Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans
Identifieur interne : 000291 ( Pmc/Corpus ); précédent : 000290; suivant : 000292Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans
Auteurs : Omar E. Cornejo ; Tristan Lefébure ; Paulina D. Pavinski Bitar ; Ping Lang ; Vincent P. Richards ; Kirsten Eilertson ; Thuy Do ; David Beighton ; Lin Zeng ; Sang-Joon Ahn ; Robert A. Burne ; Adam Siepel ; Carlos D. Bustamante ; Michael J. StanhopeSource :
- Molecular Biology and Evolution [ 0737-4038 ] ; 2012.
Abstract
Url:
DOI: 10.1093/molbev/mss278
PubMed: 23228887
PubMed Central: 3603310
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PMC:3603310Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evolutionary and Population Genomics of the Cavity Causing Bacteria <italic>Streptococcus mutans</italic>
</title>
<author><name sortKey="Cornejo, Omar E" sort="Cornejo, Omar E" uniqKey="Cornejo O" first="Omar E." last="Cornejo">Omar E. Cornejo</name>
<affiliation><nlm:aff id="mss278-AFF1">Department of Genetics, School of Medicine, Stanford University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lefebure, Tristan" sort="Lefebure, Tristan" uniqKey="Lefebure T" first="Tristan" last="Lefébure">Tristan Lefébure</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pavinski Bitar, Paulina D" sort="Pavinski Bitar, Paulina D" uniqKey="Pavinski Bitar P" first="Paulina D." last="Pavinski Bitar">Paulina D. Pavinski Bitar</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lang, Ping" sort="Lang, Ping" uniqKey="Lang P" first="Ping" last="Lang">Ping Lang</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Richards, Vincent P" sort="Richards, Vincent P" uniqKey="Richards V" first="Vincent P." last="Richards">Vincent P. Richards</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Eilertson, Kirsten" sort="Eilertson, Kirsten" uniqKey="Eilertson K" first="Kirsten" last="Eilertson">Kirsten Eilertson</name>
<affiliation><nlm:aff id="mss278-AFF3">Department of Biological Statistics and Computational Biology, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Do, Thuy" sort="Do, Thuy" uniqKey="Do T" first="Thuy" last="Do">Thuy Do</name>
<affiliation><nlm:aff id="mss278-AFF4">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 Kingdom</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Beighton, David" sort="Beighton, David" uniqKey="Beighton D" first="David" last="Beighton">David Beighton</name>
<affiliation><nlm:aff id="mss278-AFF4">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 Kingdom</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zeng, Lin" sort="Zeng, Lin" uniqKey="Zeng L" first="Lin" last="Zeng">Lin Zeng</name>
<affiliation><nlm:aff id="mss278-AFF5">Department of Oral Biology, University of Florida</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ahn, Sang Joon" sort="Ahn, Sang Joon" uniqKey="Ahn S" first="Sang-Joon" last="Ahn">Sang-Joon Ahn</name>
<affiliation><nlm:aff id="mss278-AFF5">Department of Oral Biology, University of Florida</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Burne, Robert A" sort="Burne, Robert A" uniqKey="Burne R" first="Robert A." last="Burne">Robert A. Burne</name>
<affiliation><nlm:aff id="mss278-AFF5">Department of Oral Biology, University of Florida</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Siepel, Adam" sort="Siepel, Adam" uniqKey="Siepel A" first="Adam" last="Siepel">Adam Siepel</name>
<affiliation><nlm:aff id="mss278-AFF3">Department of Biological Statistics and Computational Biology, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bustamante, Carlos D" sort="Bustamante, Carlos D" uniqKey="Bustamante C" first="Carlos D." last="Bustamante">Carlos D. Bustamante</name>
<affiliation><nlm:aff id="mss278-AFF1">Department of Genetics, School of Medicine, Stanford University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stanhope, Michael J" sort="Stanhope, Michael J" uniqKey="Stanhope M" first="Michael J." last="Stanhope">Michael J. Stanhope</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evolutionary and Population Genomics of the Cavity Causing Bacteria <italic>Streptococcus mutans</italic>
</title>
<author><name sortKey="Cornejo, Omar E" sort="Cornejo, Omar E" uniqKey="Cornejo O" first="Omar E." last="Cornejo">Omar E. Cornejo</name>
