Captivity humanizes the primate microbiome

Abstract

The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.human microbiome | primate microbiome | dietary fiber | dysbiosis | microbial ecology

Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons

“…Recently, several authors have called for greater use of wild subjects in studies of the microbiome, in part because of strong effects of captivity on host-associated microbial communities [79–81]. The study described here is, to our knowledge, only the third to investigate vaginal microbiota composition in wild primates; notably, the previous two studies were restricted to small sample sizes and lacked of information on host reproductive state [6, 77].…”

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals

“…However, captivity alters microbiome composition in mammals [12,[29][30][31], and, when animals are compared across geographic regions, host phylogenetic differences may be confounded by differences in local microbial taxa [15,32]. Thus, many of these prior studies did not have sufficient data for resolving the relative influences of various heritable and environmental factors.…”

Endothelial Dysfunction in Mexican Obese Children, is there A Role of the Gut Microbiota?

“…and Prevotella spp. in Non Human Primates (NHPs), which reflects in parallel the converge of NHPs microbiota towards the modern human microbiota, and suggests the recent loss of core microbiota in humans [24]. These bacterial genera Bacteroides spp., Prevotella spp.…”