Species identity and capture locality strongly shape the bat organ microbiome: a 16S rRNA survey across internal tissues

Bats host diverse microbial communities, yet most studies have focused on gut and skin, leaving organ-specific microbiomes poorly understood. We characterized bacterial communities in heart, liver, kidney, and spleen tissues from Neotropical bats to assess the influence of organ type, host species, sex, and locality on microbial community composition. Across 234 samples, we identified 37 bacterial phyla and 844 genera, with Firmicutes, Proteobacteria, and Bacteroidota dominating. While Staphylococcus was most abundant overall, organ-level differences were descriptive rather than statistically supported: Staphylococcus was frequent in heart, Mycoplasma in kidney and liver, and Bartonella in spleen. Alpha diversity did not vary among organs or sexes, but beta diversity was significantly structured by host species and locality, with sex exerting a weaker effect. These findings indicate that microbiome composition is shaped more by host and environment than by organ type, and that organ-specific bacterial signals should be interpreted cautiously, as they may reflect ecological variation, physiological function, or sampling factors rather than consistent tissue-level differences. Our results emphasize the need for multi-organ, multi-locality approaches to fully capture bat-associated microbial diversity and to explore the potential functional roles of key taxa in host health, disease, and conservation.