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Microb Ecol. 2018 Feb;75(2):515-527. doi: 10.1007/s00248-017-1041-8. Epub 2017 Jul 22.

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

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Microbiome Program, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA.
San Diego Zoo Institute for Conservation Research, Escondido, CA, 92027, USA.
Fanjingshan National Nature Reserve Administration, Tongren, China.
Department of Life Sciences and Systems Biology, University of Turin, 10123, Turin, Italy.
Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
Zhejiang Institute of Microbiology, Zhejiang, Hangzhou, China.
Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China.
Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA.


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.


Colobine; Diet; Gut microbiota; Phylogeny; Primate


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