Species- and site-specific genome editing in complex bacterial communities.

Archaea / genetics Bacteria / classification CRISPR-Cas Systems Gastrointestinal Microbiome / genetics Gene Editing / methods Genome, Bacterial Humans Infant Microbial Consortia / genetics RNA, Guide, Kinetoplastida Soil Microbiology

Journal

Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869

Informations de publication

Date de publication:
01 2022
Historique:
received: 08 10 2021
accepted: 29 10 2021
pubmed: 8 12 2021
medline: 23 2 2022
entrez: 7 12 2021
Statut: ppublish

Résumé

Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.

Identifiants

DOI: 10.1038/s41564-021-01014-7 PMID: 34873292 PMC: PMC9261505
pubmed: 34873292
doi: 10.1038/s41564-021-01014-7
pii: 10.1038/s41564-021-01014-7
pmc: PMC9261505
mid: NIHMS1812607
doi:

Substances chimiques

RNA, Guide 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

34-47

Subventions

Organisme : NIGMS NIH HHS
ID : F32 GM131654
Pays : United States
Organisme : NIGMS NIH HHS
ID : F32 GM134694
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI092531
Pays : United States

Commentaires et corrections

Type : CommentIn
Type : CommentIn
Type : CommentIn

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

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Auteurs

Benjamin E Rubin (BE)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
ORCID: 0000-0001-8684-2417

Spencer Diamond (S)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
ORCID: 0000-0003-4131-341X

Brady F Cress (BF)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
ORCID: 0000-0002-2948-2846

Alexander Crits-Christoph (A)

Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.

Yue Clare Lou (YC)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.

Adair L Borges (AL)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
ORCID: 0000-0002-1477-7908

Haridha Shivram (H)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.

Christine He (C)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
ORCID: 0000-0002-7119-5509

Michael Xu (M)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
ORCID: 0000-0002-1801-2611

Zeyi Zhou (Z)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
ORCID: 0000-0002-7548-9512

Sara J Smith (SJ)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.

Rachel Rovinsky (R)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.

Dylan C J Smock (DCJ)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.

Kimberly Tang (K)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
ORCID: 0000-0002-7718-2872

Trenton K Owens (TK)

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Netravathi Krishnappa (N)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.

Rohan Sachdeva (R)

Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
ORCID: 0000-0001-9284-2245

Rodolphe Barrangou (R)

Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
ORCID: 0000-0002-0648-3504

Adam M Deutschbauer (AM)

Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
ORCID: 0000-0003-2728-7622

Jillian F Banfield (JF)

Innovative Genomics Institute, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
Environmental Science, Policy and Management, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia. jbanfield@berkeley.edu.
ORCID: 0000-0001-8203-8771

Jennifer A Doudna (JA)

Innovative Genomics Institute, University of California, Berkeley, CA, USA. doudna@berkeley.edu.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. doudna@berkeley.edu.
California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA. doudna@berkeley.edu.
Department of Chemistry, University of California, Berkeley, CA, USA. doudna@berkeley.edu.
Howard Hughes Medical Institute, University of California, Berkeley, CA, USA. doudna@berkeley.edu.
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. doudna@berkeley.edu.
Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. doudna@berkeley.edu.
ORCID: 0000-0001-9161-999X

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Classifications MeSH

questionsmedicales.fr › Archéobactéries › Species- and site-specific genome editing in...
questionsmedicales.fr › Bactéries › Species- and site-specific genome editing in...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Species- and site-specific genome editing in...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Biote › Microbiote › Microbiome gastro-intestinal › Species- and site-specific genome editing in...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Génie génétique › Édition de gène › Species- and site-specific genome editing in...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Species- and site-specific genome editing in...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Species- and site-specific genome editing in...
questionsmedicales.fr › Personnes › Tranches d'âge › Nourrisson › Species- and site-specific genome editing in...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Biote › Microbiote › Consortiums microbiens › Species- and site-specific genome editing in...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › ARN guide › Species- and site-specific genome editing in...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Microbiologie de l'environnement › Microbiologie du sol › Species- and site-specific genome editing in...