<affiliation><nlm:aff id="mss278-AFF1">Department of Genetics, School of Medicine, Stanford University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lefebure, Tristan" sort="Lefebure, Tristan" uniqKey="Lefebure T" first="Tristan" last="Lefébure">Tristan Lefébure</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pavinski Bitar, Paulina D" sort="Pavinski Bitar, Paulina D" uniqKey="Pavinski Bitar P" first="Paulina D." last="Pavinski Bitar">Paulina D. Pavinski Bitar</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lang, Ping" sort="Lang, Ping" uniqKey="Lang P" first="Ping" last="Lang">Ping Lang</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Richards, Vincent P" sort="Richards, Vincent P" uniqKey="Richards V" first="Vincent P." last="Richards">Vincent P. Richards</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Eilertson, Kirsten" sort="Eilertson, Kirsten" uniqKey="Eilertson K" first="Kirsten" last="Eilertson">Kirsten Eilertson</name>
<affiliation><nlm:aff id="mss278-AFF3">Department of Biological Statistics and Computational Biology, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Do, Thuy" sort="Do, Thuy" uniqKey="Do T" first="Thuy" last="Do">Thuy Do</name>
<affiliation><nlm:aff id="mss278-AFF4">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 Kingdom</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Beighton, David" sort="Beighton, David" uniqKey="Beighton D" first="David" last="Beighton">David Beighton</name>
<affiliation><nlm:aff id="mss278-AFF4">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 Kingdom</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zeng, Lin" sort="Zeng, Lin" uniqKey="Zeng L" first="Lin" last="Zeng">Lin Zeng</name>
<affiliation><nlm:aff id="mss278-AFF5">Department of Oral Biology, University of Florida</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ahn, Sang Joon" sort="Ahn, Sang Joon" uniqKey="Ahn S" first="Sang-Joon" last="Ahn">Sang-Joon Ahn</name>
<affiliation><nlm:aff id="mss278-AFF5">Department of Oral Biology, University of Florida</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Burne, Robert A" sort="Burne, Robert A" uniqKey="Burne R" first="Robert A." last="Burne">Robert A. Burne</name>
<affiliation><nlm:aff id="mss278-AFF5">Department of Oral Biology, University of Florida</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Siepel, Adam" sort="Siepel, Adam" uniqKey="Siepel A" first="Adam" last="Siepel">Adam Siepel</name>
<affiliation><nlm:aff id="mss278-AFF3">Department of Biological Statistics and Computational Biology, Cornell University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bustamante, Carlos D" sort="Bustamante, Carlos D" uniqKey="Bustamante C" first="Carlos D." last="Bustamante">Carlos D. Bustamante</name>
<affiliation><nlm:aff id="mss278-AFF1">Department of Genetics, School of Medicine, Stanford University</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stanhope, Michael J" sort="Stanhope, Michael J" uniqKey="Stanhope M" first="Michael J." last="Stanhope">Michael J. Stanhope</name>
<affiliation><nlm:aff id="mss278-AFF2">Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Molecular Biology and Evolution</title>
<idno type="ISSN">0737-4038</idno>
<idno type="eISSN">1537-1719</idno>
<imprint><date when="2012">2012</date>
</imprint>
</series>
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<front><div type="abstract" xml:lang="en"><p><italic>Streptococcus mutans</italic>
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 <italic>S. mutans</italic>
isolates, as well as representative strains of the most closely related species to <italic>S. mutans (S. ratti, S. macaccae,</italic>
and <italic>S. criceti)</italic>
, 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 <italic>S. mutans</italic>
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 <italic>S. mutans</italic>
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 <italic>S. mutans</italic>
to its new niche, the human mouth, and with the dietary changes that accompanied the origin of agriculture.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Mol Biol Evol</journal-id>
<journal-id journal-id-type="iso-abbrev">Mol. Biol. Evol</journal-id>
<journal-id journal-id-type="publisher-id">molbev</journal-id>
<journal-id journal-id-type="hwp">molbiolevol</journal-id>
<journal-title-group><journal-title>Molecular Biology and Evolution</journal-title>
</journal-title-group>
<issn pub-type="ppub">0737-4038</issn>
<issn pub-type="epub">1537-1719</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23228887</article-id>
<article-id pub-id-type="pmc">3603310</article-id>
<article-id pub-id-type="doi">10.1093/molbev/mss278</article-id>
<article-id pub-id-type="publisher-id">mss278</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Discoveries</subject>
