Sex differences and individual variability in the captive Jamaican fruit bat (Artibeus jamaicensis) intestinal microbiome and metabolome

Although the intestinal microbiome plays an important role in mammalian health, disease, and immune function, it has not been well characterized in bats, the reservoir hosts of several highly pathogenic viruses. Here, we describe a pipeline to investigate the intestinal microbiome of captive Jamaican fruit bats ( Artibeus jamaicensis ). We observed a high degree of individual variation in addition to sex- and cohort-linked differences. The intestinal microbiome drove intestinal metabolite composition, possibly contributing to differences in immune status. This work provides a basis for future infection and field studies to examine in detail the role of the intestinal microbiome in antiviral immunity.