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• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
  • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
  • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
  • G16H20/60—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to nutrition control, e.g. diets
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
  • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
  • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
  • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
  • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/158—Expression markers

Definitions

• the disclosed methods interrogate the oral microbiome to detect microbe compositional abundance trends that may be associated with renal and/or urinary diseases in cats. Detecting, identifying and/or quantifying microbial compositional abundance trends enables a practitioner to screen for and/or indicate whether a cat has a particular renal and/or urinary disease state. Detecting and identifying renal and/or urinary disease states enables the practitioner and/or the cat’s owner to treat and/or prevent the renal/urinary disease state. [09] In some embodiments, a method is disclosed for detecting and/or indicating renal/urinary diseases in cats.
• the method may further include treating the specific renal/urinary disease and/or administering a therapeutic treatment.
• the therapeutic treatment may include administering a therapeutic compound, such as a compound designed to inhibit or encourage growth of a specific one or more microbes present in the oral microbiome of the mammal.
• the therapeutic compound includes a pre-biotic, a post-biotic, a pro-biotic, a medicament or a combination thereof.
• the therapeutic compound includes a phosphate binder, an antibiotic, a compound to control hypertension and/or blood pressure of the cat, and erythropoietin, among other therapeutic compounds.
• the therapeutic treatment may include brushing the mammal’s teeth with a topical treatment.
• each sample was scored by comparing the predictive pairwise log-ratios (pPLRs) of the sample to the mean pPLRs of controls, taking into account the direction and magnitude of the difference.
• Figures 2A-2E illustrate a distribution of the average log ratio difference scores between pairwise microbial interactions associated with CKD, struvite urinary crystals or stones, urinary calcium oxalate crystals or stones, cystine urinary crystals or stones and idiopathic cystitis and healthy cohorts.
• metagenomic DNA may be extracted by SPRI magnetic beads-based DNA extraction (MCLAB, MBC-200) using 80% ethanol for purification.
• the DNA may be quantified using a GloMax Plate Reader (Promega).
• the oral samples may be prepared for NGS using the LOTUS DNA library prep kit (IDT), the Next Ultra II FS DNA library prep kit (NEB), or another ligation or tagmentation based DNA library prep kit, following the manufacturer’s instructions.
• the oral samples may be dual-barcoded with iTRU indices.
• the prepared sequencing libraries may be quantified using a GloMax Plate Reader (Promega) and equal-mass pooled into 96-sample pools.
• a method for indicating renal/urinary disease in cats includes receiving an oral swab sample taken from a cat; performing heat treatment on the oral sample; and performing magnetic beads-based deoxyribonucleic acid (DNA) extraction on the heat- treated oral sample to extract microbial DNA that is present in the oral swab sample.
• DNA deoxyribonucleic acid
• the method may further include comparing the oral microbial profile for the cat against a database of defined microbial profiles, wherein the database identifies correlations between (i) profiles that include one or more microbes and (ii) corresponding renal/urinary diseases; based on a result of comparing the oral microbial profile against the database of defined microbial profiles, generating a risk score indicating a likelihood that the cat has a specific renal/urinary disease; and in response to generating the risk score and identifying the specific renal/urinary disease, administering a therapeutic treatment designed to treat the specific renal/urinary disease.
• the therapeutic compound includes a phosphate binder, an antibiotic, a compound to control hypertension and/or blood pressure of the cat, and erythropoietin, among other therapeutic compounds.
• the therapeutic treatment may include a dietary regimen designed to address and/or alleviate the renal/urinary disease state.
• therapeutic diets that are restricted in protein, phosphorus and sodium content, and high in water-soluble vitamins, fiber, and antioxidant concentrations, may prolong life and improve quality of life in cats with CKD.
• the dietary regimen may include switching to a wet food to help maintain proper hydration of the cat.
• the therapeutic treatment may include potassium supplementation.
• Figures 9A-9B plot the probability that samples belonging to the IBD or DM cohorts and the control samples would be classified as belonging to their respective cohorts based on each sample’s compositional abundance of predictive microbes.
• microbes identified as associated with or predictive for a condition may be further predictive for stages or grades of the condition.
• a subset of the predictive microbes for CKD can be indicative of stage 2 CKD.
• Early detection of the stage of a disease enables broader treatment options.
• use of a subset of predictive microbes for earlier detection of the stage of the disease benefits cats and owners by driving unhealthy cats to the clinic before the disease progresses beyond treatment. It also benefits veterinarians by enabling them to beher select a treatment option based on the stage or grade of the condition.
• the terms “disease” and “condition” may be used interchangeably or may be different in that the particular malady or condition may not have a known causative agent (so that etiology has not yet been worked out) and it is therefore not yet recognized as a disease but only as an undesirable condition or syndrome, wherein a more or less specific set of symptoms have been identified by clinicians.
• Table 5 [0115] Table 6. Predictive microbes alongside their taxonomic classification for idiopathic cystitis (IC). Of the 94 total predictive microbes for IC (see Table 1), approximately 8.51% are gram-positive bacteria. Note that 'candidatus' stands for well -characterized, but yet uncultured bacteria.

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• Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
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• 2022
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