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

Abstract Longitudinal studies of wildlife gut microbiomes are important for understanding the impact of ecosystem dynamics on host-associated microbial communities. We repeatedly collected dung samples over 13 months from known wild African savannah 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: (i) characterize the core gut microbiome of the sampled elephants and compare it to that reported for wild African savannah elephants in another study, and (ii) 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. Seasonal dietary shifts to grazing were associated with slightly decreased alpha diversity, as well as altered community composition, compared with periods dominated by browsing. Additionally, alpha diversity and community composition were distinct according to the individual. Time showed an interesting effect; over the course of the study, the elephant gut microbiome community composition shifted along a continuum, potentially illustrating the rapid pace at which ecological processes happen within microbial communities. Most notably, we found that increased abundance of livestock altered the 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 faeces, 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.