The resilience of the oral microbiome and lability of the hair microbiome across host environments in wild and captive lemurs

Microbiome diversity and composition in mammals is affected by the hosts environment and has been linked to important immune and physiological host functions, yet most of these data come from the gut microbiome. Research on the oral and hair microbiome in nonhuman primates has been far less common, and information from wild primates is even rarer. These overlooked patterns of environmental effects on microbial communities across the body may have important implications for a range of host functions. Therefore, in this study we characterized the gut, oral, and hair microbiomes across nine different captive and wild lemur species: Eulemur collaris, Eulemur coronatus, Eulemur mongoz, Lemur catta, Microcebus griseorufus, Microcebus murinus, Propithecus coquereli, Propithecus verreauxi, and Varecia rubra. We explored how host environment affects the microbiome diversity of these three body regions using 16S rRNA sequencing and found significant differences in microbiome composition, diversity, and environmental influence across body regions. The oral microbiome was least diverse and most resilient to different environmental effects; conversely, the hair microbiome was both most diverse and most labile. Differentially abundant bacterial taxa across oral, gut, and hair microbiota may also reflect selective regimes unique to each body region. These results emphasize the importance of accounting for body region when conducting microbiome studies. ImportanceAn organisms microbiome plays important roles in a wide variety of the host animals physiological functions, yet how these microbial communities in body regions beyond the gut are affected by the hosts environment is not clearly understood. We therefore analyzed how the oral, gut, and hair microbiomes of nine lemur species (genera Eulemur, Lemur, Microcebus, Propithecus, and Varecia) varied across wild and captive environments. We found that host environment affected the microbiomes of each body region in distinct ways, with the oral microbiome appearing conserved and more resilient to environmental effects, particularly compared to the diverse and widely variable hair microbiome. To our knowledge, this study is the most comprehensive multi-body-region analysis of the lemur microbiome to date. Our results demonstrate that the environment does not have a universal effect on the microbiome across body regions, but is instead mediated by body-region specific factors.