Ecological filtering governs bacterial community assembly and zoonotic genus distribution across body sites, host species, and seasonal life-history stages in insectivorous bats

Bats harbor diverse zoonotic bacteria, yet whether pathogen carriage reflects stable host–microbe associations or transient environmental exposure remains unresolved. We propose that bat bacterial communities are shaped by three axes of ecological filtering: body site defines the microbial niche, host species imposes ecological and phylogenetic filtering, and seasonal life-history transitions alter exposure regimes. We tested four predictions: (1) each body site would harbor a distinct community reflecting its ecological role; (2) host species would show different bacterial profiles predictable from roosting ecology and life-history traits; (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 16S rRNA gene amplicon sequencing of 2,747 oral, skin, and 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 and zoonotic transmission route: stool harbored 10-fold higher pathogen loads than oral samples, dominated by Helicobacter and Chlamydia , while skin carried vector-borne Rickettsia and Bartonella . Host species structured oral communities most strongly (PERMANOVA R² = 0.295), with species-specific pathogen profiles consistent with ecological trait differences. Hibernation microbiomes were enriched in lipid catabolism pathways consistent with host torpor physiology. Longitudinal tracking of 80 recaptured individuals over 2–3 years confirmed predominantly transient carriage, supporting seasonal environmental acquisition rather than chronic colonization.