title: Transcriptome analysis of bacteriophage communities in periodontal health and disease.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. tmsantiagorodriguez@ucsd.edu.
authors.forename: Tasha M
authors.initials: TM
authors.lastname: Santiago-Rodriguez
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. mayuri.naidu@gmail.com.
authors.forename: Mayuri
authors.initials: M
authors.lastname: Naidu
authors.affiliation: Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. sabeles@ucsd.edu.
authors.forename: Shira R
authors.initials: SR
authors.lastname: Abeles
authors.affiliation: College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA. tboehm@westernu.edu.
authors.forename: Tobias K
authors.initials: TK
authors.lastname: Boehm
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. m2ly@ucsd.edu.
authors.forename: Melissa
authors.initials: M
authors.lastname: Ly
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. dpride@ucsd.edu.|Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. dpride@ucsd.edu.
authors.forename: David T
authors.initials: DT
authors.lastname: Pride
mesh_terms: D001435:Bacteriophages / Q000145:classification / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D015967:Gene Expression Regulation, Viral; D006801:Humans; D008242:Lysogeny; D009055:Mouth / Q000821:virology*; D010510:Periodontal Diseases / Q000235:genetics / Q000821:virology*; D017423:Sequence Analysis, RNA / Q000379:methods; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins