Characterizing the Gut Microbiome of African Mammals across Geographic Variation

Abstract

The mammalian gastrointestinal microbiome contributes to a range of digestive and immune system functions. Composed of diverse bacteria, archaea, and other microbes, it facilitates immune system protection against pathogens, excretes chemical signals that interact with the nervous system, and metabolizes otherwise indigestible substrates. Herbivores specifically would be unable to extract nutrients from fibrous plant material without microbial fermentation processes that occur in the gut. The mutualistic interactions between a host and its microbiome are understood to be the product of coevolution, and host species-driven differences in the gut microbiome are frequently observed. Multiple hypotheses of specific mechanisms exist to describe this coevolution, the predominant theories suggesting that patterns of microbiome composition should parallel host phylogenies. However, environmental factors such as diet also shape microbial variability within species and individuals, sometimes dominating compositional trends irrespective of phylogeny. The relative contributions of these various factors– phylogeny and diet, as well as digestive system morphology and geography– remain unresolved, and microbial composition is likely subject to complex interactions between them. Studies examining these microbial trends in wild, diverse species across locational variation are limited, thus we aimed to characterize the gut microbiomes of 24 African mammals co-occurring in protected areas across a southeastern African longitudinal gradient. We used 16S rRNA gene sequencing to identify microbes present in fecal samples, then comparatively analyzed microbial compositions. We found that gut morphology and host phylogeny were the most significant contributors to microbial variability, though phylogenetic effects decreased notably among recently diverged host species. Geographic variation emerged at the host species level but not at a community level, and locational effects were non-uniform within species.