Evaluating the core microbiota in complex communities: a systematic investigation

Astudillo-Garcia, Carmen, Bell, James J., Webster, Nicole S., Glasl, Bettina, Jompa, Jamaluddin, Montoya, Jose M., and Taylor, Michael W. (2017) Evaluating the core microbiota in complex communities: a systematic investigation. Environmental Microbiology, 19 (4). pp. 1450-1462.

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Abstract

The study of complex microbial communities poses unique conceptual and analytical challenges, with microbial species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a core' microbiota approach, focusing only on the stable and permanent members of the community, is becoming increasingly popular. Given the various ways of defining a core microbiota, it is prudent to examine whether the definition of the core impacts upon the results obtained. Here we used complex marine sponge microbiotas and undertook a systematic evaluation of the degree to which different factors used to define the core influenced the conclusions. Significant differences in alpha- and beta-diversity were detected using some but not all core definitions. However, findings related to host specificity and environmental quality were largely insensitive to major changes in the core microbiota definition. Furthermore, none of the applied definitions altered our perception of the ecological networks summarising interactions among bacteria within the sponges. These results suggest that, while care should still be taken in interpretation, the core microbiota approach is surprisingly robust, at least for comparing microbiotas of closely related samples.

Item ID: 50651
Item Type: Article (Research - C1)
ISSN: 1462-2920
Funders: University of Auckland, Australian Research Council (ARC), Laboratory of Excellence (LABEX), Victoria University of Wellington, NZ
Projects and Grants: ARC Future Fellowship FT120100480, LABEX TULIP ANR-10-LABX-41, LABEX TULIP ANR-11-IDEX-002-02)
Date Deposited: 20 Sep 2017 10:53
FoR Codes: 06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060599 Microbiology not elsewhere classified @ 100%
SEO Codes: 96 ENVIRONMENT > 9699 Other Environment > 969999 Environment not elsewhere classified @ 100%
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