EP3519096A4 - High resolution systems, kits, apparatus, and methods for bacterial community relationship determination and other high throughput microbiology applications - Google Patents

High resolution systems, kits, apparatus, and methods for bacterial community relationship determination and other high throughput microbiology applications Download PDF

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Publication number
EP3519096A4
EP3519096A4 EP17857449.7A EP17857449A EP3519096A4 EP 3519096 A4 EP3519096 A4 EP 3519096A4 EP 17857449 A EP17857449 A EP 17857449A EP 3519096 A4 EP3519096 A4 EP 3519096A4
Authority
EP
European Patent Office
Prior art keywords
kits
methods
relationship determination
bacterial community
high resolution
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Withdrawn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
EP17857449.7A
Other languages
German (de)
French (fr)
Other versions
EP3519096A1 (en
Inventor
Peter CHRISTEY
Alexander Hallock
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.)
Isolation Bio Inc
Original Assignee
General Automation Lab Technologies 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 General Automation Lab Technologies Inc filed Critical General Automation Lab Technologies Inc
Publication of EP3519096A1 publication Critical patent/EP3519096A1/en
Publication of EP3519096A4 publication Critical patent/EP3519096A4/en
Withdrawn legal-status Critical Current

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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
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/02—Burettes; Pipettes
    • B01L3/0241—Drop counters; Drop formers
    • B01L3/0244—Drop counters; Drop formers using pins
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
    • B01L3/5085—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/54—Labware with identification means
    • B01L3/545—Labware with identification means for laboratory containers
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6869—Methods for sequencing
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00313—Reactor vessels in a multiple arrangement the reactor vessels being formed by arrays of wells in blocks
    • B01J2219/00315—Microtiter plates
    • B01J2219/00317—Microwell devices, i.e. having large numbers of wells
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/0074—Biological products
    • B01J2219/00743—Cells
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/02—Adapting objects or devices to another
    • B01L2200/025—Align devices or objects to ensure defined positions relative to each other
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/06—Fluid handling related problems
    • B01L2200/0689—Sealing
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/12—Specific details about manufacturing devices
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/14—Process control and prevention of errors
    • B01L2200/141—Preventing contamination, tampering
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/02—Identification, exchange or storage of information
    • B01L2300/021—Identification, e.g. bar codes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/06—Auxiliary integrated devices, integrated components
    • B01L2300/0627—Sensor or part of a sensor is integrated
    • B01L2300/0636—Integrated biosensor, microarrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/06—Auxiliary integrated devices, integrated components
    • B01L2300/0681—Filter
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0809—Geometry, shape and general structure rectangular shaped
    • B01L2300/0829—Multi-well plates; Microtitration plates
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0893—Geometry, shape and general structure having a very large number of wells, microfabricated wells
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/16—Surface properties and coatings
    • B01L2300/161—Control and use of surface tension forces, e.g. hydrophobic, hydrophilic
    • B01L2300/165—Specific details about hydrophobic, oleophobic surfaces
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L7/00—Heating or cooling apparatus; Heat insulating devices
    • B01L7/52—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B20/00—Methods specially adapted for identifying library members
    • C40B20/02—Identifying library members by their fixed physical location on a support or substrate

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • General Health & Medical Sciences (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Clinical Laboratory Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hematology (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP17857449.7A 2016-09-28 2017-09-28 High resolution systems, kits, apparatus, and methods for bacterial community relationship determination and other high throughput microbiology applications Withdrawn EP3519096A4 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201662400841P 2016-09-28 2016-09-28
PCT/US2017/054108 WO2018064385A1 (en) 2016-09-28 2017-09-28 High resolution systems, kits, apparatus, and methods for bacterial community relationship determination and other high throughput microbiology applications

Publications (2)

Publication Number Publication Date
EP3519096A1 EP3519096A1 (en) 2019-08-07
EP3519096A4 true EP3519096A4 (en) 2020-06-17

Family

ID=61760120

Family Applications (1)

Application Number Title Priority Date Filing Date
EP17857449.7A Withdrawn EP3519096A4 (en) 2016-09-28 2017-09-28 High resolution systems, kits, apparatus, and methods for bacterial community relationship determination and other high throughput microbiology applications

Country Status (7)

