Analysis of oral bacterial communities: comparison of HOMINGS with a tree-based approach implemented in QIIME

Effects of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans on Modeling Subgingival Microbiome and Impairment of Oral Epithelial Barrier

Periodontitis is an exemplar of dysbiosis associated with the coordinated action of multiple members within the microbial consortium. The polymicrobial synergy and dysbiosis hypothesis proposes a dynamic host-microbiome balance, with certain modulators capable of disrupting eubiosis and driving shifts towards dysbiosis within the community. However, these factors remain to be explored. We established a Porphyromonas gingivalis- or Aggregatibacter actinomycetemcomitans-modified subgingival microbiome model and 16S rRNA sequencing revealed that P. gingivalis and A. actinomycetemcomitans altered the microbiome structure and composition indicated by α and β diversity metrics. P. gingivalis increased the subgingival dysbiosis index (SDI), while A. actinomycetemcomitans resulted in a lower SDI. Furthermore, P. gingivalis-stimulated microbiomes compromised epithelium function and reduced expression of tight junction proteins, whereas A. actinomycetemcomitans yielded mild effects. In conclusion, by inoculating P. gingivalis, we created dysbiotic microcosm biofilms in vitro resembling periodontitis-related subgingival microbiota, exhibiting enhanced dysbiosis and impaired epithelium integrity.

High-Throughput Sequencing of Oral Microbiota in Candida Carriage Sjögren's Syndrome Patients: A Pilot Cross-Sectional Study

BACKGROUND

This study sought to characterize the saliva microbiota of Candida carriage Sjögren's syndrome (SS) patients compared to oral candidiasis and healthy patients by high-throughput sequencing.

METHODS

Fifteen patients were included, with five Candida carriage SS patients (decayed, missing, and filled teeth (DMFT) score 22), five oral candidiasis patients (DMFT score 17), and five caries active healthy patients (DMFT score 14). Bacterial 16S rRNA was extracted from rinsed whole saliva. PCR amplification generated DNA amplicons of the V3-V4 hypervariable region, which were sequenced on an Illumina HiSeq 2500 sequencing platform and compared and aligned to the SILVA database. Taxonomy abundance and community structure diversity was analyzed using Mothur software v1.40.0.

RESULTS

A total of 1016/1298/1085 operational taxonomic units (OTUs) were obtained from SS patients/oral candidiasis patient/healthy patients. Treponema, Lactobacillus, Streptococcus, Selenomonas, and Veillonella were the primary genera in the three groups. The most abundant significantly mutative taxonomy (OTU001) was Veillonella parvula. Microbial diversity (alpha diversity and beta diversity) was significantly increased in SS patients. ANOSIM analyses revealed significantly different microbial compositional heterogeneity in SS patients compared to oral candidiasis and healthy patients.

CONCLUSION

Microbial dysbiosis differs significantly in SS patients independent of oral Candida carriage and DMFT.

Why Should We Consider Potential Roles of Oral Bacteria in the Pathogenesis of Sjögren Syndrome?

Sjögren syndrome (SS) is a chronic autoimmune disorder that primarily targets the salivary and lacrimal glands. The pathology of these exocrine glands is characterized by periductal focal lymphocytic infiltrates, and both T cell-mediated tissue injury and autoantibodies that interfere with the secretion process underlie glandular hypofunction. In addition to these adaptive mechanisms, multiple innate immune pathways are dysregulated, particularly in the salivary gland epithelium. Our understanding of the pathogenetic mechanisms of SS has substantially improved during the past decade. In contrast to viral infection, bacterial infection has never been considered in the pathogenesis of SS. In this review, oral dysbiosis associated with SS and evidence for bacterial infection of the salivary glands in SS were reviewed. In addition, the potential contributions of bacterial infection to innate activation of ductal epithelial cells, plasmacytoid dendritic cells, and B cells and to the breach of tolerance via bystander activation of autoreactive T cells and molecular mimicry were discussed. The added roles of bacteria may extend our understanding of the pathogenetic mechanisms and therapeutic approaches for this autoimmune exocrinopathy.

Assessing the Relationship Between Nitrate-Reducing Capacity of the Oral Microbiome and Systemic Outcomes

The significance of the oral microbiome in the generation of the nitric oxide (NO) via the enterosalivary nitrate-nitrite-nitric oxide pathway is increasingly recognized, directly linking the oral microbiome to cardiometabolic outcomes influenced by NO. The objective of this chapter is to outline a strategy of identifying pathway-specific bacterial taxa or predicted genes of interest from 16S rRNA data, specifically in the enterosalivary pathway of nitrate reduction, and analyzing their relationship with cardiometabolic outcomes using multivariable regression models.

Subgingival microbiome and clinical periodontal status in an elderly cohort: The WHICAP ancillary study of oral health

BACKGROUND

There is a sparsity of data describing the periodontal microbiome in elderly individuals. We analyzed the association of subgingival bacterial profiles and clinical periodontal status in a cohort of participants in the Washington Heights-Inwood Columbia Aging Project (WHICAP).

METHODS

Dentate individuals underwent a full-mouth periodontal examination at six sites/tooth. Up to four subgingival plaque samples per person, each obtained from the mesio-lingual site of the most posterior tooth in each quadrant, were harvested and pooled. Periodontal status was classified according to the Centers for Disease Control/American Academy of Periodontology (CDC/AAP) criteria as well as based on the percentage of teeth/person with pockets ≥4 mm deep. Bacterial DNA was isolated and was processed and analyzed using Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS). Differential abundance across the periodontal phenotypes was calculated using the R package DESeq2. α- and β-diversity metrics were calculated using DADA2-based clustering.

