Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease

Abstract

Periodontitis is an inflammatory disease involving complex interactions between oral microorganisms and the host immune response. Understanding the structure of the microbiota community associated with periodontitis is essential for improving classifications and diagnoses of various types of periodontal diseases and will facilitate clinical decision-making. In this study, we used a 16S rRNA metagenomics approach to investigate and compare the compositions of the microbiota communities from 76 subgingival plagues samples, including 26 from healthy individuals and 50 from patients with periodontitis. Furthermore, we propose a novel feature selection algorithm for selecting features with more information from many variables with a combination of these features and machine learning methods were used to construct prediction models for predicting the health status of patients with periodontal disease. We identified a total of 12 phyla, 124 genera, and 355 species and observed differences between health- and periodontitis-associated bacterial communities at all phylogenetic levels. We discovered that the genera Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were more abundant in patients with periodontal disease, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter, and Granulicatella were found at higher levels in healthy controls. Using our feature selection algorithm, random forests performed better in terms of predictive power than other methods and consumed the least amount of computational time.

Topic Application of the Probiotic Streptococcus dentisani Improves Clinical and Microbiological Parameters Associated With Oral Health

“…or Kingella sp. (Jiang et al, 2013 ; Chen C. et al, 2018 ; Chen W. P. et al, 2018 ) support that probiotic administration induced a shift in bacterial composition which was clearly associated with oral health. The species-level data derived from Illumina sequencing must nevertheless be taken with caution, as short fragments of the 16S rRNA gene may provide uncertain or wrong taxonomic assignments (Claesson et al, 2010 ).…”

High-throughput DNA sequencing of microbiota at interproximal sites

“…Although Aggregatibacter actinomycetemcomitans has been several times associated with oral diseases [34], it was the little studied A. aphrophilus the species significantly more represented in the lingual region [35]. Some Aggregatibacter OTUs have been associated with intra-oral halitosis and periodontitis [24][25][26]36]. Lastly, Cardiobacterium hominis abundance has been correlated with aggressive periodontitis [37] and Colombo et al found a significant reduction in this genus after treatment [38].…”

Rapid diagnosis of periodontitis, a feasibility study using MALDI-TOF mass spectrometry

“…It was interesting to note that the 10 most differentially expressed peaks in dental plaque had lower levels of intensity in the periodontitis group. The genes Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were found to be more abundant in periodontitis patients, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter and Granulicatella were observed at higher levels in healthy subjects [45]. We hypothesize that these peaks could be associated with non-periodontal pathogens as initial colonizers that were less abundant in patients with periodontal diseases.…”

“…If the average richness of microbes in subgingival plaque from patients with periodontitis was higher than in samples from healthy subjects, the microbial communities associated with periodontal health were correlated with higher Shannon indexes [45]. Subgingival microbiota in periodontal diseases seemed to be characterized by more microbes with low relative abundance compared to healthy microbiota [45]. These findings can explain the lower level of intensity of the top 10 ranking peaks in the periodontitis group.…”

“…We hypothesize that these peaks could be associated with non-periodontal pathogens as initial colonizers that were less abundant in patients with periodontal diseases. If the average richness of microbes in subgingival plaque from patients with periodontitis was higher than in samples from healthy subjects, the microbial communities associated with periodontal health were correlated with higher Shannon indexes [45]. Subgingival microbiota in periodontal diseases seemed to be characterized by more microbes with low relative abundance compared to healthy microbiota [45].…”