Habitat disturbance affects gut microbiota communities differently in wild arboreal and ground-feeding tropical primates

Human exploitation and destruction of natural ecosystems cause extinction of wild animal species on a global scale, and loss of gut ‘micro-biodiversity’ (bacterial and fungal communities) essential for individual nutrition and health is not excluded. While previous investigations have revealed lower gut bacterial diversity in populations living in fragmented compared to intact habitats, no data are available about the other relevant gut component: the fungi (mycobiota). Given their phylogenetic affinity to humans, their conservation status and importance to tropical ecosystems, wild non-human primates make excellent models to investigate the effect of human disturbance on this micro-biodiversity. Thus, to establish whether gut bacterial and fungal communities interact and are affected by diet and/or human disturbance we measured the diversity and composition of gut bacterial and fungal communities in two wild primate species with diverse diets living in human-modified habitats compared to pristine forests within the Udzungwa Mountains of Tanzania. We analysed non-invasively collected samples of 12 groups of Procolobus gordonorum (N = 89), the Udzungwa Red Colobus, endemic and endangered arboreal primates (mainly folivorous), and five groups of Papio cynocephalus (N = 69), the Yellow Baboon of least concern (omnivorous and ground-feeding), using metataxonomic sequencing of the partial 16S rRNA gene and ITS1-ITS2. Despite large intraspecific variability, this study revealed gut bacterial diversities are associated with habitat in both Yellow Baboons and Udzungwa Red Colobus, supporting their usage as sensitive biomarkers of habitat integrity. The details of these associations depend on host physiology and dietary habits. Moreover, gut mycobiota show distinctive traits across hosts and habitat type, resembling patterns found in gut bacterial communities and highlighting the importance of investigating this relatively unexplored gut component.