Ecological Variation in Bacterial Community Composition and Zoonotic Genus Distribution Across Body Sites, Host Species, and Seasonal Life-History Stages in Insectivorous Bats

Bats harbour diverse genera containing zoonotic species, yet whether colonisation by these genera reflects stable host–microbe associations or transient environmental exposure remains unresolved. We propose that bat bacterial communities are shaped by three axes of variation: body site defines the microbial niche, host species imposes ecological and phylogenetic constraints, and seasonal life-history transitions alter exposure regimes. We tested four predictions: (1) each body site would (2) host species would show different bacterial profiles associated with differences in roosting ecology, colony density, and foraging behavior; (3) active and hibernation periods would differ in community structure and predicted metabolic function; and (4) zoonotic genera would show predominantly transient detection across years within individuals. Using 16 S rRNA gene amplicon sequencing of 2,747 oral, skin, and gut (stool) samples from eight insectivorous bat species across four seasons (2021–2024) in South Korea, all four predictions were supported. Body site was the strongest determinant of community structure: mean zoonotic genus relative abundance was 10-fold higher in gut (6.91%) than in oral samples (0.69%), dominated by Helicobacter and Chlamydia, while skin carried Rickettsia and Bartonella. Host species structured oral communities most strongly (PERMANOVA R² = 0.295), with interspecific variation in zoonotic genus composition. PICRUSt2 predicted that hibernation-associated oral taxa were enriched in fatty acid β-oxidation pathway genes, paralleling the host’s metabolic switch from carbohydrate to lipid catabolism during torpor. Longitudinal tracking of 80 recaptured individuals over 2–3 years confirmed predominantly transient carriage, supporting seasonal environmental acquisition rather than chronic colonisation.