Temporal change in the Namibian Ju|’hoansi intestinal microbiome

Abstract

The microbes which reside in our digestive tract comprise the human intestinal microbiome (IM). Many historical events have influenced the composition of our IM, such as the invention of cooking, the advent of farming and the industrial revolution. Although ancestral IMs could provide insight into the evolution of the human IM, pristine ancestral hunter-gatherer IM samples are near-impossible to acquire. Alternatively, studying contemporary hunter-gatherers might allow us to gain insight into the pre-Industrial human IM. The Ju|’hoansi hunter-gatherers of Namibia are in transition to an increasingly Western lifestyle, providing an opportunity to study the effects of westernization on the human IM. Various factors impact our IM, including diet and our interaction with the environment. In this regard, the influence of drinking water on our IM is largely unknown and necessitates further exploration. This study aims to detect temporal changes in the Ju|’hoansi IM, while also exploring the impact of water sources on their IM, and the levels of the IM volatile fatty acids. In order to do so, faecal samples were collected and subsequently sequenced from a total cohort of 40 participants taken 2 years apart in 2019 and 2021. Based on our study, we were able to identify changes in the composition of microbial communities over a 2-year period. Statistically significant differences were found in the taxonomic composition of the Ju|’hoansi IM after 2 years. Within each year, the village of residency of each participant proved significant. The richness of the Ju|’hoansi IM did not change during this time period and still reflected that of a traditional hunter-gatherer IM. From baseline to follow-up, numerous bacterial genera differentially decreased, and the core microbiome significantly decreased in species. Only one volatile fatty acid was found to have significant correlations with the Ju|’hoansi IM, decanoic acid. The nitrate concentration, Langelier saturation index and the total oxidised nitrogen in the water sources impacted the IM composition of the Ju|’hoansi, causing differentially abundant genera. Chapter 2 is a draft manuscript that will be sent to Cell Press Community Review intended for publication a in Cell Press Journal.