Abstract:
ABSTRACT 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.
IMPORTANCE 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.
KEYWORDS microbiome, Chiroptera, phylosymbiosis, Afrotropics
