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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

  • Rifkin, Riaan F.1, 2
  • Vikram, Surendra1
  • Ramond, Jean-Baptiste1, 2, 3
  • Rey-Iglesia, Alba4
  • Brand, Tina B.4
  • Porraz, Guillaume5, 6
  • Val, Aurore6, 7
  • Hall, Grant1
  • Woodborne, Stephan1, 8
  • Le Bailly, Matthieu9
  • Potgieter, Marnie1
  • Underdown, Simon J.1, 2
  • Koopman, Jessica E.1
  • Cowan, Don A.1
  • Van de Peer, Yves1, 10, 11
  • Willerslev, Eske4, 12, 13
  • Hansen, Anders J.4
  • 1 University of Pretoria, Hatfield, South Africa , Hatfield (South Africa)
  • 2 Oxford Brookes University, Oxford, UK , Oxford (United Kingdom)
  • 3 Pontificia Universidad Católica de Chile, Santiago, Chile , Santiago (Chile)
  • 4 University of Copenhagen, Hatfield, Denmark , Hatfield (Denmark)
  • 5 Université Paris-Nanterre, Paris, France , Paris (France)
  • 6 University of the Witwatersrand, Braamfontein Johannesburg, South Africa , Braamfontein Johannesburg (South Africa)
  • 7 University of Tübingen, Tübingen, Germany , Tübingen (Germany)
  • 8 iThemba LABS, Braamfontein Johannesburg, South Africa , Braamfontein Johannesburg (South Africa)
  • 9 University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France , Besancon (France)
  • 10 VIB Centre for Plant Systems Biology, Ghent, Belgium , Ghent (Belgium)
  • 11 Ghent University, Ghent, Belgium , Ghent (Belgium)
  • 12 University of Cambridge, Cambridge, UK , Cambridge (United Kingdom)
  • 13 Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK , Cambridge (United Kingdom)
Published Article
Springer (Biomed Central Ltd.)
Publication Date
May 06, 2020
DOI: 10.1186/s40168-020-00832-x
Springer Nature


BackgroundThe 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.MethodsFollowing 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.ResultsOur 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.ConclusionsOur 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.

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