The study of gut microbiome in both animals and humans living in proximity has proven crucial in understanding their coevolution, the potential for microbial transfer and the dynamics behind various diseases. Similarly, the investigation of respiratory microbiomes has been gaining popularity due to its significance and impact on respiratory health. Here, we use 16S rRNA metabarcoding to explore the respiratory microbiome of captive Asian elephants (Elephas maximus) and their mahouts (i.e., trainers and handlers) in Chitwan National Park (Nepal), with local villagers residing out of the protected area acting as control. Sputum samples were collected to characterize their bacterial composition, while its functional profile was inferred with PICRUSt2. Additionally, the occurrence of genera hosting potentially pathogenic ESKAPE-E species was evaluated. Our findings revealed high similarity in the bacterial and functional composition of the respiratory microbiome of elephants and mahouts, with Bacillota and Pseudomonadota emerging as the most abundant phyla across all host categories and the controls displaying the highest diversity. A striking difference was observed in relation to the family Bacillaceae that dominated the microbial composition of both mahouts and elephants but not controls. Genera hosting potentially pathogenic ESKAPE-E bacteria were found in all host categories, which underscores the need for in-depth analyses to identify the species involved. Our study delivers valuable insights in the respiratory microbial community of both Asian elephants and humans, thus laying the basis for further investigations on their diversity and function, unveiling their role in respiratory health of both host species.
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