EP3562956A4 - Methods, apparatuses, and systems for analyzing microorganism strains in complex heterogeneous communities, determining functional relationships and interactions thereof, and diagnostics and biostate management based thereon - Google Patents

Methods, apparatuses, and systems for analyzing microorganism strains in complex heterogeneous communities, determining functional relationships and interactions thereof, and diagnostics and biostate management based thereon Download PDF

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Publication number
EP3562956A4
EP3562956A4 EP17887981.3A EP17887981A EP3562956A4 EP 3562956 A4 EP3562956 A4 EP 3562956A4 EP 17887981 A EP17887981 A EP 17887981A EP 3562956 A4 EP3562956 A4 EP 3562956A4
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EP
European Patent Office
Prior art keywords
biostate
diagnostics
interactions
apparatuses
systems
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP17887981.3A
Other languages
German (de)
French (fr)
Other versions
EP3562956A1 (en
Inventor
Mallory EMBREE
Cameron Joseph MARTINO
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Native Microbials Inc
Original Assignee
Ascus Biosciences Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Ascus Biosciences Inc filed Critical Ascus Biosciences Inc
Publication of EP3562956A1 publication Critical patent/EP3562956A1/en
Publication of EP3562956A4 publication Critical patent/EP3562956A4/en
Withdrawn legal-status Critical Current

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56911—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
    • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
    • C12Q1/04—Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor
    • C12Q1/06—Quantitative determination
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/20—Probabilistic models
    • 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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B10/00—ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
EP17887981.3A 2016-12-28 2017-12-28 Methods, apparatuses, and systems for analyzing microorganism strains in complex heterogeneous communities, determining functional relationships and interactions thereof, and diagnostics and biostate management based thereon Withdrawn EP3562956A4 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662439804P 2016-12-28 2016-12-28
US201762560174P 2017-09-18 2017-09-18
PCT/US2017/068753 WO2018126033A1 (en) 2016-12-28 2017-12-28 Methods, apparatuses, and systems for analyzing microorganism strains in complex heterogeneous communities, determining functional relationships and interactions thereof, and diagnostics and biostate management based thereon

Publications (2)

Publication Number Publication Date
EP3562956A1 EP3562956A1 (en) 2019-11-06
EP3562956A4 true EP3562956A4 (en) 2020-10-14

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
EP17887981.3A Withdrawn EP3562956A4 (en) 2016-12-28 2017-12-28 Methods, apparatuses, and systems for analyzing microorganism strains in complex heterogeneous communities, determining functional relationships and interactions thereof, and diagnostics and biostate management based thereon

Country Status (8)

Country Link
EP (1) EP3562956A4 (en)
JP (1) JP2020507308A (en)
CN (1) CN110392738A (en)
AU (1) AU2017388532A1 (en)
CA (1) CA3048247A1 (en)
IL (1) IL267646A (en)
MX (1) MX2019007764A (en)
WO (1) WO2018126033A1 (en)

Families Citing this family (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10851399B2 (en) 2015-06-25 2020-12-01 Native Microbials, Inc. Methods, apparatuses, and systems for microorganism strain analysis of complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and selecting and synthesizing microbial ensembles based thereon
EP3314007B1 (en) 2015-06-25 2024-01-24 Native Microbials, Inc. Methods, apparatuses, and systems for analyzing microorganism strains from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and selecting and synthesizing microbial ensembles based thereon
US9938558B2 (en) 2015-06-25 2018-04-10 Ascus Biosciences, Inc. Methods, apparatuses, and systems for analyzing microorganism strains from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and selecting and synthesizing microbial ensembles based thereon
CA3010505A1 (en) 2016-01-07 2017-07-13 Ascus Biosciences, Inc. Methods for improving milk production by administration of microbial consortia
AU2017386658A1 (en) 2016-12-28 2019-07-25 Native Microbials, Inc. Methods, apparatuses, and systems for analyzing complete microorganism strains in complex heterogeneous communities, determining functional relationships and interactions thereof, and identifying and synthesizing bioreactive modificators based thereon
EP3614847A4 (en) 2017-04-28 2021-09-01 Native Microbials, Inc. Methods for supporting grain intensive and/or energy intensive diets in ruminants with a synthetic bioensemble of microbes
IL264581A (en) * 2019-01-31 2020-08-31 Segal Eran Predicting blood metabolites
EP4172851A1 (en) * 2020-06-24 2023-05-03 Université de Lausanne Means and methods for classifying microbes
KR102241357B1 (en) * 2020-10-20 2021-04-16 주식회사 에이치이엠 Method and apparatus for diagnosing colon plyp using machine learning model
CN112662795B (en) * 2021-01-26 2023-12-15 苏州系统医学研究所 Positive reference substance for detecting infectious pathogens and preparation method and application thereof
CN112951333A (en) * 2021-01-27 2021-06-11 天津大学 Evaluation method for model for predicting coronavirus resistance elimination by taking f2 phage as model virus
KR102304399B1 (en) * 2021-03-26 2021-09-24 주식회사 에이치이엠파마 Method and diagnostic apparatus for determining hyperglycemia using machine learning model
CN113096737B (en) * 2021-03-26 2023-10-31 北京源生康泰基因科技有限公司 Method and system for automatically analyzing pathogen type
KR102304402B1 (en) * 2021-03-26 2021-09-24 주식회사 에이치이엠파마 Method and diagnostic apparatus for determining obesity using machine learning model
KR20220158948A (en) * 2021-05-25 2022-12-02 주식회사 에이치이엠파마 Method and diagnostic apparatus for determining gasbloating using machine learning model
KR20220158950A (en) * 2021-05-25 2022-12-02 주식회사 에이치이엠파마 Method and diagnostic apparatus for determining gastro-intestinal tract disorder using machine learning model