RESULTS

The mean age of the 739 participants was 74.5 years, and 32% were male. Several taxa including Sneathia amnii-like sp., Peptoniphilaceae [G-1] bacterium HMT 113, Porphyromonas gingivalis, Fretibacterium fastidiosum, Filifactor alocis, and Saccharibacteria (TM7) [G-1] bacterium HMT 346 were more abundant with increasing severity of periodontitis. In contrast, species such as Veillonella parvula, Veillonella dispar, Rothia dentocariosa, and Lautropia mirabilis were more abundant in health. Microbial diversity increased in parallel with the severity and extent of periodontitis.

CONCLUSIONS

The observed subgingival bacterial patterns in these elderly individuals corroborated corresponding findings in younger cohorts and were consistent with the concept that periodontitis is associated with perturbations in the resident microbiome.

Association Between Nitrate-Reducing Oral Bacteria and Cardiometabolic Outcomes: Results From ORIGINS

Background

The enterosalivary nitrate‐nitrite‐nitric oxide pathway is an alternative pathway of nitric oxide generation, potentially linking the oral microbiome to insulin resistance and blood pressure (BP). We hypothesized that increased abundance of nitrate‐reducing oral bacteria would be associated with lower levels of cardiometabolic risk cross‐sectionally.

Methods and Results

ORIGINS (Oral Infections, Glucose Intolerance, and Insulin Resistance Study) enrolled 300 diabetes mellitus–free adults aged 20 to 55 years (mean=34±10 years) (78% women). Microbial DNA was extracted from subgingival dental plaque (n=281) and V3–V4 regions of the 16S rRNA gene were sequenced to measure the relative abundances of 20 a priori–selected taxa with nitrate‐reducing capacity. Standardized scores of each taxon's relative abundance were summed, producing a nitrate‐reducing taxa summary score (NO₃TSS) for each participant. Natural log‐transformed homeostatic model assessment of insulin resistance, plasma glucose, systolic BP, and diastolic BP were regressed on NO₃TSS in multivariable linear regressions; prediabetes mellitus and hypertension prevalence were regressed on NO₃TSS using modified Poisson regression models. Nitrate‐reducing bacterial species represented 20±16% of all measured taxa. After multivariable adjustment, a 1‐SD increase in NO₃TSS, was associated with a −0.09 (95% CI, −0.15 to −0.03) and −1.03 mg/dL (95% CI, −1.903 to −0.16) lower natural log‐transformed homeostatic model assessment of insulin resistance and plasma glucose, respectively. NO₃TSS was associated with systolic BP only among patients without hypertension; 1‐SD increase in NO₃TSS was associated with −1.53 (95% CI, −2.82 to −0.24) mm Hg lower mean systolic BP. No associations were observed with prediabetes mellitus and hypertension.

Conclusions

A higher relative abundance of oral nitrate‐reducing bacteria was associated with lower insulin resistance and plasma glucose in the full cohort and with mean systolic BP in participants with normotension.

A rapid chair-side method for the estimation of oral bacterial colonization density

AIMS

Caries and periodontal disease are associated with inadequate control of oral bacteria. Since conventional microbiological evaluations are impractical in dental clinics or public engagement activities, a rapid test for the quantification of oral bacteria represents a useful tool. We describe the development of a colour change test to rapidly estimate bacterial colonisation density in the mouth.

METHODS AND RESULTS

Volunteers rinsed with milk or milkshake. Viability indicators were added and colour changes quantified during incubation. Using milkshake and the resazurin-based solution PrestoBlue (9% v/v), the method distinguished between samples before and after brushing within 5 min. Colour changes were quantified and viable counts were obtained using oral rinses. Measured colour changes strongly correlated with total counts of both anaerobes and streptococci (Spearman's correlation coefficient of 0·782 and 0·769, respectively, P ≤ 0·001) and with perceived changes, as determined by volunteers (n = 10) visually ranking images.

CONCLUSIONS

The resazurin milkshake test can rapidly and visually quantify viable bacteria in oral samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

The resazurin milkshake test could serve as a sensitive semi-quantitative method for measuring oral bacteria in human oral rinse samples.

Sex-specific differences in the salivary microbiome of caries-active children

Background and Objectives: Dental caries is a chronic disease affecting young children and has multi-factorial risk factors. The purpose of this work was to identify sex-specific differences in the salivary microbiota within caries-active children. Design: Saliva specimens were collected from 85 children (boys: 41; girls: 44) between the ages of 2-12 years. Salivary microbial DNA was subjected to PCR amplification using V3-V4 16S rDNA-specific primers and next-generation sequencing. Results: Significant sex differences in salivary microbiota were found between caries-active boys versus caries-active girls. Neisseria flavescens, Rothia aeria, and Haemophilus pittmaniae were found at significantly higher levels in caries-active boys. In contrast, Lactococcus lactis, Selenomonas species HOT 126, Actinobaculum species HOT 183, Veillonella parvula, and Alloprevotella species HOT 473 were found at significantly higher levels in caries-active girls. Conclusion: We have found the acid-generating, cariogenic Lactococcus lactis to be much more abundant in caries-active girls than caries-active boys, indicating that this microorganism may play a more significant role in shaping the cariogenic microbiome in girls. In addition, in caries-active girls, Alloprevotella species HOT 473 was the only species that exhibited both significant sex differences (4.4-fold difference; p=0.0003) as well as high abundance in numbers (1.85% of the total microbial population).