Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?

The intestinal microbiota, an invisible organ supporting a host’s
survival, has essential roles in metabolism, immunity, growth, and
development. Since intestinal microbiota influences a host’s biology,
application of such data to wildlife conservation has gained interest.
There are standard protocols for studying the human intestinal microbiota,
but no equivalent for wildlife. A major challenge is sampling the
intestinal microbiota in an effective, unbiased way. Fecal samples are a
popular proxy for intestinal microbiota because collection is
non-invasive, convenient, and allows for longitudinal sampling. Yet, it is
unclear whether the fecal microbiota is representative of the intestinal
microbiota. In amphibians, research on sampling methodology is limited. In
this study, we characterize and compare microbiota (small intestine, large
intestine, feces) of two Hong Kong stream-dwelling frog species: Lesser
Spiny Frog (Quasipaa exilispinosa), and Hong Kong Cascade Frog (Amolops
hongkongensis). We found that both species have similar dominant phyla and
families, but diverge in terms of the dominant genera. Next, we assess the
performance of fecal microbiota in representing the intestinal microbiota
in these two species. We found that (1) microbiota of small and large
intestine differs significantly, (2) feces are not an appropriate proxy of
both intestinal sections, and (3) a set of microbial taxa significantly
differs between sample types. Our cautions equating fecal and intestinal
microbiota. Sampling feces can avoid sacrifice of an animal, but
researchers should avoid over-extrapolation and interpret results
carefully.