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Cell Host Microbe. 2017 Sep 13;22(3):411-419.e4. doi: 10.1016/j.chom.2017.08.010.

The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
2
Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195, USA.
3
Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA; Microbial Sciences Institute, Yale University School of Medicine, West Haven, CT 06516, USA.
4
Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, School of Medicine, University of Washington, Seattle, WA 98195, USA. Electronic address: mougous@uw.edu.
5
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Santa Fe Institute, Santa Fe, NM 87501, USA. Electronic address: elbo@uw.edu.

Abstract

Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1-3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1-3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1 and GA2) and strain (GA3) levels. Bacteroides fragilis GA3 is known to mediate potent inter-strain competition, and we observe GA3 enrichment among strains colonizing infant microbiomes, suggesting competition early in life. Additionally, GA3 is associated with increased Bacteroides abundance, indicating that this system confers an advantage in Bacteroides-rich ecosystems. Collectively, these analyses uncover the prevalence of T6SS-dependent competition and reveal its potential role in shaping human gut microbial composition.

KEYWORDS:

Bacteroidales; T6SS; human microbiome; infant microbiome; interbacterial competition; metagenomics; microbiome assembly; toxin; type VI secretion system

PMID:
28910638
PMCID:
PMC5679258
DOI:
10.1016/j.chom.2017.08.010
[Indexed for MEDLINE]
Free PMC Article

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