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Species- and site-specific genome editing in complex bacterial communities.
Rubin, Benjamin E; Diamond, Spencer; Cress, Brady F; Crits-Christoph, Alexander; Lou, Yue Clare; Borges, Adair L; Shivram, Haridha; He, Christine; Xu, Michael; Zhou, Zeyi; Smith, Sara J; Rovinsky, Rachel; Smock, Dylan C J; Tang, Kimberly; Owens, Trenton K; Krishnappa, Netravathi; Sachdeva, Rohan; Barrangou, Rodolphe; Deutschbauer, Adam M; Banfield, Jillian F; Doudna, Jennifer A.
Afiliação
  • Rubin BE; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Diamond S; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
  • Cress BF; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Crits-Christoph A; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
  • Lou YC; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Borges AL; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
  • Shivram H; Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
  • He C; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Xu M; Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
  • Zhou Z; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Smith SJ; Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
  • Rovinsky R; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Smock DCJ; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
  • Tang K; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Owens TK; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
  • Krishnappa N; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
  • Sachdeva R; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Barrangou R; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
  • Deutschbauer AM; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
  • Banfield JF; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
  • Doudna JA; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Nat Microbiol ; 7(1): 34-47, 2022 01.
Article em En | MEDLINE | ID: mdl-34873292
ABSTRACT
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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Microbiologia do Solo / Genoma Bacteriano / Consórcios Microbianos / Microbioma Gastrointestinal / Edição de Genes Limite: Humans / Infant Idioma: En Revista: Nat Microbiol Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Microbiologia do Solo / Genoma Bacteriano / Consórcios Microbianos / Microbioma Gastrointestinal / Edição de Genes Limite: Humans / Infant Idioma: En Revista: Nat Microbiol Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Estados Unidos