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Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome

View ORCID ProfileBenjamin D. Ross, Adrian J. Verster, Matthew C. Radey, Danica T. Schmidtke, Christopher E. Pope, Lucas R. Hoffman, Adeline M. Hajjar, S. Brook Peterson, View ORCID ProfileElhanan Borenstein, View ORCID ProfileJoseph D. Mougous
doi: https://doi.org/10.1101/471110
Benjamin D. Ross
1Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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Adrian J. Verster
2Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
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Matthew C. Radey
1Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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Danica T. Schmidtke
1Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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Christopher E. Pope
3Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
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Lucas R. Hoffman
1Department of Microbiology, University of Washington, Seattle, WA 98195, USA
3Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
4Seattle Children’s Hospital, Seattle, WA, 98105
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Adeline M. Hajjar
5Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
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S. Brook Peterson
1Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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Elhanan Borenstein
2Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
6Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
7Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel
8Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
9Santa Fe Institute, Santa Fe, NM 87501, USA
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  • For correspondence: mougous@uw.edu elbo@uw.edu
Joseph D. Mougous
1Department of Microbiology, University of Washington, Seattle, WA 98195, USA
10Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
11Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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  • For correspondence: mougous@uw.edu elbo@uw.edu
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Abstract

The impact of direct interactions between co-resident microbes on microbiome composition is not well understood. Here we report the occurrence of acquired interbacterial defense (AID) gene clusters in bacterial residents of the human gut microbiome. These clusters encode arrays of immunity genes that protect against type VI secretion toxin-mediated intra- and inter-species bacterial antagonism. Moreover, the clusters reside on mobile elements and we demonstrate that their transfer is sufficient to confer toxin resistance in vitro and in gnotobiotic mice. Finally, we identify and validate the protective capacity of a recombinase-associated AID subtype (rAID-1) present broadly in Bacteroidales genomes. These rAID-1 gene clusters have a structure suggestive of active gene acquisition and include predicted immunity factors of toxins deriving from diverse organisms. Our data suggest that neutralization of contact-dependent interbacterial antagonism via AID systems shapes human gut microbiome ecology.

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Posted July 11, 2019.
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Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome
Benjamin D. Ross, Adrian J. Verster, Matthew C. Radey, Danica T. Schmidtke, Christopher E. Pope, Lucas R. Hoffman, Adeline M. Hajjar, S. Brook Peterson, Elhanan Borenstein, Joseph D. Mougous
bioRxiv 471110; doi: https://doi.org/10.1101/471110
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Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome
Benjamin D. Ross, Adrian J. Verster, Matthew C. Radey, Danica T. Schmidtke, Christopher E. Pope, Lucas R. Hoffman, Adeline M. Hajjar, S. Brook Peterson, Elhanan Borenstein, Joseph D. Mougous
bioRxiv 471110; doi: https://doi.org/10.1101/471110

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