Abstract

Background: Human-driven environmental changes can disrupt wildlife habitats, forcing animals to adapt to fragmented or degraded ecosystems. In some cases, this leads to increased proximity between wildlife and human populations, heightening the risk of pathogen spillover. Bats, as key ecological players, are particularly sensitive to such disturbances. While some species decline in heavily altered environments, others adapt and thrive near human settlements, increasing the likelihood of encounters. Given that bats can host a wide range of zoonotic pathogens, this adaptive behavior raises important public health concerns. Despite their ecological significance and their role in zoonotic disease dynamics, the gut eukaryotes communities associated with bats remain less studied. Methods: This study focused on the Valparaíso Myotis (Myotis arescens), an insectivorous bat species endemic to central Chile that is significantly impacted by anthropogenic deforestation and habitat fragmentation. We characterized the gut eukaryotic communities of M. arescens through fecal sample analysis. Targeted microbial groups included fungi, metazoan parasites, and protists. High-throughput sequencing was employed to assess gut eukaryotes diversity, and beta diversity analysis was conducted to explore clustering patterns in relation to environmental variables, such as vegetation cover and land use types. Results: Our analyses revealed that the gut eukaryotic community of M. arescens consistently included taxa from the Apicomplexa, Ascomycota, and Basidiomycota phyla, with Apicomplexa being the most abundant. Beta diversity analysis showed distinct clustering by sampling location, with the percentage of native vegetation identified as the primary factor shaping gut eukaryotic community structure. Other influential variables included the presence of annual crops, orchards, water bodies, and urban areas. Notably, a high abundance of Apicomplexa—particularly amplicon sequence variants (ASVs) related to the genus Eimeria—was detected in bat feces across sites with varying degrees of anthropogenic disturbance. Conclusions: This study highlights the significant role of native vegetation in shaping the eukaryotic gut community of M. arescens, suggesting that gut eukaryotic composition can serve as a bioindicator of bat health and habitat quality. Among the dominant taxa, members of the genus Eimeria were frequently detected across sites with varying degrees of anthropogenic disturbance. Although Eimeria is generally considered host-specific and not zoonotic, its high prevalence in bat gut communities points to the need for further research into its ecological role and potential implications for wildlife health. Overall, these findings underscore the importance of conserving native habitats to maintain ecosystem integrity and support healthy bat populations. © 2025 Ramírez-Fernández et al