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Species frequencies according to checkerboard tests and SPARSE results.

DNADamage plots.

NJ hierarchical clustering of all major species

Excluded samples.

Relative sources of species according to checkerboard tests and SPARSE results.

Supplementary text

Abundances of reads from S. mutans and S. sobrinus that were used to create pseudo=MAGs.

Species abundances by Velsko et al., 2019 and SPARSE

K-mean clusters and PCA

Comparisons of species abundances between Velsko et al., 2019, Metaphlan and SPARSE

We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE for probabilistic, taxonomic classification of sequence reads; EToKi for assembling and polishing genomes from short-read sequences; and GrapeTree, a graphic visualizer of genetic distances between large numbers of genomes. Together, these methods support comparative analyses of genomes from ancient skeletons and modern humans. Here, we illustrate these capabilities with 784 samples from historical dental calculus, modern saliva and modern dental plaque. The analyses revealed 1591 microbial species within the oral microbiome. We anticipated that the oral complexes of Socransky et al ., which were defined in 1998, would predominate among taxa whose frequencies differed by source. However, although some species discriminated between sources, we could not confirm the existence of the complexes. The results also illustrate further functionality of our pipelines with two species that are associated with dental caries, Streptococcus mutans and Streptococcus sobrinus . They were rare in historical dental calculus but common in modern plaque, and even more common in saliva. Reconstructed draft genomes of these two species from metagenomic samples in which they were abundant were combined with modern public genomes to provide a detailed overview of their core genomic diversity. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.