher in colons derived from NCK56- and DSS-treated mice ( Figure 3G).
• IL-10 production was significantly elevated in colonic cultures derived from NCK2025 treated mice.
• IL-12, IL-6, IFNy and TNFa were significantly reduced in the colons of the mice treated with NCK2025 ( Figure 3G).
• PHA2G7 platelet activating factor acetylhydrolase
• SRF serum response factor
• TGFp TGFp
• p21 -activated kinasesPAKl RAF1, tissue inhibitor of matrix metalloproteinase (TIMP1), Tyk2] were highly regulated in colonic distal (not proximal) regions in NCK2025, but not NCK56- or DSS alone treated mice (Fig. 7A). This implies that such genes become significantly activated to exert their regulatory functions in the distal colon where DSS-induced colitis is more severe. Therapeutic effects of NCK2025 on DSS-induced colitis.
• mice were first exposed to 3% DSS before treatment with NCK56 or NCK2025. Once disease symptoms occurred, mice received NCK56 or NCK2025 for four consecutive days ( Figure 4A). Data show that both NCK56 and NCK2025 attenuated established colitis, but to a significantly different degree. Treatment of mice with NCK2025 resulted in stabilization of body weight and rapid resolution of diarrhea and blood loss, while NCK56-treated mice continued to lose weight, albeit at a slower rate, and was significantly slower to resolve diarrhea and blood loss (Figure 4A).
• cytokine analysis of the mice treated with NCK2025 shows upregulation of IL-10 and minimal release of IL-12, TNFa, IL-6 and IFNy in the colons of these mice ( Figure 4F).
• IL-12, TNFa, IFNy, and IL-6 were highly induced in the colons of mice treated with NCK56 or DSS alone, and IL-10 was minimally released in these groups of mice ( Figure 4F).
• NCK2025 that induces IL-10 in DCs and in the colonic microenvironment of treated mice, was investigated to determine if it enhances colonic CD4 FoxP3 Treg cells in C57BL/6 mice when compared to NCK56.
• figures 5 A & B show that Treg cells were significantly induced in the colons of the mice treated with NCK2025 compared to NCK56 suggesting that the suppressor effects of these cells may impact exaggerated inflammation induced by DSS at the mucosa.
• IL-10 IL-10 "7" mice develop spontaneous Thl -mediated colitis upon exposure to commensal bacteria, with deep, transmural ulcerating lesions similar to human Crohn's disease ( Berg DX et al. (1996) J Clin Invest 98(4): 1010-1020). Prior to the onset of colitis, mice were inoculated with NCK56 or NCK2025 (or no treatment as a control group) for four consecutive days. The onset of colitis was induced by treatment with piroxicam as described above.
• the cell wall and cell surface proteins of L. acidophilus comprise components that are critical for the maintenance of cell shape and activation of immune cells, including DCs (
• NCK2025 acidophilus LTA-negative mutant, NCK2025, induced regulatory signals (i.e. IL-10) and less co-stimulatory molecules (CD40, CD86) in mouse DCs, in effect converting these cells to regulatory DCs ( Belkaid Y & Oldenhove G (2008) Immunity 29(3):362- 371). Subsequent interaction of such regulatory DCs with CD4 + T cells significantly altered T cell activation. Furthermore, NCK2025 treatment ameliorated DSS-induced colitis indicating that pretreatment of the animal with this bacterial strain induced regulatory immunity that resists DSS-challenge as demonstrated by colonic histology, weight loss, reduced diarrhea and hemoccult positivity.
• IL-10 induced regulatory signals
• CD86 co-stimulatory molecules
• IL-10 modulates both innate and adaptive immune responses via its ability to exert antiinflammatory effects (Moore KW, de Waal Malefyt R, Coffman RL, & O'Garra A (2001) Annu Rev Immunol 19:683-765; Trinchieri G (2007) J Exp Med 204(2):239- 243).
• This cytokine functionally suppresses T cells by down-regulating MHC II, co- stimulatory molecules and the production of IL-12 in DCs, all of which are strongly involved in T cell differentiation and activation (Moore KW, de Waal Malefyt R, Coffman RL, & O'Garra A (2001) Annu Rev Immunol 19:683-765; de Waal Malefyt R, Abrams J, Bennett B, Figdor CG, & de Vries JE (1991) J Exp Med 174(5): 1209-1220).
• IL-10 also regulates CD8 + cytotoxic T lymphocytes (CTL), B cells and Thl polarization ( Moore KW, de Waal Malefyt R, Coffman RL, & O'Garra A (2001) Annu Rev Immunol 19:683-765) via its activated IL-10 receptors that initiate multiple signaling cascades, including Jakl, Tyk2, and Stat3 pathways in lymphocytes ( Finbloom DS & Winestock KD (1995) J Immunol 155(3): 1079-1090).
