SREL Reprint #3892

African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique

Laura E. Peirson1,2, Erin A. McKenney3, Jessica R. Patterson4, James C. Beasley4, Stéphanie Périquet-Pearce5,6, Claudine Cloete7, Madeline H. Melton4, Brennan PetersonWood4, Rubén Portas8, Ortwin Aschenborn8, and Diana J. R. Lafferty1

1Wildlife Ecology and Conservation Science Laboratory, Department of Biology, Northern Michigan University, 1401 Presque Isle Ave., Marquette, MI 49855, USA
2Conservation Medicine, Smithsonian’s National Zoo and Conservation Biology Institute, Wildlife Health Sciences, Front Royal, VA 22630, USA
3Department of Applied Ecology, North Carolina State University, Raleigh, NC 27607, USA
4Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Resources, University of Georgia, Aiken, SC 29802, USA
5Ongava Research Centre, Windhoek, Namibia
6Panthera, NY, USA
7Etosha Ecological Institute, Etosha National Park, Windhoek, Namibia
8Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research of Berlin, Alfred-Kowalke St. 17, 10315 Berlin, Germany

Abstract: Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.

Keywords: Animal gut microbiome, African carnivore, Metagenomics, Bioinformatics, Microbiome techniques

SREL Reprint #3892

Peirson, L. E., E. A. McKenney, J. R. Patterson, J. C. Beasley, S. Périquet-Pearce, C. Cloete, M. H. Melton, B. PetersonWood, R. Portas, O. Aschenborn, and D. J. R. Lafferty. 2026. African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique. Animal Microbiome 8(59).

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).