Abstract
ObjectivesThe oral microbiota plays a significant role in oral health. The present study aims to characterize variations in the oral microbiota relative to the collection site, the dynamics of biofilm accumulation, and inherent inter-individual differences.MethodsWhole stimulated saliva and tooth biofilm samples from the 16 defined tooth regions were collected after 1, 2, or 3 days without oral hygiene (accumulation time) in six healthy adults with no signs of active caries or periodontal disease. The routines and conditions before and between sample collections were carefully standardized. Genomic DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were amplified by PCR and sequenced on an Illumina MiSeq platform. Sequences were quality controlled, amplicon sequence variants (ASVs) were clustered, and taxonomic allocation was performed against the expanded Human Oral Microbiome Database (eHOMD). Microbial community profiles were analyzed by multivariate modeling and a linear discriminant analysis (LDA) effect size (LEfSe) method.ResultsThe overall species profile in saliva and tooth biofilm differed between participants, as well as sample type, with a significantly higher diversity in tooth biofilm samples than saliva. On average, 45% of the detected species were shared between the two sample types. The microbiota profile changed from the most anterior to the most posterior tooth regions regardless of whether sampling was done after 1, 2, or 3 days without oral hygiene. Increasing accumulation time led to higher numbers of detected species in both the saliva and region-specific tooth biofilm niches.ConclusionThe present study confirms that the differences between individuals dominate over sample type and the time abstaining from oral hygiene for oral microbiota shaping. Therefore, a standardized accumulation time may be less important for some research questions aiming at separating individuals. Furthermore, the amount of DNA is sufficient if at least two teeth are sampled for microbiota characterization, which allows a site-specific characterization of, for example, caries or periodontitis.
Highlights
The human body is covered by microorganisms, with the number of bacterial cells slightly outnumbering the number of somatic cells [1]
Multivariate modeling revealed that each of the participants harbored a distinct profile of sequence variants (ASVs) and taxonomically defined species in the oral cavity, even if saliva from all three accumulation times or tooth biofilm samples from the 16 tooth sites at all three sampling occasions were included in the same models
We found that the average amount of DNA ranges from 0.86 to 11.2 μg/μl for two teeth and 24.1 to 32.9 μg/μl for saliva, and that the amount of extracted DNA was sufficient for sequencing for all individual samples after 24 h of accumulation time
Summary
The human body is covered by microorganisms, with the number of bacterial cells slightly outnumbering the number of somatic cells [1]. The warm and moist environment, epithelial surfaces and hard tooth surfaces, and restorative materials and ingested foods and drinks, and crevicular fluids and saliva provide a variety of local physicochemical disparities in the oral cavity. These distinctions in preconditions for bacteria to attach and thrive manifests as site-specific eubiotic or dysbiotic multispecies biofilms [4]. Beyond the physicochemical factors mentioned above, the surface-associated biofilms in the oral cavity manifest from bacterial adhesion to the tissue or tissue-associated receptors, interspecies receptor and adhesion interactions, and bacteria cell–cell signaling [8, 10]. One factor that disturbs this sequential building of the biofilms in the oral cavity is tooth brushing and other oral hygiene measures
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