Molecular epidemiology of Eimeria spp. parasites and the faecal microbiome of Indiana bats (Myotis sodalis): a non-invasive, multiplex metabarcode survey of an endangered species

Assessing individual and population health in endangered wildlife poses unique challenges due to the lack of an adequate baseline and ethical constraints on invasive sampling. For endangered bats, minimally invasive samples like guano can often be the ethical and technical limit for studies of pathogens and the microbiome. In this study, we use multiplex metabarcode sequencing to describe the faecal microbiome and parasites of 56 Indiana bats (<i>Myotis sodalis</i>). We show evidence of a high prevalence of <i>Eimeria</i> spp. protozoan parasite and characterize associations between infection and changes to the faecal microbiome. We identify a strong and significant enrichment of <i>Clostridium</i> species in <i>Eimeria</i>-positive bats, including isolates related to <i>Clostridium perfringens</i>.