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Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species

Microbial Ecology volume 75, pages 515–527 (2018)Cite this article

An Erratum to this article was published on 11 September 2017

This article has been updated

Abstract

Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity—often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza). Monkeys were housed at five different captive institutes: Panxi Wildlife Rescue Center (Guizhou, China), Beijing Zoo, Beijing Zoo Breeding Center, Singapore Zoo, and Singapore Zoo Primate Conservation Breeding Center. Captive diets varied widely between institutions, but within an institution, all colobine monkey species were fed nearly identical or identical diets. In addition, four monkey species were present at multiple captive institutes. This allowed us to parse the effects of diet and phylogeny in these captive colobines. Gut microbial communities clustered weakly by host species and strongly by diet, and overall, colobine phylogenetic relationships were not reflected in gut microbiota analyses. Core microbiota analyses also identified several key taxa—including microbes within the Ruminococcaceae and Lachnospiraceae families—that were shared by over 90% of the monkeys in this study. Microbial species within these families include many butyrate producers that are important for GI health. These results highlight the importance of diet in captive colobines.

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Change history

  • 11 September 2017

    An erratum to this article has been published.

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Acknowledgements

We would like to thank Richard D. Howard for his support of this project, thoughtful suggestions on analysis, and review of this manuscript. Krista Nichols kindly provided laboratory space for the molecular work. We also thank Bong Suk-Kim and Gaenna Rogers for their assistance in the laboratory. Finally, we thank the reviewers for the time and thought they put into providing helpful feedback on this manuscript. This project was funded by the Margot Marsh Biodiversity Foundation (VLH, CLT), San Diego Zoo Global, the Offield Family Foundation, the Earth Microbiome Project, the Howard Hughes Medical Institute (RK), Purdue College of Veterinary Medicine International Programs (VLH), and Fanjingshan National Nature Reserve. VLH was supported by a Purdue University Andrews Fellowship and a Purdue Research Foundation Research Grant.

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Authors and Affiliations

  1. Microbiome Program, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA

    Vanessa L. Hale

  2. San Diego Zoo Institute for Conservation Research, Escondido, CA, 92027, USA

    Chia L. Tan

  3. Fanjingshan National Nature Reserve Administration, Tongren, China

    Kefeng Niu & Yeqin Yang

  4. Department of Life Sciences and Systems Biology, University of Turin, 10123, Turin, Italy

    Kefeng Niu

  5. Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA

    Rob Knight

  6. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA

    Rob Knight

  7. Zhejiang Institute of Microbiology, Zhejiang, Hangzhou, China

    Qikun Zhang

  8. Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China

    Duoying Cui

  9. Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA

    Katherine R. Amato

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Correspondence to Vanessa L. Hale.

Additional information

An erratum to this article is available at https://doi.org/10.1007/s00248-017-1070-3.

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Hale, V.L., Tan, C.L., Niu, K. et al. Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species. Microb Ecol 75, 515–527 (2018). https://doi.org/10.1007/s00248-017-1041-8

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  • DOI: https://doi.org/10.1007/s00248-017-1041-8

Keywords

  • Colobine
  • Gut microbiota
  • Diet
  • Phylogeny
  • Primate