Associations of sex, oral hygiene and smoking with oral species in distinct habitats at age 32 years.

The oral microbiome is ecologically diverse, complex, dynamic, and little understood. We describe the microbiota of four oral habitats in a birth cohort at age 32 and examine differences by sex, oral hygiene, and current smoking status, dental caries, and periodontal health. Oral biofilm samples collected from anterior labial supragingival, posterior lingual supragingival, subgingival, and tongue sites of 841 Dunedin Multidisciplinary Health and Development Study members were analysed using checkerboard DNA-DNA hybridization; focusing on 30 ecologically important bacterial species. The four habitats exhibited distinct microbial profiles that differed by sex. Streptococcus gordonii was more dominant in supragingival and tongue biofilms of males; Porphyromonas gingivalis exhibited higher relative abundance in subgingival biofilm of females. Males had higher scores than females for periodontal pathogens at supragingival sites. The relative abundance of several putative caries and periodontal pathogens differed in smokers and non-smokers. With poor oral hygiene significantly higher proportions of Gram-negative facultative anaerobes were present in subgingival biofilm and there were higher scores for the principal components characterised by putative cariogenic and periodontal pathogens at each site. Distinctive microenvironments shape oral biofilms and systematic differences exist by sex, oral hygiene, and smoking status.

Checkerboard DNA-DNA hybridization technology using digoxigenin detection.

Checkerboard DNA-DNA hybridization (CKB) is a technique that provides a simultaneous quantitative analysis of 40 microbial species against up to 28 mixed microbiota samples on a single membrane; using digoxigenin (DIG)-labeled, whole-genome DNA probes. Developed initially to study the predominantly gram-negative dental plaque microorganisms involved in periodontitis, we modified the probe species composition to focus on putative pathogens involved in the development of dental caries. CKB analysis is applicable to species from other biodiverse ecosystems and to a large number of samples. The major limitations are that high-quality DNA is required for the preparation of DIG-labeled probes and standards, and that probe specificity requires careful evaluation. Overall, CKB analysis provides a powerful ecological fingerprint of highly biodiverse microbiota based on key cultivable bacteria.