Abstract
Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status.
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Acknowledgements
We are grateful to Chad Trent and Rose Gaudreau for valuable technical support; and to Jeffrey Gordon, Julie Toplin, Roger Volker and Brendan Bohannan for helpful discussions and intellectual contributions. This work was funded by grants from the NIH (DK075549 to KG; DK081426 and DK073695 to JFR; HD22486 provided support for the Oregon Zebrafish Facility; RR012546 provided support for the Zebrafish International Resource Center), the National Science Foundation (IOB 0541733 to DMP), the University of North Carolina at Chapel Hill, the Harvard University Center for the Environment, a Harvard Digestive Disease Center Pilot and Feasibility grant to CMC, a Rubicon award from the Netherlands Organization for Scientific Research to GR, a Burroughs Wellcome Fund Investigator in the Pathogenesis of Infectious Disease Award to KG, and a Pew Scholars Program in the Biomedical Sciences Award to JFR.
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Genbank accession numbers: HM778163-HM778168, HM778178-HM780469.
Short Read Archive accession number: ERP000213.
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Roeselers, G., Mittge, E., Stephens, W. et al. Evidence for a core gut microbiota in the zebrafish. ISME J 5, 1595–1608 (2011). https://doi.org/10.1038/ismej.2011.38
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DOI: https://doi.org/10.1038/ismej.2011.38
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