Are fecal samples an appropriate proxy for amphibian intestinal microbiota?

Ivan P. Y. LAM, Jonathan FONG*

*Corresponding author for this work

Research output: Journal PublicationsJournal Article (refereed)peer-review


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 and allows for longitudinal sampling. Yet, it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In wildlife studies, research on sampling methodology is limited. In this study focusing on amphibians, we characterize and compare the 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 the microbiota of both species are similar at the level of phylum and family, but diverge at the level of genus. When we assessed the performance of fecal microbiota in representing the intestinal microbiota in these two species, we found that (1) the microbiota of small and large intestine differs significantly, (2) feces are not an appropriate proxy of either intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our findings raise caution equating fecal and intestinal microbiota in stream-dwelling frogs. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over-extrapolation and interpret results carefully.
Original languageEnglish
Article numbere10862
JournalEcology and Evolution
Issue number2
Early online date31 Jan 2024
Publication statusPublished - Feb 2024

Bibliographical note

We would like to thank a team of dedicated laboratory members from the Science Unit, Lingnan University for assistance in sampling collection—Dr. Itzue CAVIEDES-SOLIS, Brian KATONA, TAN Kai Teck Desmond, LEE Wing-Him Henry, Julia LEUNG, FOK Wing Lam Amy, and CHAN Man Ho Henry. We also thank Dr. SIN Yung Wa Simon, POON Shui Kei Emily, and CHAN Wing Sing Vincent from The University of Hong Kong for advice in laboratory work and analysis. Finally, we would like to thank our administrative staff, Mrs. CHAN Mei Yan, for help in facilitating this work.

© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

Publisher Copyright:
© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.


  • amphibian microbiome
  • fecal microbiota
  • gut microbiota
  • non-invasive sampling
  • wildlife conservation


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