Using the gut microbiota as a novel tool for examining colobine primate GI health

Katherine R. Amato, Jessica L. Metcalf, Se Jin Song, Vanessa L. Hale, Jonathan Clayton, Gail Ackermann, Greg Humphrey, Kefeng Niu, Duoying Cui, Hongxia Zhao, Mark D. Schrenzel, Chia L. Tan, Rob Knight, Josephine Braun

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


Primates of the Colobinae subfamily are highly folivorous. They possess a sacculated foregut and are believed to rely on a specialized gut microbiota to extract sufficient energy from their hard-to-digest diet. Although many colobines are endangered and would benefit from captive breeding programs, maintaining healthy captive populations of colobines can be difficult since they commonly suffer from morbidity and mortality due to gastrointestinal (GI) distress of unknown cause. While there is speculation that this GI distress may be associated with a dysbiosis of the gut microbiota, no study has directly examined the role of the gut microbiota in colobine GI health. In this study, we used high-throughput sequencing to examine the gut microbiota of three genera of colobines housed at the San Diego Zoo: doucs (Pygathrix) (N=7), colobus monkeys (Colobus) (N=4), and langurs (Trachypithecus) (N=5). Our data indicated that GI-healthy doucs, langurs, and colobus monkeys possess a distinct gut microbiota. In addition, GI-unhealthy doucs exhibited a different gut microbiota compared to GI-healthy individuals, including reduced relative abundances of anti-inflammatory Akkermansia. Finally, by comparing samples from wild and captive Asian colobines, we found that captive colobines generally exhibited higher relative abundances of potential pathogens such as Desulfovibrio and Methanobrevibacter compared to wild colobines, implying an increased risk of gut microbial dysbiosis. Together, these results suggest an association between the gut microbiota and GI illness of unknown cause in doucs. Further studies are necessary to corroborate these findings and determine cause-and-effect relationships. Additionally, we found minimal variation in the diversity and composition of the gut microbiota along the colobine GI tract, suggesting that fecal samples may be sufficient for describing the colobine gut microbiota. If these findings can be validated in wild individuals, it will facilitate the rapid expansion of colobine gut microbiome research.

Original languageEnglish (US)
Pages (from-to)225-237
Number of pages13
JournalGlobal Ecology and Conservation
StatePublished - Jul 1 2016

Bibliographical note

Funding Information:
The authors would like to acknowledge the pathologists and research technicians at the San Diego Zoo Wildlife Disease Laboratories. Also we wish to thank Fanjingshan National Nature Reserve Administration, Beijing Zoo, Zhejiang Institute of Microbiology and the following individuals: Yeqin Yang, Dunyuan Sun, Lei Shi, Weiyong Zhang, Liangui Liu, Zezhong Wang, Zhenxin Peng, Jinguo Zhang, Qikun Zhang and the staff members of the Wildlife Rescue Center of Fanjingshan National Nature Reserve for their logistical and financial support in China. Funding was provided by the Earth Microbiome Project, as well as San Diego Zoo Global and grants from the Amerman Foundation , Offield Family Foundation , Margot Marsh Biodiversity Foundation , and Morris Animal Foundation awarded to C.L.T. and/or V.L. H. for the China sample collection, and grants from the Margot Marsh Biodiversity Foundation and Mohamed bin Zayed Species Conservation Fund for sample collection in Vietnam, and the National Institutes of Health through a PharmacoNeuroImmunology Fellowship ( NIH/NIDA T32 DA007097-32 ) awarded to J.B.C. The authors would like to thank Oliver Ryder for comments on an early version of this manuscript.

Publisher Copyright:
© 2016 The Authors


  • Captive
  • Colobine
  • Dysbiosis
  • Gut microbiome
  • Zoo


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