Composición del microbioma bacteriano de murciélagos de la familia Phyllostomidae en Ecuador

Abstract

Bats are the second most numerous and diverse group of mammals after rodents. They perform key ecological functions essential for ecosystem balance and maintenance, but they also act as reservoirs for various bacterial pathogens. In Ecuador, 114 phyllostomid species have been recorded, occupying diverse dietary niches. However, despite advances in ecological, morphological, and phylogenetic studies, major gaps remain regarding their microbiome composition and its relationship to the emergence of zoonotic diseases. In this study, oral swab samples from six phyllostomid species (Carollia brevicauda, C. castanea, C. perspicillata, Sturnira ludovici, Rhinophylla alethina, and Artibeus ravus) were analyzed using nanopore sequencing of genomic RNA. A diverse bacterial microbiome was observed, with C. brevicauda and C. castanea showing the highest proportions of classified reads and the greatest microbial loads. The phylum Proteobacteria, particularly Gammaproteobacteria, predominated across all species, with Enterobacterales as the dominant order. Notably, Escherichia coli was the core and most frequent component of the microbiome. Other clinically relevant genera, including Ralstonia, Bordetella, Shigella, Salmonella, and Pseudomonas, appeared sporadically and were detected at low frequency. In this context, focusing analyses on the proteobacterial core is important for investigating digestive and immunological functions, while maintaining ongoing surveillance due to the presence of clinically relevant taxa. Metagenomic approaches provide a useful roadmap to deepen understanding of the function, stability, and zoonotic risk of the microbiome in Neotropical bats.