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ORIGINAL RESEARCH article

Front. Vet. Sci.
Sec. Animal Behavior and Welfare
Volume 12 - 2025 | doi: 10.3389/fvets.2025.1496946
This article is part of the Research Topic Advances in Methods of Biochemical Assessment and Diagnosis of Animal Welfare in Wildlife View all 6 articles

Use of fecal microbiome to understand the impact of housing conditions on metabolic stress responses in farmed saltwater crocodiles (Crocodylus porosus)

Provisionally accepted
David John Beale David John Beale 1Thao Nguyen Thao Nguyen 1Tim Dyall Tim Dyall 2Jodie van de Kamp Jodie van de Kamp 1Andrew Bissett Andrew Bissett 2Leisha Hewitt Leisha Hewitt 3Alison Small Alison Small 2*
  • 1 Environment, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
  • 2 Department of Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia
  • 3 Dr Leisha Hewitt Livestock Welfare., Franklin, Tasmania, Australia

The final, formatted version of the article will be published soon.

    Understanding the impact of housing conditions on the stress responses in farmed saltwater crocodiles (Crocodylus porosus) is crucial for optimizing welfare and management practices. This study employed a multi-omics methodology, combining targeted and untargeted LC-MS for metabolite, lipid, and hormone profiling with 16S rRNA gene sequencing for microbiome analysis, to compare stress responses and changes in faecal samples of crocodiles housed in single versus group pens. Metabolic responses to a startle test were evaluated through multivariate analysis, and changes post-stress were examined. A total of 564 metabolic features were identified. Of these, 15 metabolites were linked to the cortisol biosynthesis pathway. Metabolite origin analysis showed that 128 metabolites originated from the host, 151 from the microbiota, and 400 remained unmatched. No significant differences in faecal corticosterone levels were observed between single and group pens. However, metabolic profiling revealed distinct differences in stress responses: single pen crocodiles exhibited downregulation of certain compounds and upregulation of others, affecting pyrimidine and purine metabolism pathways when compared to grouped pen crocodiles, linked to altering energy associated induced stress. Additionally, faecal microbiome analysis indicated increased Firmicutes:Bacteroides (F:B) ratio in group-housed animals, suggesting greater stress. The study highlights that while traditional stress indicators like corticosterone levels may not differ significantly between housing conditions, metabolic and microbiome analyses provide deeper insights into stress responses. Single pens are associated with less metabolic disruption and potentially better health outcomes compared to group pens. These findings underscore the value of faecal microbiome and metabolomics in assessing animal welfare in farmed crocodiles.

    Keywords: Metabolomics, bacterial community sequencing, Corticosterone, Animal Welfare, captivity, Reptiles

    Received: 16 Sep 2024; Accepted: 13 Jan 2025.

    Copyright: © 2025 Beale, Nguyen, Dyall, van de Kamp, Bissett, Hewitt and Small. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Alison Small, Department of Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.