Body site, host species, and seasonal drivers of zoonotic bacterial distribution in Korean insectivorous bat microbiomes

Bats harbor diverse zoonotic bacteria, yet how pathogen carriage varies across body sites, host species, and seasons --- and whether individual bats maintain infections chronically --- remains largely unknown. We surveyed 2,747 oral, skin, and stool samples from eight insectivorous bat species across four seasons (2021–2024) in South Korea using 16S rRNA gene sequencing. Ten zoonotic genera were detected in 63.7% of samples. Feces harbored 10-fold higher pathogen loads than oral samples, dominated by Helicobacter and Chlamydia , while skin carried high levels of vector-borne Rickettsia and Bartonella . Three species posed distinct risks: Myotis macrodactylus stool contained Helicobacter at 14.4% relative abundance, Pipistrellus abramus --- a synanthropic species known to be house-dwelling --- carried extreme Rickettsia on skin (9.37%), and Miniopterus fuliginosus harbored the broadest pathogen diversity. Pathogen abundance peaked in summer and dropped sharply in winter, though Yersinia persisted during hibernation. Longitudinal tracking of 80 recaptured bats over 2–3 years showed that pathogen carriage was predominantly transient, indicating environmental acquisition each season rather than chronic colonization. Predicted metabolic profiles shifted between active and hibernation periods, with hibernation microbiomes enriched in lipid catabolism consistent with host torpor physiology. These results identify stool and skin as the primary transmission routes, pinpoint high-risk species and seasons, and demonstrate that population-level pathogen prevalence reflects ongoing environmental exposure --- findings directly relevant to wildlife disease surveillance and bat conservation management.