Data corresponding to publication titled "Livestock exposure, seasonal diet shifts, and age influence wild African savanna elephant gut microbiomes"

Longitudinal studies of wildlife gut microbiomes are important for understanding the impact of ecosystem dynamics and changes on host-associated microbial communities. We repeatedly collected dung samples 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 over 13 months. We then used 16S rRNA sequencing to 1) characterize the core gut microbiome of the sampled elephants and compare it to that reported for 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 in a different ecosystem. There were regular fluctuations in microbial genera such as Oribacterium and Enterococcus over time. Seasonal (late wet season) 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 the implications of such effects on wildlife health and biodiversity conservation.