Metagenomics of the modern and historical human oral microbiome with phylogenetic studies onStreptococcus mutansandStreptococcus sobrinus

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’.

Comparative Microbial Profiles of Caries and Black Extrinsic Tooth Stain in Primary Dentition

“…Considering that the perturbed microbial community of the dental plaque is the main reason behind the carious processes, the "core microbiome of caries" have been proposed in order to better understand the microbial community in the occurrence and development of caries [Kressirer et al, 2018;Kazemtabrizi et al, 2020]. Several highly acidogenic and acid-tolerant bacteria have been considered as "core microbiome" associated with caries, including Streptococcus mutans, Streptococcus sobrinus, and certain Lactobacillus, Bifidobacterium, and Scardovia [Saraithong et al, 2015;Neves et al, 2017;Achtman and Zhou, 2020]. When it comes to Streptococcus mutans, it was regarded as one of the major etiological agents of human dental caries with its capacity to orchestrate changes in the plaque microbiome via the extracellular polysaccharide matrix and acid production [Lemos et al, 2019].…”

Insights into health and disease from ancient biomolecules

“…Despite the expectation that such a major lifestyle change should result in a microbiome shift as detected in prior gut microbiome studies [24], Eisenhofer et al [23] observed that the microbiome variation changed little between these periods, with a noteworthy exception of Edo-period differences between the sexes, which they propose reflects traditional cultural practices. In the third article, Achtman & Zhou [25] discuss recently developed bioinformatic tools for investigating microbial diversity in metagenomic datasets, and they use these to examine the oral microbiome from ancient dental calculus in addition to modern saliva and dental calculus samples across a broad geographical region. In doing so, they cast doubt on the existence of the traditional oral complexes of bacteria, such as the red complex, defined by Socransky et al [26] and illustrate the importance of using new genomic methods to assess taxon diversity in the oral microbiome.…”

VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections

“… Streptococcus mutans is a ubiquitous species of the oral microbiome of modern humans [9, 36, 37]. Besides its important role in cariogenesis, S.…”