Oral microbial diversity in 18th century African individuals from South Carolina

Abstract

As part of the Anson Street African Burial Ground Project, we characterized the oral microbiomes of twelve 18th century African-descended individuals (Ancestors) from Charleston, South Carolina, USA, to study their oral health and diet. We found that their oral microbiome composition resembled that of other historic (18th-19th century) dental calculus samples but differed from that of modern samples, and was not influenced by indicators of oral health and wear observed in the dentition. Phylogenetic analysis of the oral bacteria, Tannerella forsythia and Pseudoramibacter alactolyticus, revealed varied patterns of lineage diversity and replacement in the Americas, with the Ancestors carrying strains similar to historic period Europeans and Africans. Functional profiling of metabolic pathways suggested that the Ancestors consumed a diet low in animal protein. Overall, our study reveals important insights into the oral microbial histories of African-descended individuals, particularly oral health and diet in colonial North American enslavement contexts.

Fig. 1. The Anson Street African Burial Ground site displaying burial numbering and dental calculus information.

The Ancestors from whom dental calculus was sampled and sequenced are highlighted in red, and those where dental calculus was sampled but were not sequenced due to low recovery are highlighted in blue. The Ancestors with no dental calculus are denoted in grey. The tooth or teeth with dental calculus deposits that were collected from each Ancestor are shown. Pie charts display the results from the SourceTracker analysis. The original site map was published in Fleskes et al. .

Fig. 2. MetaPhlAn4 results.

A A heatmap showing the 25 most abundant species. B The histogram indicates total number of taxa identified for each Ancestor.

Fig. 3. Bi-Plot analysis of the MetaPhlAn4 mean relative abundances for the Anson Street Ancestors.

A Bi-Plot analysis, with black arrows representing the top 10 species with the highest PCA loadings, and grey arrows representing the top 10 species with negative PCA loadings. B The table of species corresponding to the arrows, matching the arrow numbers.

Fig. 4. Comparative PCA analysis of the Metaphalan4 mean relative abundances at the species level.

A PCA depicting the Anson Street Ancestors and comparative reference populations. The legend and color symbols are denoted on the bottom of the plot and are additionally shared with subpanel C. B A PCA analysis, with coloring representing the number of identified species. Legend symbols are denoted in the same subpanel. C A Bi-Plot analysis, with arrows denoting the top 10 species with the highest and lowest PCA loadings shown in the corresponding table. Legend and color symbols are shown above the plot.

Fig. 5. Maximum Likelihood tree of Tannerella forsythia strains.

An alignment of 26,922 homozygous, bi-allelic SNPs was used. The tree was built using IQ-TREE and the K3PU + F + ASC + R2 model. The tree was rooted using canine T. forsythia strains. Brown circles indicate branches with greater than 95% bootstrap support, estimated using 1000 ultrafast bootstraps. Strains are color-coded based on location, symbols are used to denote temporal context, and the country of origin is shown in parentheses. The strain reconstructed from Ancestor Tima [CHS31], is colored in red.

Fig. 6. Maximum Likelihood tree of Pseudoramibacter alactolyticus strains.

An alignment of 3,083 homozygous, bi-allelic SNPs with a maximum of 10% missing data was used. The tree was built with IQ-TREE using the K3Pu+F + ASC + R2 model. A strain reconstructed from a wild-borne chimpanzee was used as the outgroup. Brown circles indicate branches with greater than 95% bootstrap support from 1,000 ultrafast bootstrap replicates. The color of each strain corresponds to geographic origin and the symbols equate to temporal context. Strains reconstructed from Ancestors Lima [CHS03] and Nina [CHS20] are colored in red.

Fig. 7. Functional analysis of animal protein consumption.

HUMAnN3 gene family abundances aggregated based on high-meat or high-plant consumption. Pairwise Wilcoxon rank sum tests for significance with p-values < 0.05 are indicated below the graph by asterisks. The number of genes in each population are displayed above each bar and detailed statistics are outlined in Supplementary Data 18.