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APPLIED MICROBIOLOGY

DART takes aim at community editing

Nature Microbiology volume 7, pages 8–9 (2022)Cite this article

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An Author Correction to this article was published on 06 January 2022

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Advances in CRISPR–Cas tools coupled with innovative screening and bioinformatic pipelines make it possible to conduct strain-specific and site-specific genome editing within a microbial community without the need for prior culturing or engineering.

Microbiome studies rely heavily on sequencing methods to identify changes or patterns in microbial communities that can point to functional consequences, such as pathogenic processes in the host. Often, the holy grail of such studies is to identify individual key bacteria, or key groups of related bacteria, that can be targeted to prevent or resolve disease or disease complications. However, reaching that conclusion, and the ultimate therapeutic interventions, requires complex experimentation, including the ability to isolate the organism(s) of interest from the host and genetically modify genes suspected to confer the phenotype of interest. From a practical standpoint, however, existing bacterial cultivation and engineering approaches are fraught with challenges because (1) many bacteria have not yet been successfully grown outside their native environments; (2) most microorganisms with biomedical, environmental and industrial potential coexist and interact with other organisms in communities; (3) not all bacteria are amenable to genetic engineering; and (4) strains engineered in isolation may not deliver the genetically modified phenotype when they are re-introduced into the microbiome. Therefore, a widely applicable and scalable strategy for bacterial genome editing of targeted organisms within their natural communities is needed.

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Fig. 1: Conceptual overview of the ET-seq and VcDART toolkit for bacterial genomic editing.

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Authors and Affiliations

  1. The Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA

    Connie W. Y. Ha

  2. F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA

    Suzanne Devkota

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  1. Connie W. Y. Ha
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  2. Suzanne Devkota
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Correspondence to Suzanne Devkota.

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Ha, C.W.Y., Devkota, S. DART takes aim at community editing. Nat Microbiol 7, 8–9 (2022). https://doi.org/10.1038/s41564-021-01017-4

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  • DOI: https://doi.org/10.1038/s41564-021-01017-4

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