The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

Abstract

The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.

A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo

“…Hence, if gorilla dietary diversity in the zoo exceeded that of Cameroonian gorillas during the dry season, that may explain our results. This mechanism has been suggested in another study of zoo great apes reporting similar patterns 55 . Nevertheless, studies of gorillas have come to different conclusions about the influence of seasonality on gut microbiome diversity 19,57 and comparative studies of NHPs suggest that the influence of seasonality on the gut bacteriome among unconfined primates is less than that of host phylogeny.…”

“…Flexilinea was much less abundant in zoo gorillas than in Cameroonian gorillas; that pattern was reversed in chimpanzees, with higher relative abundance among zoo chimpanzees. Differences in this taxon between gorillas and chimpanzees, and within gorillas across seasons, have been previously associated with diet 19,55 . Although we cannot link its relative abundance to a specific ape dietary component in this study, our interviews and the literature suggest that zoo gorillas had reduced leafy material in their diets compared to those in Cameroon, whereas zoo chimpanzees had more leafy material in their diets compared to Cameroonian chimpanzees.…”

“…Nevertheless, three studies have conversely found higher alpha diversity among zoo animals. Campbell and colleagues concluded that gorillas and chimpanzees housed at an American zoo displayed higher gut microbial richness compared to those living in a Congolese forest 55 . For other animal taxa, McKenzie and colleagues observed higher gut www.nature.com/scientificreports/ microbial alpha diversity among zoo-housed Rhinocerotidae family (Ceratotherium simum and Diceros bicomis) and hypothesized specific host biological traits to explain this result; they did not evaluate specific environmental conditions under which these animals were sampled .…”

The Essence of Health and Longevity

“…Literature indicates that animals (gorillas, chimpanzees) that live in human proximity adapt human microbiome from their caretakers. [21] It is the proximity of relationships among biologic systems that lead to similarities of diseases; e.g. wives of men with major cardiovascular disease risk factors, namely hypertension, diabetes, etc., often develop the same disease.…”

Host genetic and environmental factors shape the human gut resistome

“…Although evidence remains sparse [14,15], direct exposure to livestock 100 has been linked to an increase in the number of ARG within the human gut [16]. 101 Furthermore, other environmental or lifestyle factors have also been linked to gut 102 resistome variation [17]. For example, significant gut resistome associations with travel 103 [18] and pet ownership [19] suggest that a multitude of factors could be at play.…”