Human–wildlife interfaces are increasingly recognized as critical zones for pathogen exchange, microbial adaptation, and emerging infectious disease risks. Among these interfaces, the close relationships between captive wildlife and their caretakers are particularly important yet remain understudied. Asian elephants (Elephas maximus) hold deep cultural, economic, and conservation significance across South and Southeast Asia, and many live in human-managed settings where daily interactions with mahouts create unique opportunities for bidirectional microbial transmission. Despite growing concern about respiratory pathogens affecting both elephants and people, the respiratory tract microbiome of elephants has never been comprehensively characterized, limiting our understanding of microbial sharing, potential zoonotic risks, and implications for conservation medicine.
This study represents the first effort to profile and compare the respiratory microbiomes of captive elephants and their human handlers in Chitwan National Park, Nepal. By analyzing nasal swab microbiota from elephants, their mahouts, and unrelated human controls, we identify distinct microbial community structures associated with close human–animal contact. Notably, elephants and their mahouts exhibited a higher degree of microbiome similarity to each other than to non-mahout human controls, suggesting that sustained proximity, shared environments, and daily caregiving activities facilitate microbial exchange.
A striking finding was the high abundance of Bacillaceae—including several genera commonly associated with environmental persistence and spore formation—in both elephants and mahouts, but not in unrelated humans. This pattern points to shared environmental exposures specific to the elephant–mahout interface. Additionally, we detected taxa potentially including ESKAPE-E bacteria, a group of clinically important and often multidrug-resistant pathogens. Their presence in either elephants or humans, even at low relative abundance, underscores the need for targeted surveillance and risk-aware management practices in captive wildlife systems.
Overall, our findings highlight the respiratory microbiome as a valuable lens for understanding human–elephant interactions, with important implications for One Health, conservation medicine, and the management of captive wildlife populations.