Williams, Catryn; (2020) Evolution of the primate gut microbiome. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

The importance of the gut microbiome to an individual’s health and disease state is becoming increasingly apparent. So far studies have focussed primarily on humans, however relatively little is known about other mammals, including our closest relatives, the non-human primates. Using 16S rRNA sequencing and bioinformatics analyses, this thesis explores how various factors affect and determine the gut microbiome of an individual primate. The thesis begins with gut microbiome variation within a single species, the common chimpanzee (Pan troglodytes), by comparing two geographically distinct chimpanzee populations of different subspecies living in Issa and Gashaka. Within Issa, collection site was shown to be a factor that distinguishes microbiome composition in samples, although this is likely to be variation within a single chimpanzee community over time rather than two separate chimpanzee communities. The two subspecies at Issa and Gashaka showed recognisably different gut microbiomes to each other, indicating that the gut microbiomes of these primates varied with chimpanzee subspecies. Variation between multiple primate species’ living at Issa is next considered, as well as how living in sympatry with other primates impacts the gut, by comparing three free-living species in Issa. Results here showed that each of the three primate species living at Issa showed distinct gut microbiomes. Whilst the red tailed monkey microbiomes were not significantly more similar to either the Issa or Gashaka chimpanzees, the yellow baboons had microbiomes that were more similar to the sympatric chimpanzees at Issa than to the chimpanzees at Gashaka. The second half of the thesis focuses on how life in captivity might impact the gut microbiome. The gut microbiota of captive chimpanzees are compared to free-living populations to determine the effects of captivity, and a comparison of these animals with a population comprising the descendants of chimpanzees that were released from captivity provides an opportunity to consider the effects of reintroduction efforts on the gut. Results here showed that gut microbiomes of the Rubondo chimpanzees shared less in common with the native Gashaka and Issa chimpanzees than these two native populations shared with each other. Furthermore, the Rubondo chimpanzees showed gut microbiomes that were significantly more similar to captive primates living in the UK than to other free-living chimpanzees at Issa and Gashaka, despite the Rubondo population sampled in 2013 having never lived in captivity themselves. This implies that captivity causes heritable changes in the gut microbiome that release alone is not sufficient to counteract without proximity to other free-living members of that species. The thesis finally performs a large-scale comparison of captive primates from across the whole Order, asking whether host species or captive location has the greater impact on determining gut communities. This chapter finds that variation occurs between zoos, outweighing the effect of host species for some Families of primates, whilst for other primate Families, host species-specific microbiomes are recognisable regardless of captive location. The results of this chapter suggest that captivity affects different Families within the primate Order to different extents The thesis concludes by discussing what these studies tell us overall about how the gut microbiome is influenced.

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