Livestock may be rewriting elephants' gut microbiomes in Kenya's protected reserves

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Sharing habitat with livestock is changing elephants' gut bacteria in ways that could be harmful to their health, according to new research conducted by San Diego Zoo Wildlife Alliance in collaboration with Save the Elephants. The study, appearing in Royal Society Open Science, tracked known individual elephants in the Samburu and Buffalo Springs National Reserves in Northern Kenya and found that when livestock numbers increased in the reserves, the elephants' gut microbiomes shifted significantly. Microbes commonly found in livestock became more abundant in elephant guts, while beneficial microbes decreased.

"Our analysis revealed that the elephants' gut microbiomes changed when they shared the reserves with more livestock. We observed increases in the amount of the methane-producing genus Methanobrevibacter of Kingdom Archaea, known as prevalent in livestock feces, and decreases in bacterial genera like Roseburia that are known as beneficial to human health," said Jenna Parker, Assistant Professor of Conservation Biology at Lake Superior State University and lead author of the study.

"We are not sure if these changes are harmful, but they are concerning because changes in gut microbiomes often signal health problems," Parker added.

These findings have significance beyond elephant conservation. Livestock now comprise the majority of Earth's mammalian biomass, meaning livestock-associated microbiome changes could be occurring in wildlife populations worldwide—an environmental impact that has largely gone unnoticed. This is therefore a significant step forward in the discovery of how other species are being affected by the presence of livestock across shared landscapes.

"The health of wildlife, livestock, and humans are interconnected, and more work is needed to better understand how each of these systems impacts the health of the others," said Candace Williams, previously a Senior Researcher at San Diego Zoo Wildlife Alliance, and currently Technical Services Manager, Oxford Nanopore Technologies.

The research was conducted against a backdrop of increasing pressures in the reserves, where livestock numbers fluctuate with seasonal changes and intensifying drought conditions driven by climate change.

"The often negative impacts on wildlife populations and their refuges from human encroachment are well documented, but this study highlights that previously unrecognized, more subtle impacts also occur. Holistic understanding of the interplay between wildlife, humans and their livestock is a critical area of investigation and can benefit all actors in these systems," stated George Wittemyer, Chief Scientist for Save the Elephants and a professor at Colorado State University.

Publication details

Jenna Marie Parker et al, Livestock exposure, seasonal diet shifts, host individual and time correlate with wild African savannah elephant gut microbiome diversity, Royal Society Open Science (2026). DOI: 10.1098/rsos.251569

Journal information: Royal Society Open Science

Key concepts

ElephantsHost Microbial InteractionsGastrointestinal Microbiome

Provided by San Diego Zoo Wildlife Alliance