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Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota

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Abstract

Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.

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Data Availability

The unfiltered sequence data used in this study has been deposited in the NCBI Short Read Archive under accession number PRJNA528765.

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Acknowledgments

Coyote carcasses were provided by Bill, Duncan, and Malcolm Abercrombie of Animal Damage Control, Inc., and SS would like to thank Dana Sanderson and several undergraduate volunteers at the University of Alberta for assistance with coyote necropsies.

Code Availability

The R scripts and all material(code and workspace) is available (present tense) in the linked GitHub repository https://github.com/sasugden/Coyote_intestinal_biogeography.

Funding

This study was supported by Discovery Grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) to CCSC (RGPIN-2017-05915) and LYS (RGPIN-2019-04399).

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  1. Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

    Scott Sugden, Colleen Cassady St. Clair & Lisa Y. Stein

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  1. Scott Sugden
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Correspondence to Scott Sugden.

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Sugden, S., St. Clair, C.C. & Stein, L.Y. Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota. Microb Ecol 81, 240–252 (2021). https://doi.org/10.1007/s00248-020-01547-0

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