Journal article
Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans
Molecular biology and evolution, Vol.30(4), pp.881-893
04/2013
Handle:
https://hdl.handle.net/2376/112307
PMCID: PMC3603310
PMID: 23228887
Abstract
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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Details
- Title
- Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans
- Creators
- Omar E Cornejo - Department of Genetics, School of Medicine, Stanford UniversityTristan Lefébure - Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell UniversityPaulina D Pavinski Bitar - Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell UniversityPing Lang - Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell UniversityVincent P Richards - Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell UniversityKirsten Eilertson - Department of Biological Statistics and Computational Biology, Cornell UniversityThuy Do - Department of Microbiology, King’s College London Dental Institute and NIHR Biomedical Research Centre at Guy's and St. Thomas’s NHS Foundation Trust, Guy’s Hospital, London, United KingdomDavid Beighton - Department of Microbiology, King’s College London Dental Institute and NIHR Biomedical Research Centre at Guy's and St. Thomas’s NHS Foundation Trust, Guy’s Hospital, London, United KingdomLin Zeng - Department of Oral Biology, University of FloridaSang-Joon Ahn - Department of Oral Biology, University of FloridaRobert A Burne - Department of Oral Biology, University of FloridaAdam Siepel - Department of Biological Statistics and Computational Biology, Cornell UniversityCarlos D Bustamante - Department of Genetics, School of Medicine, Stanford UniversityMichael J Stanhope - Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
- Publication Details
- Molecular biology and evolution, Vol.30(4), pp.881-893
- Academic Unit
- Biological Sciences, School of
- Publisher
- Oxford University Press
- Identifiers
- 99900547669101842
- Language
- English
- Resource Type
- Journal article