Abstract
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’.
Highlights
Multiple research areas have undergone revolutionary changes in the last 10 years due to broad accessibility to high-throughput DNA sequencing at reduced costs
We address the question of which microbial taxa are uniformly present in human saliva, dental plaque and dental calculus, and which are specific to individual niches
We identified 17 public archives containing 1016 sets of metagenomic sequences from 791 oral samples from a variety of global sources which had been obtained from modern human saliva, modern human dental plaque or historical dental calculus
Summary
Multiple research areas have undergone revolutionary changes in the last 10 years due to broad accessibility to high-throughput DNA sequencing at reduced costs. Recent evaluations have demonstrated that current taxonomic classifiers either lack sufficient sensitivity for species-level assignments or suffer from false positives, and that they overestimate the number of species in the metagenome [29,30,31] Both tendencies are especially problematic for the identification of microbial species which are only present at low-abundance, e.g. detecting pathogens in ancient metagenomic samples. SPARSE accounts for the existing bias in reference databases [29,33] by sorting all complete genomes of Bacteria, Archaea, Viruses and Protozoa in RefSeq into sequence similarity-based hierarchical clusters with a cutoff of 99% average nucleotide identity (ANI99%) It subsequently extracts a representative subset from those clusters, consisting of one genome per ANI95% cluster because ANI95% is a common cutoff for individual bacterial species [34,35]. We examine the population genomic structures of Streptococcus mutans and Streptococcus sobrinus, which are associated with dental caries in some human populations [39,40,41]
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