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
Posted on 07.05.2020 - 09:30
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.
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Rifkin, Riaan F.; Vikram, Surendra; Ramond, Jean-Baptiste; Rey-Iglesia, Alba; Brand, Tina B.; Porraz, Guillaume; 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. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4967438.v1
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AUTHORS (17)
RR
Riaan F. Rifkin
SV
Surendra Vikram
JR
Jean-Baptiste Ramond
AR
Alba Rey-Iglesia
TB
Tina B. Brand
GP
Guillaume Porraz
AV
Aurore Val
GH
Grant Hall
SW
Stephan Woodborne
ML
Matthieu Le Bailly
MP
Marnie Potgieter
SU
Simon J. Underdown
JK
Jessica E. Koopman
DC
Don A. Cowan
YV
Yves Van de Peer
EW
Eske Willerslev
AH
Anders J. Hansen