Transcriptome analysis of bacteriophage communities in periodontal health and disease
Identifieur interne : 000C02 ( Main/Exploration ); précédent : 000C01; suivant : 000C03Transcriptome analysis of bacteriophage communities in periodontal health and disease
Auteurs : Tasha M. Santiago-Rodriguez [États-Unis] ; Mayuri Naidu [États-Unis] ; Shira R. Abeles [États-Unis] ; Tobias K. Boehm [États-Unis] ; Melissa Ly [États-Unis] ; David T. Pride [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
The role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identified in these communities have been bacteriophages that predate upon cellular microbiota rather than the human host. Phages have the capacity to lyse their hosts or provide them with selective advantages through lysogenic conversion, which could help determine the structure of co-existing bacterial communities. Because conditions such as periodontitis are associated with altered bacterial biota, phage mediated perturbations of bacterial communities have been hypothesized to play a role in promoting periodontal disease. Oral phage communities also differ significantly between periodontal health and disease, but the gene expression of oral phage communities has not been previously examined.
Here, we provide the first report of gene expression profiles from the oral bacteriophage community using RNA sequencing, and find that oral phages are more highly expressed in subjects with relative periodontal health. While lysins were highly expressed, the high proportion of integrases expressed suggests that prophages may account for a considerable proportion of oral phage gene expression. Many of the transcriptome reads matched phages found in the oral cavities of the subjects studied, indicating that phages may account for a substantial proportion of oral gene expression. Reads homologous to siphoviruses that infect Firmicutes were amongst the most prevalent transcriptome reads identified in both periodontal health and disease. Some genes from the phage lytic module were significantly more highly expressed in subjects with periodontal disease, suggesting that periodontitis may favor the expression of some lytic phages.
As we explore the contributions of viruses to the human microbiome, the data presented here suggest varying expression of bacteriophage communities in oral health and disease.
The online version of this article (doi:10.1186/s12864-015-1781-0) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1781-0
PubMed: 26215258
PubMed Central: 4515923
Affiliations:
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Santiago-Rodriguez</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla</wicri:cityArea></affiliation></author><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="Aff1">Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Abeles, Shira R" sort="Abeles, Shira R" uniqKey="Abeles S" first="Shira R." last="Abeles">Shira R. 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Santiago-Rodriguez</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla</wicri:cityArea></affiliation></author><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="Aff1">Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Abeles, Shira R" sort="Abeles, Shira R" uniqKey="Abeles S" first="Shira R." last="Abeles">Shira R. 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Boehm</name><affiliation wicri:level="2"><nlm:aff id="Aff3">College of Dental Medicine, Western University of Health Sciences, Pomona, CA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>College of Dental Medicine, Western University of Health Sciences, Pomona</wicri:cityArea></affiliation></author><author><name sortKey="Ly, Melissa" sort="Ly, Melissa" uniqKey="Ly M" first="Melissa" last="Ly">Melissa Ly</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla</wicri:cityArea></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="Aff1">Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identified in these communities have been bacteriophages that predate upon cellular microbiota rather than the human host. Phages have the capacity to lyse their hosts or provide them with selective advantages through lysogenic conversion, which could help determine the structure of co-existing bacterial communities. Because conditions such as periodontitis are associated with altered bacterial biota, phage mediated perturbations of bacterial communities have been hypothesized to play a role in promoting periodontal disease. Oral phage communities also differ significantly between periodontal health and disease, but the gene expression of oral phage communities has not been previously examined.</p></sec><sec><title>Results</title><p>Here, we provide the first report of gene expression profiles from the oral bacteriophage community using RNA sequencing, and find that oral phages are more highly expressed in subjects with relative periodontal health. While lysins were highly expressed, the high proportion of integrases expressed suggests that prophages may account for a considerable proportion of oral phage gene expression. Many of the transcriptome reads matched phages found in the oral cavities of the subjects studied, indicating that phages may account for a substantial proportion of oral gene expression. Reads homologous to siphoviruses that infect Firmicutes were amongst the most prevalent transcriptome reads identified in both periodontal health and disease. Some genes from the phage lytic module were significantly more highly expressed in subjects with periodontal disease, suggesting that periodontitis may favor the expression of some lytic phages.</p></sec><sec><title>Conclusions</title><p>As we explore the contributions of viruses to the human microbiome, the data presented here suggest varying expression of bacteriophage communities in oral health and disease.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1781-0) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Eke, Pi" uniqKey="Eke P">PI Eke</name></author><author><name sortKey="Thornton Evans, G" uniqKey="Thornton Evans G">G Thornton-Evans</name></author><author><name sortKey="Dye, B" uniqKey="Dye B">B Dye</name></author><author><name sortKey="Genco, R" uniqKey="Genco R">R 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