Heritage Cases

The human gastrointestinal tract (GI) harbours a dynamic population of bacteria, archaea, fungi, protozoa and viruses; the intestinal microbiota. This collection of microorganisms, comprising the human intestinal microbiome (IM) (1) performs critical functions in digestion, development, behaviour and immunity (2, 3). Modifications of the core IM composition (dysbiosis) have been associated with the pathogenesis of inflammatory diseases and infections (3, 4), including autoimmune and allergic diseases, obesity, inflammatory bowel disease and diabetes (5). Despite its clinical importance, the factors that contribute to changes in IM taxonomic composition and functionality, are not entirely understood (6, 7). This is attributed to the fact that most of what is known about the human IM, is based on contemporary industrialised and ‘traditional’ human societies (8-10). In evolutionary terms, our species have subsisted by hunting and gathering for >90% of our existence (11). Evidence derived from the analyses of the IMs of traditional societies, including the Tanzanian Hadza hunter-gatherers (8), the Venezuelan Yanomami Amerindians (5), the BaAka Pygmies in the Central African Republic (12) and the Arctic Inuit (13) are thus widely viewed as representing ‘snapshots’ of ancient human IM composition. However, as exposure to Western diets, medicines and microbes cannot be excluded, one must be cautious about the use of these ethnographic cohorts as proxies for prehistoric human IMs (14). The transformation of the IMs of present-day humans to their current ‘modernised’ state commenced millennia ago, with the advent of the Neolithic, which, at c. 12,000 years ago (kya), resulted in the first major human dietary transition (15). But precisely how our IMs changed following the advent of the Neolithic, and the Industrial Revolution after c. AD 1760, remains ambiguous (16-18). In this regard, the analyses of ancient human IMs provide a unique view into the co-evolution of microbes and human hosts, host microbial ecology and changing human IM-related health states through time. Despite the fact that African populations are not underrepresented in studies concerning ‘traditional’ human IMs (8, 12), there is, currently, no information concerning the taxonomy and metabolic capacity of ancestral (i.e., archaeologically-derived) African IM composition. Accordingly, and to gain insight into the ancient African human IM, and the prehistoric incidence of intestinal parasites, pathogenic microbes and antibiotic resistance genes, we aim to apply the recently-devised multi-proxy analytical protocol (including shotgun metagenome sequencing, SEM analyses, intestinal parasitic analyses, 14C dating, and isotope analyses) to these ancient samples. This study, currently under review at Science Advances, involved the comparison with ancient (Ötzi), traditional (Hadza and Malawian) and contemporary ‘Western’ (Italian) IM datasets. The results indicate that the IM of the BRS individual represents a unique taxonomic and metabolic configuration observed in neither contemporary African, nor European, populations. The extraction and analyses of aDNA from African prehistoric samples is challenging, primarily because no suitable aDNA extraction facilities currently exist in Africa. Globally, there are more than 62 laboratories dedicated to aDNA research. Given the fact that sub-Saharan Africa should form the very focus of aDNA research it is curious that, excluding Antarctica, Africa is the only continent on which no aDNA dedicated facilities exist. Although the Centre for Microbial Ecology and Genomics (CMEG) has mastered the extraction of environmental DNA from soils derived from the Namib Desert and Antarctica, archaeological sample processing must take place at a suitable international facility. Accordingly, appropriate collaborative analytical arrangements have been made with the Centre for GeoGenetics (CGG) (Genetic Identification and Discovery Group (GID)) at the Natural History Museum in Copenhagen, Denmark. The five palaeo-faecal specimens will therefore be exported to Denmark and analyse in the ‘clean’ laboratory fascilities at the CGG.