Fecal microbiomes of non-human primates in Western Uganda reveal species-specific communities largely resistant to habitat perturbation - PubMed (original) (raw)

doi: 10.1002/ajp.22238. Epub 2013 Nov 27.

Colin A Chapman, Geoffrey Weny, Alex Tumukunde, David Hyeroba, Kelly Klotz, Avery S Koblings, David N M Mbora, Melissa Cregger, Bryan A White, Steven R Leigh, Tony L Goldberg

Affiliations

Fecal microbiomes of non-human primates in Western Uganda reveal species-specific communities largely resistant to habitat perturbation

Aleia I McCord et al. Am J Primatol. 2014 Apr.

Abstract

Primate gastrointestinal microbial communities are becoming increasingly appreciated for their relevance to comparative medicine and conservation, but the factors that structure primate "microbiomes" remain controversial. This study examined a community of primates in Kibale National Park, Uganda, to assess the relative importance of host species and location in structuring gastrointestinal microbiomes. Fecal samples were collected from primates in intact forest and from primates in highly disturbed forest fragments. People and livestock living nearby were also included, as was a geographically distant population of related red colobus in Kenya. A culture-free microbial community fingerprinting technique was used to analyze fecal microbiomes from 124 individual red colobus (Procolobus rufomitratus), 100 individual black-and-white colobus (Colobus guereza), 111 individual red-tailed guenons (Cercopithecus ascanius), 578 human volunteers, and 364 domestic animals, including cattle (Bos indicus and B. indicus × B. taurus crosses), goats (Caprus hircus), sheep (Ovis aries), and pigs (Sus scrofa). Microbiomes sorted strongly by host species, and forest fragmentation did not alter this pattern. Microbiomes of Kenyan red colobus sorted distinctly from microbiomes of Ugandan red colobus, but microbiomes from these two red colobus populations clustered more closely with each other than with any other species. Microbiomes from red colobus and black-and-white colobus were more differentiated than would be predicted by the phylogenetic relatedness of these two species, perhaps reflecting heretofore underappreciated differences in digestive physiology between the species. Within Kibale, social group membership influenced intra-specific variation among microbiomes. However, intra-specific variation was higher among primates in forest fragments than among primates in intact forest, perhaps reflecting the physical separation of fragments. These results suggest that, in this system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance.

Keywords: Cercopithecinae; Colobinae; Uganda; forest fragmentation; microbiome; non-human primate.

© 2013 Wiley Periodicals, Inc.

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Figures

Fig. 1

Fig. 1

Non-metric multi-dimensional scaling ordination based on Bray–Curtis similarity matrix for fecal microbiomes of three primate species from Kibale National Park (KNP) and surrounding forest fragments: red colobus (RC), black-and-white colobus (BW), and red-tailed guenon (RT). Red colobus from Tana River National Park, Kenya (TRNPR) are included for comparison. Each point represents the fecal microbiome of an individual primate. Two-dimensional stress value indicates moderate fidelity of original Bray–Curtis similarity matrix as represented in 2D space.

Fig. 2

Fig. 2

Non-metric multi-dimensional scaling ordination based on Bray–Curtis similarity matrix comparing the fecal microbiomes of people, livestock, and non-human primates (BW, black-and-white colobus; RC, red colobus; RT, red-tailed guenon) from the Kibale area. Red colobus from Tana River National Park, Kenya (TRNPR) are included for comparison. Each point represents the fecal microbiome of an individual. Two-dimensional stress value indicates moderate fidelity of original Bray–Curtis similarity matrix as represented in 2D space.

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