Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans
Open accessAbstract
Streptococcus mutans is widely recognized as one of the key etiological agents of human dental caries. Despite its role in this important disease, our present knowledge of gene content variability across the species and its relationship to adaptation is minimal. Estimates of its demographic history are not available. In this study, we generated genome sequences of 57 S. mutans isolates, as well as representative strains of the most closely related species to S. mutans (S. ratti, S. macaccae, and S. criceti), to identify the overall structure and potential adaptive features of the dispensable and core components of the genome. We also performed population genetic analyses on the core genome of the species aimed at understanding the demographic history, and impact of selection shaping its genetic variation. The maximum gene content divergence among strains was approximately 23%, with the majority of strains diverging by 5-15%. The core genome consisted of 1,490 genes and the pan-genome approximately 3,296. Maximum likelihood analysis of the synonymous site frequency spectrum (SFS) suggested that the S. mutans population started expanding exponentially approximately 10,000 years ago (95% confidence interval [CI]: 3,268-14,344 years ago), coincidental with the onset of human agriculture. Analysis of the replacement SFS indicated that a majority of these substitutions are under strong negative selection, and the remainder evolved neutrally. A set of 14 genes was identified as being under positive selection, most of which were involved in either sugar metabolism or acid tolerance. Analysis of the core genome suggested that among 73 genes present in all isolates of S. mutans but absent in other species of the mutans taxonomic group, the majority can be associated with metabolic processes that could have contributed to the successful adaptation of S. mutans to its new niche, the human mouth, and with the dietary changes that accompanied the origin of agriculture.
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Changes in diet were paralleled by pathologic changes to the oral microbiota, including greater representation of acid-producing and acid-tolerant organisms and periodontal pathogens.
“Such changes in diet were paralleled by pathologic changes to the oral microbiota, including greater representation of acid‐producing and acid‐tolerant organisms and periodontal pathogens.17, 22, 24, 25”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [25]
Population genomics studies predict that the S mutans population started growing exponentially 10,000 years ago, around the advent of human agriculture.
“population genomics studies predict that the S mutans population started growing exponentially 10,000 years ago, around the advent of human agriculture.”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [25]
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References 97 · Cited by 198
Research works printed but not linked: 3
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- Authors
- Cornejo, O. E., Lefébure, T., Pavinski Bitar, P. D., Lang, P., Richards, V. P., Eilertson, K., Do, T., Beighton, D., Zeng, L., Ahn, S.-J., Burne, R. A., Siepel, A., Bustamante, C. D., & Stanhope, M. J.
- Affiliations
- Stanford Medicine (US)
- Cornell University (US)
- Guy's Hospital (GB)
- University of Florida (US)
- Corresponding author
- Stanhope, Michael J.
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-12-10
- Volume
- 30
- Issue
- 4
- Pages
- 881-893
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3603310
- OpenAlex
- W2143645881
- Cited by
- 198
- References
- 97
- Citations by year
- 2026: 9 · 2025: 10 · 2024: 8 · 2023: 8 · 2022: 14 · 2021: 13 · 2020: 16 · 2019: 19 · 2018: 16 · 2017: 21 · 2016: 18 · 2015: 21 · 2014: 10 · 2013: 15
- FWCI
- 17.69
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- HAL (submittedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (R01AI073368, AI073368)
- Topics
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- Streptococcus mutans, dental caries, pan-genome, core genome, demographic history, demographic expansion, positive selection, negative selection, sugar metabolism, acid resistance, oral microbiota, origins of agriculture, mutans streptococci
- MeSH terms
- Adaptation, Biological, Dental Caries, Gene Frequency, Humans, Models, Genetic, Recombination, Genetic, Selection, Genetic, Streptococcus mutans, Linkage Disequilibrium, Likelihood Functions, Genome, Bacterial, Evolution, Molecular, Polymorphism, Single Nucleotide, Carbohydrate Metabolism, Metagenomics
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