Country Link
EP (1) EP3519096A4 (en)
JP (1) JP2019531730A (en)
CN (1) CN109843435A (en)
AU (1) AU2017335897A1 (en)
CA (1) CA3037631A1 (en)
IL (1) IL265540A (en)
WO (1) WO2018064385A1 (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111483096B (en) * 2019-12-10 2022-04-08 中国科学院亚热带农业生态研究所 Rhizosphere channel micro-fluidic chip, colloidal block thereof and mold for manufacturing colloidal block
WO2021241721A1 (en) * 2020-05-29 2021-12-02 国立研究開発法人理化学研究所 Method for treating cell population and method for analyzing genes included in cell population
EP3939699A1 (en) * 2020-07-17 2022-01-19 Biomillenia SAS Growth modulation
WO2024135694A1 (en) * 2022-12-23 2024-06-27 ペプチドリーム株式会社 Dna amplification method using pcr

Citations (4)

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Publication number Priority date Publication date Assignee Title
WO2005010169A2 (en) * 2003-07-23 2005-02-03 Diversa Corporation High throughput or capillary-based screening for a bioactivity or biomolecule
EP2805769A1 (en) * 2013-05-24 2014-11-26 European Molecular Biology Laboratory Methods for nano-scale single cell analysis
US20160010085A1 (en) * 2013-03-07 2016-01-14 Snu R&Db Foundation Heterologous dna barcoding method
WO2016138496A1 (en) * 2015-02-27 2016-09-01 Cellular Research, Inc. Spatially addressable molecular barcoding

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WO1998045406A1 (en) * 1997-04-09 1998-10-15 Minnesota Mining And Manufacturing Company Method and devices for partitioning biological sample liquids into microvolumes
WO2003044484A2 (en) * 2001-11-16 2003-05-30 Sloan-Kettering Institute For Cancer Research High-density cell microarrays for parallel functional determinations
CN1313622C (en) * 2002-08-02 2007-05-02 赵翀 High-flux cell biological chip testing technology and reagent case
CN1444043A (en) * 2002-12-25 2003-09-24 帕弗瑞生物技术(北京)有限公司 Individuation specific immunocytofunction determination method
JPWO2005090549A1 (en) * 2004-03-19 2008-02-07 ジェノミディア株式会社 Microwell for cell culture
CN1920559A (en) * 2005-08-24 2007-02-28 赵翀 Cellular biological technique, reagent kits and preparation device
PL2007910T3 (en) * 2006-03-31 2017-04-28 Mobidiag Oy Method and microarray for detecting herpesviruses
EP4357493A3 (en) * 2013-06-27 2024-07-24 10X Genomics, Inc. Compositions and methods for sample processing
US10633714B2 (en) * 2013-07-21 2020-04-28 Pendulum Therapeutics, Inc. Methods and systems for microbiome characterization, monitoring and treatment
ES2711168T3 (en) * 2013-08-28 2019-04-30 Becton Dickinson Co Massive parallel analysis of individual cells
WO2015112352A2 (en) * 2014-01-25 2015-07-30 uBiome, Inc. Method and system for microbiome analysis
US20190102512A1 (en) * 2014-11-17 2019-04-04 Yeda Research And Development Co., Ltd. Method of analyzing microbiome
CA3184363C (en) * 2015-04-21 2024-01-02 Isolation Bio Inc. High resolution systems, kits, apparatus, and methods for high throughput microbiology applications

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2005010169A2 (en) * 2003-07-23 2005-02-03 Diversa Corporation High throughput or capillary-based screening for a bioactivity or biomolecule
US20160010085A1 (en) * 2013-03-07 2016-01-14 Snu R&Db Foundation Heterologous dna barcoding method
EP2805769A1 (en) * 2013-05-24 2014-11-26 European Molecular Biology Laboratory Methods for nano-scale single cell analysis
WO2016138496A1 (en) * 2015-02-27 2016-09-01 Cellular Research, Inc. Spatially addressable molecular barcoding

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
J.DAISY VANITHA ET AL: "Evaluation of microplate Alamar blue assay for drug susceptibility testing of Mycobacterium avium complex isolates", DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE, vol. 49, no. 3, 1 July 2004 (2004-07-01), AMSTERDAM, NL, pages 179 - 182, XP055288738, ISSN: 0732-8893, DOI: 10.1016/j.diagmicrobio.2004.04.003 *
LIANG MA ET AL: "Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, vol. 111, no. 27, 25 June 2014 (2014-06-25), US, pages 9768 - 9773, XP055362053, ISSN: 0027-8424, DOI: 10.1073/pnas.1404753111 *
See also references of WO2018064385A1 *

Also Published As

Publication number Publication date
JP2019531730A (en) 2019-11-07
EP3519096A1 (en) 2019-08-07
CA3037631A1 (en) 2018-04-05
CN109843435A (en) 2019-06-04
WO2018064385A1 (en) 2018-04-05
IL265540A (en) 2019-05-30
AU2017335897A1 (en) 2019-04-04

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