Species- and site-specific genome editing in complex bacterial communities
| Autor: | 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 |
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| Rok vydání: | 2021 |
| Předmět: |
Microbiology (medical)
Immunology Microbial Consortia Applied Microbiology and Biotechnology Microbiology Article Genetics 2.2 Factors relating to the physical environment Humans Clustered Regularly Interspaced Short Palindromic Repeats Kinetoplastida Aetiology Soil Microbiology Gene Editing Genome Bacteria Microbiota Prevention Human Genome Bacterial Infant Cell Biology Archaea Gastrointestinal Microbiome Medical Microbiology RNA CRISPR-Cas Systems Infection Guide Genome Bacterial Biotechnology RNA Guide Kinetoplastida |
| Zdroj: | Nature microbiology, vol 7, iss 1 Nat Microbiol |
| ISSN: | 2058-5276 |
| Popis: | Knowledge of microbial gene functions comes from manipulating the DNA of individual strains in isolation from their natural communities. While this approach to microbial genetics has been foundational, its requirement for culturable microorganisms has left the majority of microbes and their interactions genetically unexplored. Here, we describe a generalizable strategy for editing the genomes of specific organisms within microbial communities. We identified genetically tractable bacteria within a community using Environmental Transformation Sequencing (ET-Seq), an approach in which non-targeted transposon integrations are mapped and quantified following community delivery. We next developed and used DNA-editing All-in-one RNA-guided CRISPR-Cas Transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-Seq, enabling organism- and locus-specific genetic manipulation within the community context. To illustrate the utility of our approach, we selectively edited closely related strains, measured gene fitness, and enriched targeted members within soil and infant gut microbiota. These results establish a new paradigm for targeted community editing relevant to research and applications on medical, agricultural, and industrial microbiomes. |
| Databáze: | OpenAIRE |
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