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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

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, et al.
(2020) MICROBIOME. 8(1).
Author
Organization
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 (otzi) 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.
Keywords
Ancient DNA, Human evolution, Molecular ecology, Intestinal microbiome, Taxonomic composition, Metabolic capacity, KeyWords Plus:CHAIN CHLORINATED PARAFFINS, GUT MICROBIOTA, DNA, PATTERNS, DAMAGE, IMPACT, ENTEROTYPES, RESISTANCE, DIVERSITY, DYSBIOSIS

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Citation

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MLA
Rifkin, Riaan F., 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, vol. 8, no. 1, 2020, doi:10.1186/s40168-020-00832-x.
APA
Rifkin, R. F., Vikram, S., Ramond, J.-B., Rey-Iglesia, A., Brand, T. B., Porraz, G., … Hansen, A. J. (2020). 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, 8(1). https://doi.org/10.1186/s40168-020-00832-x
Chicago author-date
Rifkin, Riaan F., Surendra Vikram, Jean-Baptiste Ramond, Alba Rey-Iglesia, Tina B. Brand, Guillaume Porraz, Aurore Val, et al. 2020. “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 8 (1). https://doi.org/10.1186/s40168-020-00832-x.
Chicago author-date (all authors)
Rifkin, Riaan F., 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, and Anders J. Hansen. 2020. “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 8 (1). doi:10.1186/s40168-020-00832-x.
Vancouver
1.
Rifkin RF, Vikram S, Ramond J-B, Rey-Iglesia A, Brand TB, Porraz G, 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(1).
IEEE
[1]
R. F. Rifkin 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, vol. 8, no. 1, 2020.
@article{8661527,
  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 (otzi) 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.}},
  articleno    = {{62}},
  author       = {{Rifkin, Riaan F. and Vikram, Surendra and Ramond, Jean-Baptiste and Rey-Iglesia, Alba and Brand, Tina B. and Porraz, Guillaume and Val, Aurore and Hall, Grant and Woodborne, Stephan and Le Bailly, Matthieu and Potgieter, Marnie and Underdown, Simon J. and Koopman, Jessica E. and Cowan, Don A. and Van de Peer, Yves and Willerslev, Eske and Hansen, Anders J.}},
  issn         = {{2049-2618}},
  journal      = {{MICROBIOME}},
  keywords     = {{Ancient DNA,Human evolution,Molecular ecology,Intestinal microbiome,Taxonomic composition,Metabolic capacity,KeyWords Plus:CHAIN CHLORINATED PARAFFINS,GUT MICROBIOTA,DNA,PATTERNS,DAMAGE,IMPACT,ENTEROTYPES,RESISTANCE,DIVERSITY,DYSBIOSIS}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{23}},
  title        = {{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}},
  url          = {{http://dx.doi.org/10.1186/s40168-020-00832-x}},
  volume       = {{8}},
  year         = {{2020}},
}
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