Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

Riaan F Rifkin , Surendra Vikram , Jean-Baptiste Ramond , Alba Rey-Iglesia , Tina B Brand , Guillaume E Porraz (1, 2) , Aurore Val , Grant Hall , Stephan Woodborne , Matthieu Le Bailly , Marnie Potgieter , Simon J Underdown , Jessica E Koopman , Don A Cowan , Yves van de Peer , Eske Willerslev , Anders J Hansen

1 CNRS - Centre National de la Recherche Scientifique
2 LAMPEA - Laboratoire méditerranéen de préhistoire Europe-Afrique

Background: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. Results: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.

Mots clés: Ancient DNA; Human evolution; Molecular ecology; Intestinal microbiome; Taxonomic composition; Metabolic capacity

Domaines: Sciences de l'Homme et Société

Riaan F Rifkin, Surendra Vikram, Jean-Baptiste Ramond, Alba Rey-Iglesia, Tina B Brand, et al.. Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome. Microbiome, 2020, 8, ⟨10.1186/s40168-020-00832-x⟩. ⟨hal-03094233⟩