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Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus
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Achtman, Mark and Zhou, Zhemin (2020) Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus. Philosophical Transactions of the Royal Society B: Biological Sciences, 375 (1812). 20190573. doi:10.1098/rstb.2019.0573 ISSN 0962-8436.
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WRAP-metagenomics-oral-microbiome-phylogenetic-Streptococcus-mutans-sobrinus-Zhou-2020.pdf - Accepted Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (976Kb) | Preview |
Official URL: https://doi.org/10.1098/rstb.2019.0573
Abstract
We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE [1] for probabilistic, taxonomic classification of sequence reads, EToKi [2] for assembling and polishing genomes from short read sequences, and GrapeTree [3], 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 [2,4]. 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. [5] 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.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QP Physiology R Medicine > RK Dentistry |
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Library of Congress Subject Headings (LCSH): | Metagenomics, DNA, Fossil, Dental plaque, Dental calculus, Saliva | |||||||||
| Journal or Publication Title: | Philosophical Transactions of the Royal Society B: Biological Sciences | |||||||||
| Publisher: | The Royal Society Publishing | |||||||||
| ISSN: | 0962-8436 | |||||||||
| Official Date: | 5 October 2020 | |||||||||
| Dates: |
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| Volume: | 375 | |||||||||
| Number: | 1812 | |||||||||
| Article Number: | 20190573 | |||||||||
| DOI: | 10.1098/rstb.2019.0573 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 2 September 2020 | |||||||||
| Date of first compliant Open Access: | 2 September 2020 | |||||||||
| RIOXX Funder/Project Grant: |
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