The taxonomic diversity of the Ju|'hoansi hunter-gatherer intestinal microbiome in Tsumkwe, Namibia

Abstract

The intestinal microbiome (IM) comprises all the microorganisms in the human gastro-intestinal tract, including bacteria, fungi, viruses, archaea and protozoans. Over millennia, these microorganisms have formed intimate relationships with the human host, providing the host with benefits such as optimal nutrient absorption and the priming of the immune system. The relationship between host and microbe has developed over at least 200,000 years of human evolutionary history, providing humanity with a means of faster, more flexible adaptation than their own genomes would allow. The advent of Westernisation has brought about many lifestyle changes, some of which are causing changes in IM community structure and function, which may have unforeseen and adverse consequences for human health. The IMs of traditional societies have been studied as examples of the “pre-Westernised” human IM, so that IM changes in response to Westernisation, and the consequences thereof, can be elucidated. In Chapter 1, some of the factors that have been found to impact the composition and function of the human IM, are discussed, as well as how various lifestyle factors differ between traditional and Western societies, leading to the differences in IM structure observed between these two societies. The bioinformatic and statistical approaches employed in microbiome studies are summarised and critically compared. Studies investigating changes in IM composition have either investigated the IM differences between traditional and Western populations or examined how IM composition changes in response to certain lifestyle factors, largely in a Western context. Furthermore, no IM data has been collected from traditional societies within southern Africa. Chapter 2 aims to fill this knowledge gap, through the analysis of 40 faecal samples derived from the Ju|’hoansi San/Bushman hunter-gatherers who reside in north-eastern Namibia. This community is in the process of Westernisation, presenting an opportunity to study the evolution of the IM from a traditional to a Western lifestyle. IM composition within the Ju|’hoansi community is also analysed with respect to 1) the ages of research participants, 2) their former use of antibiotic treatment for tuberculosis, 3) their biological sex, 4) whether diarrhoea is or had been experienced following the consumption of certain foods, 5) whether participants have ever experienced an intestinal infection, 6) their former or current use of malaria medication, 7) their exposure to local, regional and international travel, and 8) the villages of primary residency of each research participant. The Ju|’hoansi IM was comparable to those of other hunter-gatherer societies, being enriched for Prevotella, Blautia, Faecalibacterium, Succinivibrio and Treponema. No significant differences were found in terms of any lifestyle v factors, except for village of primary residence. Chapter 2 aims to serve as a baseline characterisation of the Ju|’hoansi IM from which to conduct future research pertaining to the evolution of the IM during the process of Westernisation. Chapter 2 is written in the format of a draft article intended for publication in Cell Press Community Review. Finally, Chapter 3 provides a brief summary of the work carried out in this dissertation, addresses the limitations of the study, and offers insight into future research concerning the Ju|’hoansi IM.