The microbiome of captive hamadryas baboons

Abstract

Background: The hamadryas baboon (Papio hamadryas) is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. In contrast to the widely studied human microbiome, there is a paucity of information on the host-associated microbiomes of nonhuman primates (NHPs). Here, our goal was to understand the microbial composition throughout different body sites of cohabiting baboons. Results: We analyzed 170 oral, oropharyngeal, cervical, uterine, vaginal, nasal and rectal samples from 16 hamadryas baboons via 16S rRNA gene sequencing. Additionally, raw Miseq sequencing data from 1041 comparable publicly available samples from the human oral cavity, gut and vagina were reanalyzed using the same pipeline. We compared the baboon and human microbiome of the oral cavity, gut and vagina, showing that the baboon microbiome is distinct from the human. Baboon cohabitants share similar microbial profiles in their cervix, uterus, vagina, and gut. The oral cavity, gut and vagina shared more bacterial amplicon sequence variants (ASVs) in group living baboons than in humans. The shared ASVs had significantly positive correlations between most body sites, suggesting a potential bacterial exchange throughout the body. No significant differences in gut microbiome composition were detected within the maternity line and between maternity lines, suggesting that the offspring gut microbiota is shaped primarily through bacterial exchange among cohabitants. Finally, Lactobacillus was not so predominant in baboon vagina as in the human vagina but was the most abundant genus in the baboon gut. Conclusions: This study is the first to provide comprehensive analyses of the baboon microbiota across different body sites. We contrast this to human body sites and find substantially different microbiomes. This group of cohabitating baboons generally showed higher microbial diversity and remarkable similarities between body sites than were observed in humans. These data and findings from one group of baboons can form the basis of future microbiome studies in baboons and be used as a reference in research where the microbiome is expected to impact human modeling with baboons.

The gut microbiota of gibbons across host genus and captive site in China

“…We also observed a high proportion of Spirochaetes in the gut of Hoolock gibbons at Beijing Zoo (24.1%) and Hylobates gibbon at Shanghai Zoo (21.3%). Spirochaetes is an opportunistic pathogen, which is extremely rare in modern humans but commonly found in Hadza hunter‐gatherers (Schnorr et al, 2014) and the gut of captive baboons (Li et al, 2020).…”

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand

“…The order Pasteurellales are normally commensal microbes on mucous membranes of the upper respiratory tract 35 . They also had been recently identified in oral microbiota of captive baboons 36 . In contrast, the oral microbiota of wild macaques was enriched by the group of environmental bacteria such as phylum Verrucomicrobia, phylum Nitrospirae, Fusobacteria and various members of class Alphaproteobacteria.…”

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health

“…Spirochetes were more abundant (45.72%) in the intestines of captive skywalker hoolock gibbons. Such high proportions of spirochetes have not been reported in the gut of other captive primates—northern white‐cheeked gibbons ( Nomascus leucogenys ), <5% (Jia et al, 2018); chimpanzee ( Pan troglodytes troglodytes ) and gorilla ( Gorilla gorilla gorilla ), ~25% (Campbell et al, 2020); and hamadryas baboon ( Papio hamadryas ), <10% (Li et al, 2020). The enrichment of Spirochetes here was mainly caused by abundant Treponema .…”