Animal microbiomes influence host nutrition, physiology, and immunity, but the influence of host phylogeny versus diet is not well understood. Bats, the second most speciose group of mammals, vary in their feeding niche, but it is currently unclear how strongly host diets modulate the microbiome communities compared with the effect of evolutionary history. We used 16S rRNA microbiome profiling to test the following hypotheses: (1) does the host phylogeny have a measurable effect on bacterial community composition? (2) and how strong is that effect relative to dietary ecology?
Results/Conclusions
Using a machine-learning approach combining data from the microbiome, host ecology, and host evolutionary history from 19 species of Neotropical bats, we found that host ecology has a stronger influence on microbiome structure than host evolutionary history. Studying these processes in wildlife hosts can help improve our understanding of why some species possess certain bacterial communities and others do not. Because microbiomes are increasingly recognized as inseparable elements from hosts, preventing disruptions in these communities may be an underappreciated axis of host conservation.