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.
Description:
Additional file 1: Figure S1. Additional information concerning the
archaeological provenance of the BRS faecal specimen. Figure S2.
Processing of the faecal specimen at the Centre for GeoGenetics,
Copenhagen, Denmark. Figure S3. Dot-plot indicating the occurrence of
statistically-significant C-T p-values. Figure S4. Biplot of δ13C and δ15N
stable isotope values obtained for the BRS specimen. Figure S5. SEM
analysis detected bacterial cells, plant fragments and saprophytic organisms.
Figure S6. Heat-map indicating differences in taxonomic community
structure for IM datasets. Figure S7. Comparing ‘relative abundance’
and ‘presence-absence’ as taxonomic representation. Figure S8. Comparison
of the incidence of the twenty-four authenticated ancient IM
taxa. Figure S9. Heat-map indicating the presence of fifteen functional
ARGs identified.
Additional file 2: Table S1. Sequence reads for environmental- and
subsistence-related taxa detected. Table S2. Information concerning 14C
Accelerator Mass Spectrometry (AMS) dating. Table S3a. Processing
protocol and results for isotope analyses. Table S3b. Results for isotope
analyses (Merck standard). Table S3c. Results for isotope analyses (DLValine
standard). Table S4. Abundance of bacterial taxonomic categories
in the IM datasets. Table S5. Sequence read-length distribution for taxa
identified in this study. Table S6. Significant KEGG pathways in the comparative
IM datasets analysed. Table S7. Relative abundance of eighteen
significant KEGG pathways in the IM cohorts. Table S8. Enrichment and
depletion of KO metabolic gene categories in the comparative IM sample
cohorts based on p-value (p=<0.05) designation. Table S9. Enrichment
and depletion of KO metabolic gene categories in the comparative IM
sample cohorts based on false discovery rate (FDR) corrected p-values
(q=<0.05). Table S10. Enrichment and depletion of KO metabolic gene
categories in the ancient and modern comparative IM sample cohort as
calculated for the twenty-four authenticated ancient IM taxa. Table S11.
Comparison of relative abundance of antibiotic resistance genes in the
comparative IM cohorts. Table S12. Raw and filtered high-quality sequence
read counts as related to the comparative IM datasets. Table
S13. Information concerning the comparative NCBI genomes used during
this study.
