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ISME J. 2016 Mar;10(3):655-64. doi: 10.1038/ismej.2015.142. Epub 2015 Aug 21.

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development.

Author information

1
Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
2
Department of Pathology, University of Utah, Salt Lake City, UT, USA.
3
Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
4
Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
5
Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.

Abstract

Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct sub-groups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.

PMID:
26296066
PMCID:
PMC4817674
DOI:
10.1038/ismej.2015.142
[Indexed for MEDLINE]
Free PMC Article

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