Bacterial diversity in the oral cavity of 10 healthy individuals

Abstract

The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11 368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.

Signature of Microbial Dysbiosis in Periodontitis

“…Capnocytophaga and Leptotrichia were not included because of their high rates of prevalence in CP samples (more than 90%; data not shown). Species belonging to the genus Rothia have been repeatedly described as being members of oral communities associated with periodontal health (26)(27)(28)(29)(30)(31) or at least as being more predominant in health (28). In the same way, Corynebacterium appeared to be more associated with healthy subgingival biofilm (32,33).…”

The oral metagenome in health and disease

“…A total of 4254 16S rRNA sequences were obtained (Supplementary Table 1), giving a similar picture of diversity to that obtained through 16S rRNA PCR-dependent procedures (Bik et al, 2010), although the relative proportions of each taxonomic group were different (Figure 1 Figure 1 Bacterial diversity in the oral cavity. The graph on the left shows the relative frequency of different bacterial taxa, based on the assignment of the DNA reads by the PhymmBL software and by 16S rRNA reads extracted from the metagenome, and compared with the PCR results obtained by Bik et al (2010). The graph on the right indicates the relative contribution of each taxonomic group to the coding potential of the ecosystem, based on the COGs functional classification system.…”

Association between living environment and human oral viral ecology

“…Although not every subject in the SHH demonstrated this trend, the viruses in households nos.1, 3 and 4 shared a significantly greater than expected fraction of homologous reads (Table 3). Although it seems plausible that virome constituents and viral exposures would directly reflect the bacterial communities present, we chose not to evaluate the bacterial communities for the following reasons: (1) we previously have demonstrated that inverse relationships exist between certain viruses and their host bacteria in the human oral cavity (Pride et al, 2012a), (2) much of the variation in CRISPR communities likely exists at the strain level and thus cannot be evaluated through 16S rRNA sequencing, and (3) there have already been relatively thorough evaluations of the bacterial communities present in saliva (Bachrach et al, 2003;Lazarevic et al, 2009;Nasidze et al, 2009;Bik et al, 2010;Pride et al, 2011a;Pride et al, 2011). Thus, we do not believe that sequencing of 16S rRNA would clarify the effects of bacteria on the viral community constituents within households.…”