Data from: Synchronized shift of oral, fecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

Seasonal reproduction is a period of extreme physiological and behavioral
changes, yet we know little about how it may affect host microbial
communities (i.e. microbiota) and pathogen transmission. Here, we
investigated shifts of the bacterial microbiota in saliva, urine and
faeces during the seasonal reproduction of bats in South Africa, and test
for an interaction in shedding patterns of both bacterial (Leptospira) and
viral (adeno- and herpes-viruses) agents. Based on a comparative approach
in two cave-dwelling bat species and high-throughput sequencing of the 16S
rRNA gene, we demonstrated a clear signature in microbiota changes over
the reproduction season, consistent across the multiple body habitats
investigated, and associated with sex, age and reproductive condition of
bats. We observed in parallel highly dynamic shedding patterns for both
bacteria and viruses, but did not find a significant association between
viral shedding and bacterial microbiota composition. Indeed, only
Leptospira shedding was associated with alterations in both the diversity
and composition of the urinary microbiota. These results illustrate how
seasonal reproduction in bats substantially affects microbiota composition
and infection dynamics, and have broad implications for the understanding
of disease ecology in important reservoir hosts, such as bats.