A comparison of nonlethal sampling methods for amphibian gut microbiome analyses

Jia Zhou, Tiffanie Maree Nelson, Carlos Rodriguez Lopez, Roshmi Rekha Sarma, Shao Jia Zhou, Lee Ann Rollins

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.

Original languageEnglish
Pages (from-to)844-855
Number of pages12
JournalMolecular Ecology Resources
Issue number4
StatePublished - Jul 1 2020

Bibliographical note

Funding Information:
This project was supported by The Holsworth Wildlife Research Endowment (Ecological Society of Australia) and Adelaide Graduate Research Scholarship (University of Adelaide) to J.Z., and a Scientia Fellowship to L.A.R. (UNSW). Animals were provided from an experiment funded through an ARC Discovery grant awarded to collaborator Richard Shine and L.A.R. (DP160102991). We would like to thank our colleagues from the University of Adelaide, University of New South Wales, Macquarie University, and others who provided insights and expertise that greatly assisted the research.

Publisher Copyright:
© 2020 John Wiley & Sons Ltd


  • 16S rRNA
  • Illumina
  • amphibian
  • cane toad
  • gut microbiota

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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