• L. acidophilus presents a unique display of S-layer proteins that profoundly alter DC functions (Konstantinov SR, et al. (2008) Proc Natl Acad Sci USA
• the S-layer of L. acidophilus is composed of three S-layer A, B and X genes (Goh YJ, et al. (2009) Appl Environ Microbiol 75(10):3093-3105, Goh YJ & Klaenhammer TR (2009) Front Biosci 14:1362-1386) whereupon the "self assembling" S-layer proteins A or B are the major proteins covering the surface of this bacterium.
• Gene modification in an allochthonous bacterium that does not permanently colonize the gut may offer more therapeutic options when immune responses are regulated (i.e. active IBD) or left unperturbed (i.e. intestinal infections) by administering probiotic microbes. This would facilitate development of therapeutic vehicles that may optimize the regulation of oral immune responses. Accordingly, establishing such a probiotic intervention against autoimmune diseases must be carefully orchestrated from various immunological perspectives to achieve better clinical outcomes.
• inflammation should not be constant as inflammation is a part of regular immunity (Nathan C (2002) Nature 420(6917): 846- 852).
• a bacterium that colonizes the gut may impair immune responses that are required to maintain the intestinal regulatory/co-stimulatory immune balance.
• the inflammation process allows for recognition of the pathogen, and activation of innate and adaptive immune responses that facilitate recovery from infection.
• inflammation orchestrating series of events must be properly phased and regulated to achieve microbe elimination yet prevent unnecessary tissue damage due to presence of various immune cascades and the pathogen.
• Such an inflammatory process can be controlled via specific checkpoints and feedback loops that can provoke escalation, suppression or regulation of the inflammatory response.
• Such positive and negative feedback loops rely on a variety of molecules that mediate inflammatory responses, ultimately playing a regulatory role in its control.
• an active immunity that mobilizes signals toward bacterial clearance requires optimal cellular co-stimulation controlled by regulatory signals (i.e. IL-10) that is partly induced by inflammatory signals.
• targeted preventive or therapeutic strategies will be effective when cellular interactions are understood, in depth, and critical molecules identified that culminate in autoimmunity, inflammation, or anti-inflammatory responses.
• Piroxicam and Sulindac were obtained from Sigma (St. Louis, MO).
• Dextran Sulfate Sodium (DSS) was obtained from MP Biochemicals (Solon, OH).
• NS- 398 was obtained from Cayman Chemical Company (Ann Arbor, MI).
• Monoclonal antibodies for CD4, CD25, FoxP3, CD3, CDl lc, CDl lb, CD40, CD80, CD86, IL-10, and mouse GM-CSF were purchased from Invitrogen (Carlsbad, California) and eBioscience (San Diego, CA).
• L. acidophilus NCK56 and NCK2025 were inoculated at 1% and propagated in de Man, Rogosa, and Sharpe broth (MRS, Difco) at 37°C for 15 h. Subsequently, 1 ml of each culture was transferred to 50 ml of fresh MRS and incubated at 37°C for 18 hrs. The number of colony- forming units (CFU) of L.
• acidophilus strains was determined by measuring the optical density at 600 nm (Greene JD & Klaenhammer TR (1994) Appl Environ Microbiol 60(12):4487-4494). Cells were harvested by centrifugation, washed twice with sterile PBS, resuspended at 5x10 CFU/ml PBS containing 20% glycerol, and subsequently stored at -80 until used to stimulate immature DCs (1 : 1) in vitro.
• mice grown bacteria for 48 hrs were washed twice with sterile PBS, resuspended at 5xl0 9 /ml of PBS, and used for oral inoculation of mice (5x10 cfu/100 ⁇ PBS/mouse).
• mice Six to 8-week-old C57BL/6, and IL-10 "7" (C57BL/6 background) mice were purchased from Jackson Laboratories (Bar Harbor, ME), and Germantown, NY. Mice were maintained in microisolator cages under specific pathogen-free,
• NCK56 was constructed with a deletion of phosphoglycerol transferase (LBA0447) using standard integration and excision methods, tools and strains (Pfeiler EA & Klaenhammer TR (2009) Appl Environ Microbiol 75(18):6013-6016, Russell WM & Klaenhammer TR (2001) Appl Environ Microbiol 67(9):4361-4364).
• a pORI28 deletion vector was constructed containing two targeting fragments, Dell SphI and
• LTA Biochemical Analysis L. acidophilus NCK56 (5xl0 8 /cfu/10 ml) and NCK2025 (5xl0 8 /cfu/10 ml) were propagated from frozen stocks (-80°C) in deMan, Rogosa, and Sharpe broth (MRS, Difco, Lawrence, KS) without ERM at 37°C.
