Structure and Function of Oral Microbial Community in Periodontitis Based on Integrated Data

Abstract

ObjectiveMicroorganisms play a key role in the initiation and progression of periodontal disease. Research studies have focused on seeking specific microorganisms for diagnosing and monitoring the outcome of periodontitis treatment. Large samples may help to discover novel potential biomarkers and capture the common characteristics among different periodontitis patients. This study examines how to screen and merge high-quality periodontitis-related sequence datasets from several similar projects to analyze and mine the potential information comprehensively.MethodsIn all, 943 subgingival samples from nine publications were included based on predetermined screening criteria. A uniform pipeline (QIIME2) was applied to clean the raw sequence datasets and merge them together. Microbial structure, biomarkers, and correlation network were explored between periodontitis and healthy individuals. The microbiota patterns at different periodontal pocket depths were described. Additionally, potential microbial functions and metabolic pathways were predicted using PICRUSt to assess the differences between health and periodontitis.ResultsThe subgingival microbial communities and functions in subjects with periodontitis were significantly different from those in healthy subjects. Treponema, TG5, Desulfobulbus, Catonella, Bacteroides, Aggregatibacter, Peptostreptococcus, and Eikenella were periodontitis biomarkers, while Veillonella, Corynebacterium, Neisseria, Rothia, Paludibacter, Capnocytophaga, and Kingella were signature of healthy periodontium. With the variation of pocket depth from shallow to deep pocket, the proportion of Spirochaetes, Bacteroidetes, TM7, and Fusobacteria increased, whereas that of Proteobacteria and Actinobacteria decreased. Synergistic relationships were observed among different pathobionts and negative relationships were noted between periodontal pathobionts and healthy microbiota.ConclusionThis study shows significant differences in the oral microbial community and potential metabolic pathways between the periodontitis and healthy groups. Our integrated analysis provides potential biomarkers and directions for in-depth research. Moreover, a new method for integrating similar sequence data is shown here that can be applied to other microbial-related areas.

Periodontal Disease: The Good, The Bad, and The Unknown

“…Many studies have investigated the abundance of certain phyla and genera that differentiate between periodontal health and disease. Although many discrepancies exist between studies, a shift in relative proportions of the four most abundant phyla, including Bacteroidetes, Actinobacteria, Proteobacteria and Firmicutes, and more specifically a decrease in the abundance of Proteobacteria and Actinobacteria and increased abundance of Bacteroidetes and Firmicutes in periodontitis, is unvarying amongst different investigators ( Griffen et al., 2012 ; Wang et al., 2013 ; Cai et al., 2021 ). On a genus level, Treponema is overrepresented in periodontal disease ( Abusleme et al., 2013 ; Cai et al., 2021 ), and conversely Rothia, Actinomyces , and Neisseria dominate communities of health ( Abusleme et al., 2013 ; Rosier et al., 2020 ; Cai et al., 2021 ).…”

“…Although many discrepancies exist between studies, a shift in relative proportions of the four most abundant phyla, including Bacteroidetes, Actinobacteria, Proteobacteria and Firmicutes, and more specifically a decrease in the abundance of Proteobacteria and Actinobacteria and increased abundance of Bacteroidetes and Firmicutes in periodontitis, is unvarying amongst different investigators ( Griffen et al., 2012 ; Wang et al., 2013 ; Cai et al., 2021 ). On a genus level, Treponema is overrepresented in periodontal disease ( Abusleme et al., 2013 ; Cai et al., 2021 ), and conversely Rothia, Actinomyces , and Neisseria dominate communities of health ( Abusleme et al., 2013 ; Rosier et al., 2020 ; Cai et al., 2021 ). As the understanding of the species involved in the etiology of periodontitis grows, the relationship between such pathogens, pathobionts, and oral symbionts among and across one another has revealed a complex network comprised of antagonistic and synergistic interactions among members of the oral microbiome.…”

“…Metagenomic analysis of collective data from nine peer-reviewed publications, in which a total of 943 subgingival samples from periodontitis-afflicted and healthy subjects identified enriched pathways exclusive to each cohort: significant differences ( p<0.05 ) in cell motility, cellular processing and signaling, nucleotide metabolism, metabolism of cofactors and vitamins, and nervous system function were significantly different, with an increase in bacterial motility proteins and assembly among periodontitis patients. Additionally, a significant difference (p<0.05) was identified for the synthesis and degradation of ketone bodies, nitrogen metabolism, and sulfur metabolism ( Cai et al., 2021 ).…”

Dental Materials for Oral Microbiota Dysbiosis: An Update

“…It is obvious that the dysbiosis of the microbiota causes differences in metabolic pathways and functions. Elevated levels of bacterial motility proteins and flagellar assembly may imply an increased invasive capacity of pathogenic bacteria in periodontitis ( Cai et al., 2021 ). Studies have shown that bacterial phenolic acid metabolites, especially phenylacetate and volatile sulfur compounds were positively associated with periodontal exploration depth ( Liebsch et al., 2019 ; Abdullah et al., 2020 ).…”

Chemotherapy-associated oral microbiome changes in breast cancer patients

“…Moreover, the effects of the oral microbiome on oral and dental health are well characterized ( 21 , 22 ). Upon the dysbiosis of the oral community, pathogenic taxa like Porhyromonas , Prevotella , Veillonella , or Actinomyces my take over and cause critical illnesses ( 13 , 23 ).…”