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 Porraz,
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
Affiliations
Riaan F. Rifkin
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Surendra Vikram
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Jean-Baptiste Ramond
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Alba Rey-Iglesia
Centre for GeoGenetics, GLOBE Institute, University of Copenhagen
Tina B. Brand
Centre for GeoGenetics, GLOBE Institute, University of Copenhagen
Guillaume Porraz
CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre
Aurore Val
Evolutionary Studies Institute, University of the Witwatersrand
Grant Hall
Mammal Research Institute, University of Pretoria
Stephan Woodborne
Mammal Research Institute, University of Pretoria
Matthieu Le Bailly
University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment
Marnie Potgieter
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Simon J. Underdown
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Jessica E. Koopman
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Don A. Cowan
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Yves Van de Peer
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria
Eske Willerslev
Centre for GeoGenetics, GLOBE Institute, University of Copenhagen
Anders J. Hansen
Centre for GeoGenetics, GLOBE Institute, University of Copenhagen
Abstract 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. Conclusions Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.
