article · mSystems
An examination of the gut, oral, and skin microbiomes of 497 Afrotropical bats spanning 31 species indicates that ecological conditions, rather than evolutionary history, primarily govern bacterial community structure. Across more than 1,200 bacterial amplicon libraries, chiropteran phylogeny shows no correlation with microbial dissimilarity across the three anatomical sites. Host species identity and geographic locality instead emerge as principal predictors of bacterial composition. Additionally, bacterial richness demonstrates a positive correlation with elevation, and gut microbial communities differ significantly between frugivorous and insectivorous bats. These results demonstrate that bats do not display the typical phylosymbiosis observed in other mammals. Instead, external habitat factors, dietary traits, and local environments predominantly shape the distribution and diversity of bacterial symbionts across diverse anatomical niches in bat hosts.
Understanding the mechanisms that shape wildlife microbiomes clarifies how animal health connects to the surrounding environment. Because bats do not follow the evolutionary host-microbe patterns typical of other mammals, this research shows that external ecological pressures and habitats exert a stronger influence on bat-associated bacteria, providing a vital comparative baseline for ecological health and systems biology studies across broad mammalian scales.
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Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals.<b>IMPORTANCE</b> This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity-but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.
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DOI: 10.1128/msystems.00511-19
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