Characterization of bacteriophage communities and CRISPR profiles from dental plaque
Identifieur interne : 000971 ( Main/Exploration ); précédent : 000970; suivant : 000972Characterization 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
Affiliations:
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Abeles</name><affiliation wicri:level="2"><nlm:aff id="I2">Department of Medicine, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Boehm, Tobias K" sort="Boehm, Tobias K" uniqKey="Boehm T" first="Tobias K" last="Boehm">Tobias K. Boehm</name><affiliation wicri:level="2"><nlm:aff id="I3">College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Dental Medicine, Western University of Health Sciences, Pomona, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Pride, David T" sort="Pride, David T" uniqKey="Pride D" first="David T" last="Pride">David T. Pride</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Pathology, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Department of Medicine, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24981669</idno><idno type="pmc">4104742</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104742</idno><idno type="RBID">PMC:4104742</idno><idno type="doi">10.1186/1471-2180-14-175</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000265</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000265</idno><idno type="wicri:Area/Pmc/Curation">000265</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000265</idno><idno type="wicri:Area/Pmc/Checkpoint">000436</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000436</idno><idno type="wicri:Area/Ncbi/Merge">000F18</idno><idno type="wicri:Area/Ncbi/Curation">000F18</idno><idno type="wicri:Area/Ncbi/Checkpoint">000F18</idno><idno type="wicri:Area/Main/Merge">000973</idno><idno type="wicri:Area/Main/Curation">000971</idno><idno type="wicri:Area/Main/Exploration">000971</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterization of bacteriophage communities and CRISPR profiles from dental plaque</title><author><name sortKey="Naidu, Mayuri" sort="Naidu, Mayuri" uniqKey="Naidu M" first="Mayuri" last="Naidu">Mayuri Naidu</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Pathology, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Robles Sikisaka, Refugio" sort="Robles Sikisaka, Refugio" uniqKey="Robles Sikisaka R" first="Refugio" last="Robles-Sikisaka">Refugio Robles-Sikisaka</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Pathology, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Abeles, Shira R" sort="Abeles, Shira R" uniqKey="Abeles S" first="Shira R" last="Abeles">Shira R. Abeles</name><affiliation wicri:level="2"><nlm:aff id="I2">Department of Medicine, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Boehm, Tobias K" sort="Boehm, Tobias K" uniqKey="Boehm T" first="Tobias K" last="Boehm">Tobias K. Boehm</name><affiliation wicri:level="2"><nlm:aff id="I3">College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Dental Medicine, Western University of Health Sciences, Pomona, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Pride, David T" sort="Pride, David T" uniqKey="Pride D" first="David T" last="Pride">David T. Pride</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Pathology, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Department of Medicine, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">BMC Microbiology</title><idno type="eISSN">1471-2180</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bik, Em" uniqKey="Bik E">EM Bik</name></author><author><name sortKey="Long, Cd" uniqKey="Long C">CD Long</name></author><author><name sortKey="Armitage, Gc" uniqKey="Armitage G">GC Armitage</name></author><author><name sortKey="Loomer, P" uniqKey="Loomer P">P Loomer</name></author><author><name sortKey="Emerson, J" uniqKey="Emerson J">J Emerson</name></author><author><name sortKey="Mongodin, Ef" uniqKey="Mongodin E">EF Mongodin</name></author><author><name sortKey="Nelson, Ke" uniqKey="Nelson K">KE Nelson</name></author><author><name 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sortKey="Mcdonald, D" uniqKey="Mcdonald D">D McDonald</name></author><author><name sortKey="Muegge, Bd" uniqKey="Muegge B">BD Muegge</name></author><author><name sortKey="Pirrung, M" uniqKey="Pirrung M">M Pirrung</name></author><author><name sortKey="Reeder, J" uniqKey="Reeder J">J Reeder</name></author><author><name sortKey="Sevinsky, Jr" uniqKey="Sevinsky J">JR Sevinsky</name></author><author><name sortKey="Turnbaugh, Pj" uniqKey="Turnbaugh P">PJ Turnbaugh</name></author><author><name sortKey="Walters, Wa" uniqKey="Walters W">WA Walters</name></author><author><name sortKey="Widmann, J" uniqKey="Widmann J">J Widmann</name></author><author><name sortKey="Yatsunenko, T" uniqKey="Yatsunenko T">T Yatsunenko</name></author><author><name sortKey="Zaneveld, J" uniqKey="Zaneveld J">J Zaneveld</name></author><author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shannon, P" uniqKey="Shannon P">P Shannon</name></author><author><name sortKey="Markiel, A" uniqKey="Markiel A">A Markiel</name></author><author><name sortKey="Ozier, O" uniqKey="Ozier O">O Ozier</name></author><author><name sortKey="Baliga, Ns" uniqKey="Baliga N">NS Baliga</name></author><author><name sortKey="Wang, Jt" uniqKey="Wang J">JT Wang</name></author><author><name sortKey="Ramage, D" uniqKey="Ramage D">D Ramage</name></author><author><name sortKey="Amin, N" uniqKey="Amin N">N Amin</name></author><author><name sortKey="Schwikowski, B" uniqKey="Schwikowski B">B Schwikowski</name></author><author><name sortKey="Ideker, T" uniqKey="Ideker T">T Ideker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stothard, P" uniqKey="Stothard P">P Stothard</name></author><author><name sortKey="Wishart, Ds" uniqKey="Wishart D">DS Wishart</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Naidu, Mayuri" sort="Naidu, Mayuri" uniqKey="Naidu M" first="Mayuri" last="Naidu">Mayuri Naidu</name></region><name sortKey="Abeles, Shira R" sort="Abeles, Shira R" uniqKey="Abeles S" first="Shira R" last="Abeles">Shira R. Abeles</name><name sortKey="Boehm, Tobias K" sort="Boehm, Tobias K" uniqKey="Boehm T" first="Tobias K" last="Boehm">Tobias K. Boehm</name><name sortKey="Pride, David T" sort="Pride, David T" uniqKey="Pride D" first="David T" last="Pride">David T. Pride</name><name sortKey="Pride, David T" sort="Pride, David T" uniqKey="Pride D" first="David T" last="Pride">David T. Pride</name><name sortKey="Robles Sikisaka, Refugio" sort="Robles Sikisaka, Refugio" uniqKey="Robles Sikisaka R" first="Refugio" last="Robles-Sikisaka">Refugio Robles-Sikisaka</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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