Taxonomic and functional profiling of bat guano microbiota from hiking trail-associated tunnels: a potential risk for human health?

Metagenomic studies have significantly expanded our understanding of the bacterial communities present in bat guano. Several studies have reported the presence of common human pathogenic bacteria, including enteric foodborne species, zoonotic pathogens, unusual Gram-negative bacteria, and multidrug-resistant strains. These findings have reinforced the perception of bat guano as a potential reservoir of pathogens. Despite this, research conducted in sites with frequent human contact remains limited. Caves and tunnels such as those along the Camino del Hierro in northeastern Spain represent environments with regular human exposure, making them areas of particular interest from a public health perspective. In this study, we conducted an extensive analysis of the guano microbiome during both the breeding season and hibernation period in bats inhabiting this touristic site, using shotgun metagenomics and a comprehensive bioinformatic pipeline. Our results revealed marked differences in the relative microbial composition across samples from fresh and desiccated bat guano. The most abundant viral order detected was Herpesvirales, while among bacterial genera, Bacillus, Burkholderia, Lactobacillus, Pseudomonas, Salmonella and Streptococcus were dominant. The presence of these taxa in the tunnels poses a potential risk not only to visitors but also to park staff who are regularly exposed to bat guano, particularly due to the presence of species associated with various human viral and bacterial diseases. No significant differences were observed in the overall abundance of detected organisms between seasons. However, distinct seasonal patterns emerged when analyzing metabolic pathways and virulence factors. During the breeding season, there was a notable predominance of metabolic pathways related to cell proliferation, along with virulence factors associated with strategies for surface attachment and biofilm formation. Overall, our findings highlight an underrecognized and unmonitored risk of pathogen transmission for both visitors and personnel at this tourist site, underscoring the need for increased awareness and further investigation into the health implications of human-bat interactions in such environments.