Transcriptome analysis of bacteriophage communities in periodontal health and disease

Abstract

BackgroundThe 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.ResultsHere, 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.ConclusionsAs 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1781-0) contains supplementary material, which is available to authorized users.

Host‐microbe interactions: Profiles in the transcriptome, the proteome, and the metabolome

“…However, genes from lytic phages were highly expressed in saliva from individuals with periodontal disease. 15 Lytic phages were also significant in subgingival biofilms of individuals with periodontal disease. 24 Although current research on periodontitis and the associated transcriptome is limited, recent studies have shown promising results that may be beneficial to the diagnosis of periodontal disease via the development of gene biomarkers.…”

“…Transcriptomics, or meta‐transcriptomics, has helped to elucidate the role of various RNA subtypes in periodontal health and disease. The main methods currently used in transcriptomic studies include RNA sequencing and microarray analyses (Table ). RNA sequencing effectively demonstrates periodontitis‐related gene expression .…”

“…The main methods currently used in transcriptomic studies include RNA sequencing and microarray analyses 3,[8][9][10][11][12][13][14][15][16][17][18][19] (Table 1). RNA sequencing effectively demonstrates periodontitis-related gene expression.…”

Emerging Technologies for Gut Microbiome Research

“…This could serve as a diagnostic tool to detect signs of dysbiosis prior to the onset of disease. Finally, transcriptome data can provide information about bacteriophage prevalence and activity within the community, which is often overlooked [47]. …”

Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions

“…Several intriguing studies have revealed phages as the most abundant members of the human oral cavity (10 8 virus like particles per mL of saliva) (22, 26), with distinct communities at sites of disease (27, 28), capable of augmenting the bacterial arsenal of pathogenic genes (29, 30). These studies have relied on the shotgun metagenomic approach, in part because one of the defining features of viral genomes is the lack of a universally conserved sequence.…”