Asian Pacific Journal of Tropical Biomedicine
Ecological and biological determinants of fecal bacterial diversity in bats across four continents and phylogenetic screening for pathogen‑affiliated bacterial lineages
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Abstract:
Objective: To characterize the diversity and composition of bacterial communities in bat fecal samples under distinct ecological and biological conditions and to investigate the phylogenetic relationships of selected bacterial lineages with clinically relevant taxa. Methods: Publicly available 16S rRNA gene sequencing data from 194 fecal samples covering 20 bat species from South America, Europe, Asia, and Africa were reanalyzed using DADA2 and the SILVA database. Alpha and beta diversity, taxonomic composition, and community differences according to host diet, habitat, sex, and geographic region were evaluated. Phylogenetic analyses were performed on amplicon sequence variants assigned to Pseudomonas, Staphylococcus, Clostridium, and Streptococcus. Results: A total of 3 778 110 reads passed quality filtering, representing 123 bacterial families and 203 genera. Proteobacteria (57%) and Firmicutes (40%) predominated, with Pseudomonas, Staphylococcus, and Carnobacterium among the most abundant genera. Microbial composition and diversity varied significantly according to diet, habitat, sex, and geographic region. Frugivorous bats showed the highest alpha diversity, whereas piscivorous bats showed the lowest, and Rousettus aegyptiacus exhibited the greatest bacterial richness. Bats inhabiting forest and cave habitats possessed higher bacterial richness, while communities from freshwater and coastal aquatic habitats were less diverse. Males showed higher relative abundance of Staphylococcus, whereas females were enriched in Pseudomonas. Distinct taxonomic signatures were linked to dietary guilds. Insectivorous bats were enriched in Gammaproteobacteria, Pseudomonadales, and Moraxellaceae; frugivorous bats were enriched in Lactobacillales and Streptococcus; and piscivorous bats were enriched in Firmicutes, including Staphylococcaceae and Clostridium. Sixty-two genera containing species with recognized pathogenic potential were identified. Phylogenetic analyses revealed amplicon sequence variants affiliated with Pseudomonas, Clostridium, and Streptococcus clustering with or related to clinically relevant lineages, such as Clostridioides difficile and Streptococcus pneumoniae. Conclusions: Bat fecal bacterial communities are highly diverse and vary significantly under different ecological and biological conditions. Detection of bacterial genera containing clinically relevant species and the phylogenetic proximity of selected amplicon sequence variants to known pathogens support further genomic, functional, and epidemiological studies to clarify their pathogenic and zoonotic relevance.
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Project Supported:
the Fundacao Amazonia de Amparo a Estudos e Pesquisas (FAPESPA, grant number 2014/15440- 7); the Sao Paulo Research Foundation (FAPESP, grant number 13/08135-2); the National Council for Scientific and Technological Development (CNPq, grant numbers 421516/2025-9, PS); and the Coordination for the Improvement of Higher Education Personnel (CAPES, Finance Code 001).
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