Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis

Abstract

The phylogenetic characteristics of microbial communities associated with periodontitis have been well studied, however, little is known about the functional endowments of this ecosystem. The present study examined 73 microbial assemblages from 25 individuals with generalized chronic periodontitis and 25 periodontally healthy individuals using whole genome shotgun sequencing. Core metabolic networks were computed from taxa and genes identified in at least 80% of individuals in each group. 50% of genes and species identified in health formed part of the core microbiome, while the disease-associated core microbiome contained 33% of genes and only 1% of taxa. Clinically healthy sites in individuals with periodontitis were more aligned with sites with disease than with health. 68% of the health-associated metagenome was dedicated to energy utilization through oxidative pathways, while in disease; fermentation and methanogenesis were predominant energy transfer mechanisms. Expanded functionality was observed in periodontitis, with unique- or over-representation of genes encoding for fermentation, antibiotic resistance, detoxification stress, adhesion, invasion and intracellular resistance, proteolysis, quorum sensing, Type III/IV secretion systems, phages and toxins in the disease-associated core microbiome. However, different species or consortia contributed to these functions in each individual. Several genes, but not species, demonstrated robust discriminating power between health and disease.

Metagenomic Sequencing of Stage 3 Periodontitis Reveals Phenotype-Specific Taxonomic and Functional Features of the Subgingival Microbiome

“…Therefore, the variance in the microbiome could not be explained by disease severity. This dispersion was more apparent in taxonomy than in the functional pro les, corroborating our earlier nding that the microbiome associated with periodontitis is taxonomically heterogenous but functionally congruent [20]. This was also corroborated by identifying a set of putative periodontal pathogens and perturbed functions common to all three diseases, suggesting that certain genes and taxa are broadly associated with the disease process.…”

“…34 nonsmoking, normoglycemic individuals with Stage 3 periodontitis as de ned by the 2017 classi cation [19], were recruited and informed consent or assent with parental approval was obtained as appropriate. Additionally, sequences from 25 stage 3 periodontitis and 25 periodontally healthy controls from a previous study [20] were reanalyzed. Periodontal health was de ned as clinical attachment loss (CAL) ≤ 1 mm, probing pocket depths (PD) ≤ 3 mm, mean gingival index <1.…”

Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs

“…Thus, our analysis supports a model where a variety of different bacteria may drive the metabolic process, supporting the polymicrobial dysbiotic nature of the periodontal disease (Darveau, 2010;Hajishengallis and Lamont, 2012;Rosier et al, 2014;Szafrański et al, 2015). Furthermore, our findings also support the notion that periodontitis occurs despite idiosyncratic differences between individuals as long as the community undergoes a switch in its functional and metabolic signals (Dabdoub et al, 2016).…”

Comparison of Sampling Techniques For qPCR Quantification of Periodontal Pathogens

“…Curette samples yielded on average 2.75x10 8 bacteria and paper points 6.76x10 7 bacteria in absence of gingival bleeding and in presence of gingival bleeding only 1.74x10 4 bacteria. The maximum number of bacteria recovered by paper points in presence of gingival bleeding was 2.88x10 5 , which is much smaller compared by the other types. The mean counts and the detection range of A. actinomycetemcomitans and T. denticola are listed in table 2.…”

“…The equilibrium between the host and microbial cells is very dynamic and absolutely necessary for the normal oral tissues functions. Perturbations by various environmental factors leads to establishment of a dysbiotic microbial community with elevated virulence potential and evade the local defense system [3][4][5]. Such mechanisms are responsible for oral diseases like caries, endodontic infections, gingivitis and periodontitis [6].…”