Metagenomic and metatranscriptomic analysis of saliva reveals disease-associated microbiota in patients with periodontitis and dental caries

Oral health: Signals from gene activity in saliva Genetic analysis of saliva reveals the activity of bacteria linked to gum disease and tooth decay and may prove useful in early diagnosis. Daniel Belstrøm and colleagues at the University of Copenhagen, Denmark, with co-workers at Nanyang Technological University in Singapore, analyzed saliva from 10 patients with periodontitis gum disease, 10 with dental caries and 10 with good oral health. DNA analysis revealed which bacteria were present, while examining RNA revealed which bacterial genes were most active. The procedure identified greater abundance and activity of bacteria linked to each specific oral condition in the oral disease groups, and also found distinctive bacterial activity in those people with good oral health. Further studies should investigate the possibility of testing bacterial gene activity in saliva to identify oral diseases before they become clinically evident

Transcriptome analysis of bacteriophage communities in periodontal health and disease

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1781-0) contains supplementary material, which is available to authorized users