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.

Autor:	Rifkin RF; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. riaanrifkin@gmail.com.; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK. riaanrifkin@gmail.com., Vikram S; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa., Ramond JB; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.; Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile., Rey-Iglesia A; Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark., Brand TB; Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark., Porraz G; CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre, Paris, France.; Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa., Val A; Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa.; Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany., Hall G; Mammal Research Institute, University of Pretoria, Hatfield, South Africa., Woodborne S; Mammal Research Institute, University of Pretoria, Hatfield, South Africa.; iThemba LABS, Braamfontein Johannesburg, South Africa., Le Bailly M; University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France., Potgieter M; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa., Underdown SJ; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK., Koopman JE; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa., Cowan DA; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa., Van de Peer Y; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.; VIB Centre for Plant Systems Biology, Ghent, Belgium.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium., Willerslev E; Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark.; GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.; Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK., Hansen AJ; Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark. ajhansen@snm.ku.dk.
Jazyk:	angličtina
Zdroj:	Microbiome [Microbiome] 2020 May 06; Vol. 8 (1), pp. 62. Date of Electronic Publication: 2020 May 06.
DOI:	10.1186/s40168-020-00832-x
Abstrakt:	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.
Databáze:	MEDLINE
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