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

被引：0
作者：
Benjamin E. Rubin
Spencer Diamond
Brady F. Cress
Alexander Crits-Christoph
Yue Clare Lou
Adair L. Borges
Haridha Shivram
Christine He
Michael Xu
Zeyi Zhou
Sara J. Smith
Rachel Rovinsky
Dylan C. J. Smock
Kimberly Tang
Trenton K. Owens
Netravathi Krishnappa
Rohan Sachdeva
Rodolphe Barrangou
Adam M. Deutschbauer
Jillian F. Banfield
Jennifer A. Doudna
机构：
[1] University of California,Innovative Genomics Institute
[2] University of California,Department of Molecular and Cell Biology
[3] University of California,Department of Earth and Planetary Science
[4] University of California,Department of Plant and Microbial Biology
[5] University of California,Environmental Science, Policy and Management
[6] Lawrence Berkeley National Laboratory,Environmental Genomics and Systems Biology Division
[7] North Carolina State University,Department of Food, Bioprocessing and Nutrition Sciences
[8] University of Melbourne,School of Earth Sciences
[9] University of California,California Institute for Quantitative Biosciences
[10] University of California,Department of Chemistry
[11] University of California,Howard Hughes Medical Institute
[12] Lawrence Berkeley National Laboratory,Molecular Biophysics & Integrated Bioimaging Division
[13] Gladstone-UCSF Institute of Genomic Immunology,undefined
来源：
Nature Microbiology | 2022年 / 7卷
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摘要：
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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页码：34 / 47
页数：13
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