Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health

Abstract

Background Important alterations exist in the microbiomes of supragingival biofilm and saliva samples from adolescent patients developing induced or spontaneous gingivitis relative to healthy controls. These and the relationships to dental health are not fully understood yet. Subjects and Methods Supragingival biofilm samples (n = 36) were collected from the teeth of 9 adolescents with gingivitis induced by orthodontic appliances, as well as dental plaques (n = 40) from 10 adolescents with spontaneous gingivitis, in addition to similar samples (n = 36) from 9 healthy controls. The bacterial metagenomes were analyzed by 16S rRNA gene amplicon sequencing. Salivary microbiomes of the same persons were characterized by shotgun metagenome sequencing. The data sets were examined using advanced bioinformatics workflows and two reference databases. Results The composition and diversity of bacterial communities did not differ extensively among the three study groups. Nevertheless, the relative abundances of the genera Fusobacterium, Akkermansia, Treponema, and Campylobacter were prominently higher in gingivitis patients versus controls. In contrast, the genera Lautropia, Kingella, Neisseria, Actinomyces, and Rothia were significantly more abundant in controls than in either of the two gingivitis groups. Conclusions The abundance pattern of certain taxa rather than individual strains shows characteristic features of potential diagnostic value. Stringent bioinformatics treatment of the sequencing data is mandatory to avoid unintentional misinterpretations.

Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms

“…First, an unstimulated saliva sample was collected into a sterile plastic tube from each subject using a simple drooling method as in our previous studies ( Wirth et al., 2020 ; Wirth et al., 2021 ). The samples were stored at -80°C until DNA isolation.…”

“…DNA extractions were carried out from both sample types by using the Macherey-Nagel (Düren, Germany) NucleoSpin Soil DNA kit (Macherey-Nagel: 740780.250). Sample preparation and quality estimation were performed according to Wirth et al. (2021) .…”

“…Briefly, the hypervariable V3-V4 region of the 16S rRNA gene was PCR-amplified, and DNA sequencing was carried out on an Illumina MiSeq machine using V2 sequencing chemistry (MiSeq Reagent Kit v2) (500 cycles). Detailed description of the applied method can be found in our previous article ( Wirth et al., 2021 ).…”

“…Amplicon sequencing data were handled in house-developed bioinformatics pipeline, containing five modules ( Wirth et al., 2021 ). 0pt?>1) Sequencing preparation: join paired end fastq reads ($cat).…”

“…Both read-based and genome-centric strategies were applied for the shotgun metagenome data analysis of saliva samples. Metagenomics data were analyzed with the workflow published in our previous study ( Wirth et al., 2021 ). This contained the following main steps: 1) Raw sequence filtering: low-quality reads were filtered by Prinseq ( Schmieder and Edwards, 2011 ) (default parameters, minlen: 100), and the quality of filtered sequences was checked with FastQC program.…”