• Cells were treated with Tris-buffered ammonium chloride to lyse erythrocytes. Subsequently, B cells, T cells, IA + cells, and Gr-1 + granulocytes were removed positively by specific antibodies against CD19, CD3, MHC II and Gr-1 (PharMingen, San Diego, CA). The remaining cells were I-A ⁇ , and were cultured in RPMI 1640 complete medium plus 10% fetal bovine serum (FBS) with mouse GM-CSF alone (25 ng/ml) in 6-well plates for 6 days. Every other day cultures were fed with fresh media containing GM-CSF. On day 6, cells were harvested and used for different experiments.
• FBS fetal bovine serum
• NCK56 or NCK2025 was administrated (at 5x 10 8 CFU/100 ⁇ /mouse) to C57BL/6 mice for four consecutive days. A week later, mice were sacrificed to isolate mesenteric LNs of each group of mice. Mesenteric T cells were enriched by negative magnetic bead depletion.
• NCK56 or NCK2025 treated and untreated DCs (10 4 /well of 96-well plate) were cultured at graded doses with isolated mesenteric LN CD4 + T cells (10 5 /well) for 5 days in serum free media. Afterwards, 25 ⁇ of each well of 96-well plate were harvested and frozen for cytokine analysis. Cells were then pulsed for the last 16 h with 0.5 ⁇
• mice For vaccination/prevention studies, groups of C57BL/6 mice (10 mice/group) were inoculated orally with NCK56 or NCK2025 (5x10 cfu/100 ⁇ PBS/mouse) for four consecutive days. These groups of mice and the control mice received one 6-day cycle of 3% DSS in drinking water, followed by 1 day of regular drinking water and then were sacrificed on day 8. Acute colitis was observed after the first cycle of DSS in the non-inoculated group. Disease progression, including weight lost, diarrhea and fecal hemoccult blood positivity (FOB), was monitored throughout the study. Thereafter, mice were sacrificed and colon cross-sectional Swiss rolls were fixed in 10% formaldehyde and embedded in paraffin.
• NCK56 or NCK2025 5x10 cfu/100 ⁇ PBS/mouse
• Colonic Tissue Cultures Colonic tissue cultures were performed as previously described (Sellon RK, et al. (1998) Infect Immun 66(11):5224-5231). Briefly, colonic tissues of each mouse group treated with L. acidophilus strains before or after 3% DSS application were thoroughly cleaned with cold PBS. Tissues were cut into 1-cm pieces and shaken in complete RPMI 1640 containing gentamicin (50 ⁇ g/ml) for 30 minutes at 280 rpm. Colonic tissues were cultured in RPMI 1640 medium supplemented with 5% fetal calf serum (FCS), 50 ⁇ g/ml gentamicin, and 1%
• FCS fetal calf serum
• IL-10 Colitis Groups of C57BL/6 IL-10 "7" (10/group) were transferred from pathogen free housing to conventional housing and allowed to acclimate for 1 week. Mice were then inoculated with NCK56 or NCK2025 (5xl0 8 cfu/100 ⁇ PBS/mouse) for four consecutive days and then fed low dose piroxicam for 1 week, followed by high dose piroxicam for 1 week to accelerate and synchronize the onset of colitis, as previously described (Berg DJ, et al. (2002) Gastroenterology 123(5): 1527-1542).
• mice After 2 weeks on standard chow (day 28), mice were sacrificed, and colon cross- sectional Swiss rolls were fixed in 10% formaldehyde and embedded in paraffin. Tissue sections (4 ⁇ ) were stained with H&E, and blindly scored on a scale from 0 to 4, as described previously (Berg DJ, et al. (2002) Gastroenterology 123(5): 1527-1542).
• L. acidophilus treated- and untreated-DCs (5xl0 5 ) were incubated with surface marker monoclonal antibodies for 30 minutes at 4°C, washed extensively with PBS plus 0.1 % FCS, fixed with 0.1 % paraformaldehyde, and analyzed by a FACSCalibur four-laser cytometry by using standard CELLQUEST acquisition analysis software (Becton Dickinson). At least 10 4 gated events per condition were acquired.
• mice/group were inoculated with NCK56 or NCK2025 (5x10 cfu/100 ⁇ of sterile PBS/mouse) for 4 consecutive days.
• Lymphocytes were enriched using Percol and stained with anti-CD4 FITC, CD25 APC antibodies and 7AAD. Subsequently, stained cells were fixed, permeabilized, stained with anti-FoxP3 PE or isotype antibodies and analyzed by FACSCalibur.
• CAAAGCGTCAAATCTCAGAGGAT; Reverse-ACACCCCAGAAGCATCACATG were selected for regions spanning intron junctions to exclude amplification of genomic DNA.
• Results reflect the fold increase relative to the control sample using the ddCT method using Gapdh as the endogenous control (Forward- GTCGTGGATCTGACGTGCC; Reverse-TGCCTGCTTCACCACCTTC).

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