Livestock exposure, seasonal diet shifts, host individual and time correlate with wild African savannah elephant gut microbiome diversity

Authors: PARKER, JENNA - San Diego Zoo; WILLIAMS, CANDACE - San Diego Zoo; Deel, Heather; LITITIYA, DAVID - Save The Elephants; GOLDENBERG, SHIFRA - San Diego Zoo; SUKUNA, DAVID - Save The Elephants; D'AMMANDO, GIACOMO - Save The Elephants; DABALLEN, DAVID - Save The Elephants; OWEN, MEGAN - San Diego Zoo; TUBBS, CHRISTOPHER - San Diego Zoo; EZENWA, VANESSA - Yale University; MULINDI, SHARON - Kenya Wildlife Service; WITTEMYER, GEORGE - Colorado State University

Submitted to: Royal Society Open Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2026
Publication Date: 4/8/2026
Citation: Parker, J.M., Williams, C.L., Deel, H.L., Lititiya, D., Goldenberg, S.Z., Sukuna, D.A., D'Ammando, G., Daballen, D., Owen, M., Tubbs, C.W., Ezenwa, V., Mulindi, S.R., Wittemyer, G. 2026. Livestock exposure, seasonal diet shifts, host individual and time correlate with wild African savannah elephant gut microbiome diversity. Royal Society Open Science. 13(4). Article e251569. https://doi.org/10.1098/rsos.251569.
DOI: https://doi.org/10.1098/rsos.251569

Interpretive Summary: The bacterial communities of elephant guts could be important for their health and behavior, but the mechanisms of this are unknown. It is possible that factors including age, captivity, diet, season of the year, differences in habitat, and the presence of livestock are influential to the elephant gut microbiome, but it is unknown whether and how this can affect elephant health. To begin to address these uncertainties, dung samples were collected over 13 months from African savanna elephants who are part of a long-term monitoring project in the Samburu and Buffalo Springs National Reserves of Kenya. After characterization of the bacterial communities, it was shown that there were fluctuations in some bacterial species over time. Additionally, the presence and abundance of livestock changed the composition of the elephant gut bacterial communities. The study also showed that young elephant calves had different gut bacterial communities than older elephants. This study warrants further investigation into how elephant surroundings affect their microbiome, and whether this is concerning for their health and conservation.

Technical Abstract: Longitudinal studies of wildlife gut microbiomes are important to understanding the impact of changing ecosystems on host-associated microbial communities. We collected dung samples over 13 months from known wild African savanna elephants (Loxodonta africana) who are the subjects of a long-term monitoring project in the Samburu and Buffalo Springs National Reserves of Kenya. We then used 16S rRNA sequencing to 1) characterize the core gut microbiome of the sampled elephants and compare it to that of wild African savanna elephants in another study, 2) assess changes in individuals’ gut microbiomes over time, and 3) determine whether factors at the host-level (individual, age, sex); community-level (degree of livestock exposure); and ecosystem-level (seasonal changes causing dietary shifts from browse to grass) affect elephant gut microbiomes. We found considerable overlap among taxa in the core microbiome of the wild elephants we sampled and those of another study. There were regular fluctuations in microbial genera such as Oribacterium and Enterococcus over time. Seasonal dietary shifts to grazing were associated with decreased alpha diversity and altered community composition compared to periods dominated by browsing. Additionally, the gut microbiome communities of elephant calves were distinct from those of older elephants, with implications for rehabilitating young elephant orphans. Most notably, we found increased abundance of livestock correlated with decreased alpha diversity and altered community composition of the elephants’ gut microbiomes. Greater livestock numbers were associated with increases in genera such as Methanobrevibacter, a genus prevalent in livestock rumen and feces, and decreases in genera such as Roseburia, which is known as beneficial to human health. Our findings suggest the need for more research into how human activities affect wild microbiomes, and whether this is concerning for health and conserving biodiversity.