EP3562956A4 - METHODS, APPARATUS AND SYSTEMS FOR ANALYZING STRAINS OF MICRO-ORGANISMS IN COMPLEX HETEROGENEOUS COMMUNITIES, DETERMINING THEIR INTERACTIONS AND FUNCTIONAL RELATIONSHIPS, AND MANAGEMENT OF DIAGNOSTICS AND BIOLOGICAL STATES BASED ON THEM - Google Patents

METHODS, APPARATUS AND SYSTEMS FOR ANALYZING STRAINS OF MICRO-ORGANISMS IN COMPLEX HETEROGENEOUS COMMUNITIES, DETERMINING THEIR INTERACTIONS AND FUNCTIONAL RELATIONSHIPS, AND MANAGEMENT OF DIAGNOSTICS AND BIOLOGICAL STATES BASED ON THEM 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Withdrawn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)
English (en)
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Withdrawn legal-status Critical Current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

Landscapes

  • 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)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
EP17887981.3A 2016-12-28 2017-12-28 METHODS, APPARATUS AND SYSTEMS FOR ANALYZING STRAINS OF MICRO-ORGANISMS IN COMPLEX HETEROGENEOUS COMMUNITIES, DETERMINING THEIR INTERACTIONS AND FUNCTIONAL RELATIONSHIPS, AND MANAGEMENT OF DIAGNOSTICS AND BIOLOGICAL STATES BASED ON THEM 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

ID=62710026

Family Applications (1)

Application Number Title Priority Date Filing Date
EP17887981.3A Withdrawn EP3562956A4 (en) 2016-12-28 2017-12-28 METHODS, APPARATUS AND SYSTEMS FOR ANALYZING STRAINS OF MICRO-ORGANISMS IN COMPLEX HETEROGENEOUS COMMUNITIES, DETERMINING THEIR INTERACTIONS AND FUNCTIONAL RELATIONSHIPS, AND MANAGEMENT OF DIAGNOSTICS AND BIOLOGICAL STATES BASED ON THEM

Country Status (8)

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

Families Citing this family (17)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
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
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
NZ743958A (en) 2016-01-07 2023-07-28 Native Microbials Inc Methods for improving milk production by administration of microbial consortia
AU2017388535A1 (en) 2016-12-28 2019-07-25 Native Microbials, 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
JP2020504620A (ja) 2016-12-28 2020-02-13 アスカス バイオサイエンシーズ， インコーポレイテッド 複雑な不均一コミュニティの完全微生物株の解析、その機能的関連性及び相互作用の決定、ならびにそれに基づく生物反応性の改変剤の同定及び合成、のための方法、装置、及びシステム
EP3614847A4 (en) 2017-04-28 2021-09-01 Native Microbials, Inc. PROCESSES PROMOTING ENERGY AND / OR CEREAL RICH DIETS BY MEANS OF A SYNTHETIC BIO-SET OF MICROBES
IL264581A (he) * 2019-01-31 2020-08-31 Segal Eran צפי של מטבולטים בדם
EP4172851A1 (en) * 2020-06-24 2023-05-03 Université de Lausanne Means and methods for classifying microbes
KR102241357B1 (ko) * 2020-10-20 2021-04-16 주식회사 에이치이엠 머신러닝 모델을 이용하여 대장용종을 진단하는 방법 및 장치
CN112662795B (zh) * 2021-01-26 2023-12-15 苏州系统医学研究所 用于感染性病原体检测的阳性对照品及其制备方法与应用
CN112951333A (zh) * 2021-01-27 2021-06-11 天津大学 以f2噬菌体为模式病毒预测冠状病毒消抗模型评价方法
CN113096737B (zh) * 2021-03-26 2023-10-31 北京源生康泰基因科技有限公司 一种用于对病原体类型进行自动分析的方法及系统
KR102304402B1 (ko) * 2021-03-26 2021-09-24 주식회사 에이치이엠파마 머신러닝 모델을 이용하여 비만 여부를 판별하는 방법 및 진단 장치
KR102304399B1 (ko) * 2021-03-26 2021-09-24 주식회사 에이치이엠파마 머신러닝 모델을 이용하여 고혈당을 판별하는 방법 및 진단 장치
KR20220158950A (ko) * 2021-05-25 2022-12-02 주식회사 에이치이엠파마 머신러닝 모델을 이용하여 소화기 장애 유무를 판별하는 방법 및 진단 장치
KR20220158948A (ko) * 2021-05-25 2022-12-02 주식회사 에이치이엠파마 머신러닝 모델을 이용하여 복부팽만 유무를 판별하는 방법 및 진단 장치

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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 (zh) * 2015-04-15 2015-08-05 江苏师范大学 一种提高奶牛产奶量的微生态制剂
UY36754A (es) * 2015-06-25 2016-11-30 Ascus Biosciences Inc Métodos, aparatos y sistemas para analizar cepas de microorganismos de comunidades heterogéneas complejas, predecir e identificar relaciones e interacciones funcionales de estas, y seleccionar y sintetizar conjuntos microbianos basados en estas

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CA2908112C (en) * 2008-12-02 2019-07-02 Dupont Nutrition Biosciences Aps Enterococcus faecium strains and methods for improving ruminant health and performance
CN104171413B (zh) * 2014-08-01 2016-04-13 农业部沼气科学研究所 一种含厌氧菌K.paraultunense KD-1发酵液和羽毛粉的肉型家禽饲料

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CN104814278A (zh) * 2015-04-15 2015-08-05 江苏师范大学 一种提高奶牛产奶量的微生态制剂
UY36754A (es) * 2015-06-25 2016-11-30 Ascus Biosciences Inc Métodos, aparatos y sistemas para analizar cepas de microorganismos de comunidades heterogéneas complejas, predecir e identificar relaciones e interacciones funcionales de estas, y seleccionar y sintetizar conjuntos microbianos basados en estas
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

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See also references of WO2018126033A1 *

Also Published As

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

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