</subj-group>
</article-categories>
<title-group><article-title>Evolutionary and Population Genomics of the Cavity Causing Bacteria <italic>Streptococcus mutans</italic>
</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Cornejo</surname>
<given-names>Omar E.</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lefébure</surname>
<given-names>Tristan</given-names>
</name>
<xref ref-type="author-notes" rid="mss278-FN1"><sup>†</sup>
</xref>
<xref ref-type="aff" rid="mss278-AFF2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pavinski Bitar</surname>
<given-names>Paulina D.</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lang</surname>
<given-names>Ping</given-names>
</name>
<xref ref-type="author-notes" rid="mss278-FN3"><sup>‡</sup>
</xref>
<xref ref-type="aff" rid="mss278-AFF2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Richards</surname>
<given-names>Vincent P.</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Eilertson</surname>
<given-names>Kirsten</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Do</surname>
<given-names>Thuy</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Beighton</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zeng</surname>
<given-names>Lin</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ahn</surname>
<given-names>Sang-Joon</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Burne</surname>
<given-names>Robert A.</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Siepel</surname>
<given-names>Adam</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bustamante</surname>
<given-names>Carlos D.</given-names>
</name>
<xref ref-type="aff" rid="mss278-AFF1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stanhope</surname>
<given-names>Michael J.</given-names>
</name>
<xref ref-type="corresp" rid="mss278-COR1">*</xref>
<xref ref-type="aff" rid="mss278-AFF2"><sup>2</sup>
</xref>
</contrib>
</contrib-group>
<aff id="mss278-AFF1"><sup>1</sup>
Department of Genetics, School of Medicine, Stanford University</aff>
<aff id="mss278-AFF2"><sup>2</sup>
Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University</aff>
<aff id="mss278-AFF3"><sup>3</sup>
Department of Biological Statistics and Computational Biology, Cornell University</aff>
<aff id="mss278-AFF4"><sup>4</sup>
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 Kingdom</aff>
<aff id="mss278-AFF5"><sup>5</sup>
Department of Oral Biology, University of Florida</aff>
<author-notes><fn id="mss278-FN1"><p><sup>†</sup>
Present address: Université de Lyon; CNRS, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, Villeurbanne, F-69622, France</p>
</fn>
<fn id="mss278-FN4"><p><sup>‡</sup>
Present address: Department of Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY</p>
</fn>
<corresp id="mss278-COR1"><bold>*Corresponding author:</bold>
E-mail: <email>mjs297@cornell.edu</email>
.</corresp>
<fn id="mss278-FN3"><p><bold>Associate editor:</bold>
Ryan Hernandez</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>4</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>10</day>
<month>12</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>1</day>
<month>4</month>
<year>2014</year>
</pub-date>
<pmc-comment> PMC Release delay is 12 months and 0 days and was based on the
. </pmc-comment>
<volume>30</volume>
<issue>4</issue>
<fpage>881</fpage>
<lpage>893</lpage>
<permissions><copyright-statement>© The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com</copyright-statement>
<copyright-year>2012</copyright-year>
</permissions>
<abstract><p><italic>Streptococcus mutans</italic>
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 <italic>S. mutans</italic>
isolates, as well as representative strains of the most closely related species to <italic>S. mutans (S. ratti, S. macaccae,</italic>
and <italic>S. criceti)</italic>
, 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 <italic>S. mutans</italic>
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 <italic>S. mutans</italic>
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 <italic>S. mutans</italic>
to its new niche, the human mouth, and with the dietary changes that accompanied the origin of agriculture.</p>
</abstract>
<kwd-group><kwd><italic>Streptococcus mutans</italic>
</kwd>
<kwd>demographic inference</kwd>
<kwd>cavities</kwd>
<kwd>bacterial evolution</kwd>
<kwd>pan and core genome</kwd>
<kwd>infectious disease</kwd>
</kwd-group>
<counts><page-count count="13"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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