A cross-families evaluation of using fecal samples as a method to study the amphibian gut microbiome

The gut microbiota plays an important role in animals. Fecal samples are often used to study the gut microbiota because they are convenient to collect, allow for longitudinal sampling, and often necessary when studying rare and endangered species. In this study, we evaluate the effectiveness of using fecal samples by characterizing and comparing the microbiota of feces and the gut (small intestine mucosa, large intestine mucosa) for representatives of seven amphibian families. This includes the first data from a salamander species. Additionally, we compared fecal samples before (pre-feces) and after egestion to understand the microbiota change when there is a delay in collection and preservation (< 24 h). We find that fecal samples significantly differ from both small intestine and large intestine mucosal samples largely based on abundance. The relationship between fecal and gut microbiota differs slightly between species, indicating an influence of host identity. Also, the microbiota of pre-feces and feces significantly differ, indicating a measurable change can occur less than 24 h after egestion. These results help us better understand the relationship between gut and fecal microbiota for amphibians, as well as guide the fieldwork design and data interpretation of future studies.