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 PDFInfo
- 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
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- apparatuses
- systems
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Classifications
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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
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- 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
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- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Engineering & Computer Science (AREA)
- Physics & Mathematics (AREA)
- Chemical & Material Sciences (AREA)
- Molecular Biology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Immunology (AREA)
- Biotechnology (AREA)
- General Health & Medical Sciences (AREA)
- Biophysics (AREA)
- Urology & Nephrology (AREA)
- Analytical Chemistry (AREA)
- Hematology (AREA)
- Biomedical Technology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Organic Chemistry (AREA)
- Theoretical Computer Science (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Biochemistry (AREA)
- Medical Informatics (AREA)
- Evolutionary Biology (AREA)
- Microbiology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Physiology (AREA)
- Zoology (AREA)
- Cell Biology (AREA)
- Medicinal Chemistry (AREA)
- Virology (AREA)
- General Physics & Mathematics (AREA)
- Pathology (AREA)
- Probability & Statistics with Applications (AREA)
- Food Science & Technology (AREA)
- Genetics & Genomics (AREA)
- Wood Science & Technology (AREA)
- Tropical Medicine & Parasitology (AREA)
- General Engineering & Computer Science (AREA)
- Toxicology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Medicines Containing Material From Animals Or Micro-Organisms (AREA)
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
ID=62710026
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 (17)
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 |
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 |
AU2016282996A1 (en) | 2015-06-25 | 2018-01-18 | 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 |
NZ743958A (en) | 2016-01-07 | 2023-07-28 | Native Microbials Inc | Methods for improving milk production by administration of microbial consortia |
CA3048246A1 (en) | 2016-12-28 | 2018-07-05 | Ascus Biosciences, 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 |
EP3562955A4 (en) | 2016-12-28 | 2020-08-12 | Ascus Biosciences, Inc. | Methods, apparatuses, and systems for microorganism strain analysis of complex heterogeneous communities with tracer analytics, determination of functional relationships and interactions thereof, and synthesis of microbial ensembles including dosed microbial ensembles and inoculative microbial ensembles |
CN110913702A (en) | 2017-04-28 | 2020-03-24 | 埃斯库斯生物科技股份公司 | Method for supporting a cereal fortifier and/or energy fortifier diet in ruminants using an artificial pool of microorganisms |
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 |
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 |
KR102304399B1 (en) * | 2021-03-26 | 2021-09-24 | 주식회사 에이치이엠파마 | Method and diagnostic apparatus for determining hyperglycemia 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 |
KR20220158948A (en) * | 2021-05-25 | 2022-12-02 | 주식회사 에이치이엠파마 | Method and diagnostic apparatus for determining gasbloating using machine learning model |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
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 |
Family Cites Families (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
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 |
-
2017
- 2017-12-28 JP JP2019535790A patent/JP2020507308A/en active Pending
- 2017-12-28 CA CA3048247A patent/CA3048247A1/en not_active Abandoned
- 2017-12-28 AU AU2017388532A patent/AU2017388532A1/en not_active Abandoned
- 2017-12-28 WO PCT/US2017/068753 patent/WO2018126033A1/en unknown
- 2017-12-28 CN CN201780087481.6A patent/CN110392738A/en active Pending
- 2017-12-28 EP EP17887981.3A patent/EP3562956A4/en not_active Withdrawn
- 2017-12-28 MX MX2019007764A patent/MX2019007764A/en unknown
-
2019
- 2019-06-25 IL IL267646A patent/IL267646A/en unknown
Patent Citations (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
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)
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 |
---|---|
WO2018126033A1 (en) | 2018-07-05 |
IL267646A (en) | 2019-08-29 |
AU2017388532A1 (en) | 2019-07-25 |
CN110392738A (en) | 2019-10-29 |
EP3562956A1 (en) | 2019-11-06 |
JP2020507308A (en) | 2020-03-12 |
CA3048247A1 (en) | 2018-07-05 |
MX2019007764A (en) | 2019-10-15 |
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Ipc: A23K 50/10 20160101ALI20200904BHEP Ipc: A23K 50/75 20160101ALI20200904BHEP Ipc: A23K 10/18 20160101ALI20200904BHEP Ipc: G16B 5/00 20190101ALI20200904BHEP Ipc: C12Q 1/06 20060101AFI20200904BHEP |
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