Composition, Ecology and Natural History of the Great Ape Mycobiome
Microbial Ecology and Applied Microbiology
Final Report Abstract
The microorganisms living in close association with humans and animals have been extensively researched in the recent decades. Researchers can identify thousands of different bacterial species that inhabit the gut and other body surfaces of humans and their closest relatives, the great apes. However, the fungal members of the microbiome and their evolutionary origin were long understudied. Here, we used DNA sequencing of faecal material of wild great apes collected along their full African geographic range to characterise the fungi that potentially colonize great ape guts and ask which ecological factors contribute to colonization patterns. We analysed DNA from more than 900 faecal samples from the Pan African Programme (PanAf), with roughly 50%, 40%, and 10% originating from chimpanzees, gorillas, and bonobos, respectively. Together with the NGS Competence Center Tübingen, we subjected all samples to amplification and sequencing of two genomic regions that are commonly used to determine fungal presence and phylogenetic relationships. We observed a vast richness of fungal genomic material. While the number of different fungi detected in any individual sample was on average higher than what is found in human studies, we must assume that many of these fungi were not residents of the ape guts but entered the samples after defecation. Importantly, we could not find evidence for a shared coremycobiome, either across all sampled ape species or even within the species. We did find strong effects of geography, both in terms of distance and habitat type. In addition, roughly half of the samples were also analysed by shotgun sequencing. This gave us greater confidence in the abovementioned findings and allowed more detailed characterisation of the fungi. While we could not find a direct correlation between the remains of dietary plants detectable in the faecal material and the fungi, our analyses of potential lifestyles of the detected fungi pointed to most of them being diet-derived (if not coincidentally detected on faecal material), rather than consistent members of the chimpanzee gut microbiome. Relating the patterns observed for fungal colonization to the bacterial presence seen in the very same samples, we found evidence for direct interactions of the bacteria with the fungi. Overall, this study has generated a large collection of ape mycobiome data with unprecedented spatial coverage, which is a valuable resource to be integrated in the deep collection of socio-demographic, genetic, dietary, behavioural and ecological data within the PanAf project to further our understanding of inter- and intraspecific variation in great apes.
