The gut microbiome of Madagascar's lemurs from forest fragments in the central highlands

The gut microbiome is now understood to play essential roles in host nutrition and health and has become a dominant research focus in primatology. Over the past decade, research has clarified the evolutionary traits that govern gut microbiome structure across species and the ecological traits that further influence consortia within them. Nevertheless, we stand to gain resolution by sampling hosts in understudied habitats. We focus on the lemurs of Madagascar's central highlands. Madagascar's highlands have a deep history as heterogeneous grassland-forest mosaics, but due to significant anthropogenic modification, have long been overlooked as lemur habitat. We collected fecal samples from Verreaux's sifakas (Propithecus verreauxi), common brown lemurs (Eulemur fulvus), and Goodman's mouse lemurs (Microcebus lehilahytsara) inhabiting two protected areas in the highlands and used amplicon sequencing to determine gut microbiome diversity and membership. As expected, the lemurs harbored distinct gut consortia tuned to their feeding strategies. Mouse lemurs harbored abundant Bifidobacterium and Alloprevotella that are implicated in gum metabolism, sifakas harbored abundant Lachnospiraceae that are implicated in leaf-fiber metabolism, and brown lemurs harbored diverse consortia with abundant WCBH1-41 that could be associated with frugivory in harsh seasons and habitats. Within brown lemurs, a suite of bacteria varied between seed-packed and leaf-packed feces, a proxy for dietary intakes, collected from the same group over days. Our results underscore the evolutionary and ecological factors that govern primate gut microbiomes. More broadly, we showcase the forests of Madagascar's central highlands as rich habitat for future research of lemur ecology and evolution.