Characterization of bacteriophage communities and CRISPR profiles from dental plaque
Identifieur interne : 000265 ( Pmc/Curation ); précédent : 000264; suivant : 000266Characterization of bacteriophage communities and CRISPR profiles from dental plaque
Auteurs : Mayuri Naidu [États-Unis] ; Refugio Robles-Sikisaka [États-Unis] ; Shira R. Abeles [États-Unis] ; Tobias K. Boehm [États-Unis] ; David T. Pride [États-Unis]Source :
- BMC Microbiology [ 1471-2180 ] ; 2014.
Abstract
Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.
We found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.
Our findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized.
Url:
DOI: 10.1186/1471-2180-14-175
PubMed: 24981669
PubMed Central: 4104742
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.</p>
</sec>
<sec><title>Results</title>
<p>We found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.</p>
</sec>
<sec><title>Conclusions</title>
<p>Our findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized.</p>
</sec>
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<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Microbiol</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Microbiol</journal-id>
<journal-title-group><journal-title>BMC Microbiology</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2180</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24981669</article-id>
<article-id pub-id-type="pmc">4104742</article-id>
<article-id pub-id-type="publisher-id">1471-2180-14-175</article-id>
<article-id pub-id-type="doi">10.1186/1471-2180-14-175</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Characterization of bacteriophage communities and CRISPR profiles from dental plaque</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Naidu</surname>
<given-names>Mayuri</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>mayuri.naidu@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Robles-Sikisaka</surname>
<given-names>Refugio</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>refugio.robles1@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Abeles</surname>
<given-names>Shira R</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>sabeles@ucsd.edu</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Boehm</surname>
<given-names>Tobias K</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>tboehm@westernu.edu</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A5"><name><surname>Pride</surname>
<given-names>David T</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>dpride@ucsd.edu</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Pathology, University of California, San Diego, CA, USA</aff>
<aff id="I2"><label>2</label>
Department of Medicine, University of California, San Diego, CA, USA</aff>
<aff id="I3"><label>3</label>
College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA</aff>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>30</day>
<month>6</month>
<year>2014</year>
</pub-date>
<volume>14</volume>
<fpage>175</fpage>
<lpage>175</lpage>
<history><date date-type="received"><day>24</day>
<month>9</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>26</day>
<month>6</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Naidu et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>Naidu et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2180/14/175"></self-uri>
<abstract><sec><title>Background</title>
<p>Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.</p>
</sec>
<sec><title>Results</title>
<p>We found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.</p>
</sec>
<sec><title>Conclusions</title>
<p>Our findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized.</p>
</sec>
</abstract>
<kwd-group><kwd>Oral biofilm</kwd>
<kwd>Virus</kwd>
<kwd>Virome</kwd>
<kwd>Microbiome</kwd>
<kwd>Dental plaque</kwd>
<kwd>CRISPR</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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