Citations (3)

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US20130121968A1 (en) * 2011-10-03 2013-05-16 Atossa Genetics, Inc. Methods of combining metagenome and the metatranscriptome in multiplex profiles
CN104814278A (en) * 2015-04-15 2015-08-05 江苏师范大学 A micro-ecological preparation for improving milk yields of dairy cows
UY36754A (en) * 2015-06-25 2016-11-30 Ascus Biosciences Inc METHODS, APPLIANCES AND SYSTEMS FOR ANALYZING COMPACT HETEROGENIC MICROORGANISM VINTAGES, PREACHING AND IDENTIFYING FUNCTIONAL RELATIONS AND INTERACTIONS OF THESE, AND SELECTING AND SYNTHEIZING MICROBIAL SETS BASED ON THESE

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CA2745643C (en) * 2008-12-02 2015-12-01 Danisco A/S A bacillus pumilus strain and methods for improving ruminant health and performance
CN104171413B (en) * 2014-08-01 2016-04-13 农业部沼气科学研究所 A kind of meat type poultry feed containing anaerobic bacteria K.paraultunense KD-1 zymotic fluid and feather meal

Patent Citations (4)

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US20130121968A1 (en) * 2011-10-03 2013-05-16 Atossa Genetics, Inc. Methods of combining metagenome and the metatranscriptome in multiplex profiles
CN104814278A (en) * 2015-04-15 2015-08-05 江苏师范大学 A micro-ecological preparation for improving milk yields of dairy cows
UY36754A (en) * 2015-06-25 2016-11-30 Ascus Biosciences Inc METHODS, APPLIANCES AND SYSTEMS FOR ANALYZING COMPACT HETEROGENIC MICROORGANISM VINTAGES, PREACHING AND IDENTIFYING FUNCTIONAL RELATIONS AND INTERACTIONS OF THESE, AND SELECTING AND SYNTHEIZING MICROBIAL SETS BASED ON THESE
WO2016210251A1 (en) * 2015-06-25 2016-12-29 Ascus Biosciences, Inc. Methods, apparatuses, and systems for analyzing microorganism strains from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and selecting and synthesizing microbial ensembles based thereon

Non-Patent Citations (6)

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Title
ANDREAS BREMGES ET AL: "Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant", GIGASCIENCE, vol. 4, no. 1, 30 July 2015 (2015-07-30), XP055458912, DOI: 10.1186/s13742-015-0073-6 *
BOYANG JI ET AL: "From next-generation sequencing to systematic modeling of the gut microbiome", FRONTIERS IN GENETICS, vol. 6, 23 June 2015 (2015-06-23), XP055727043, DOI: 10.3389/fgene.2015.00219 *
CORINNE FERRIER MAURICE ET AL: "Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome", CELL, vol. 152, no. 1-2, 1 January 2013 (2013-01-01), pages 39 - 50, XP055458905, ISSN: 0092-8674, DOI: 10.1016/j.cell.2012.10.052 *
KELSEA A. JEWELL ET AL: "Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 81, no. 14, 1 May 2015 (2015-05-01), US, pages 4697 - 4710, XP055396829, ISSN: 0099-2240, DOI: 10.1128/AEM.00720-15 *
PAVEL PETRENKO ET AL: "MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes", BMC BIOLOGY, vol. 13, no. 1, 5 November 2015 (2015-11-05), XP055458828, DOI: 10.1186/s12915-015-0195-4 *
See also references of WO2018126033A1 *

Also Published As

Publication number Publication date
AU2017388532A1 (en) 2019-07-25
MX2019007764A (en) 2019-10-15
CN110392738A (en) 2019-10-29
JP2020507308A (en) 2020-03-12
EP3562956A1 (en) 2019-11-06
WO2018126033A1 (en) 2018-07-05
CA3048247A1 (en) 2018-07-05
IL267646A (en) 2019-08-29

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