Therefore, we examined the gut microbial communities within a subspecies of chimpanzees ( Pan troglodytes schweinfurthii), a monophyletic clade of approximately the same age as modern humans. One potential issue when comparing microbiotae across chimpanzees and humans is the large difference in levels of intraspecific genetic variation between the two groups: chimpanzees classify into multiple subspecies that diversified over the last 1.5 million years, whereas the ancestry of all modern humans can be traced to population bottlenecks that occurred over the last 200,000 years. To test for the presence of enterotypes in a non-human ape, we investigated the gut microbial communities within chimpanzees. Furthermore, through analyses of longitudinal samples, we show that the microbial signatures of chimpanzee enterotypes are stable over time, but that individual hosts shift among enterotypes over periods longer than one year. Here we show that the gut microbiotae of chimpanzees assort into enterotypes that are compositionally analogous to those in humans, supporting the hypothesis that enterotypic variation was present before the divergence of humans and chimpanzees. Given the co-diversification between gut microbiotae and their great ape hosts, the presence of compositionally similar enterotypes in humans and other great ape species, despite their present-day differences in diets and geographic distributions, would be consistent with the origination of enterotypes before the divergence of the human lineage. Therefore, characterization of the gut microbial communities within populations of non-human great apes provides insights into the origins of the human enterotypes. But if enterotypes are the product of more ancient features, such as host immune system or gut physiology, they are likely to have originated before or during the diversification of the great ape species. If the formation of enterotypes is driven by the varied diets of human hosts, enterotypes could have arisen in the human lineage over relatively recent timescales. The assignment of the human gut microbiotae into discrete enterotypes raises several questions about the origins and evolution of these compositionally distinct microbial communities. Whereas initially no relationship was detected between enterotypes and specific features of the host (such as age, health status, body morphotype, provenance or gender), recent work has revealed associations between enterotype and long-term diet: the Bacteroides-dominant enterotype is prevalent in individuals whose diets are high in animal fat and protein, whereas the Prevotella–dominant enterotype prevails in individuals with high carbohydrate diets. The gut microbial communities in contemporary populations of humans have been partitioned into three clusters, termed ‘enterotypes’, each of which is characterized by a distinct set of overrepresented bacterial genera.
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