Relationship between periodontitis-associated subgingival microbiota and clinical inflammation by 16S pyrosequencing

Microbiological and functional traits of peri-implant mucositis and correlation with disease severity

Osseointegrated dental implants replace missing teeth and create an artificial surface for biofilms of complex microbial communities to grow. These biofilms on implants and dental surfaces can trigger infection and inflammation in the surrounding tissue. This study investigated the microbial characteristics of peri-implant mucositis (PM) and explored the correlation between microbial ecological imbalance, community function, and disease severity by comparing the submucosal microflora from PM with those of healthy inter-subject implants and intra-subject gingivitis (G) within a group of 32 individuals. We analyzed submucosal plaques from PM, healthy implant (HI), and G sites using metagenome shotgun sequencing. The bacterial diversity of HIs was higher than that of PM, according to the Simpson index. Beta diversity revealed differences in taxonomic and functional compositions across the groups. Linear discriminant analysis of the effect size identified 15 genera and 37 species as biomarkers that distinguished PM from HIs. Pathways involving cell motility and protein processing in the endoplasmic reticulum were upregulated in PM, while pathways related to the metabolism of cofactors and vitamins were downregulated. Microbial dysbiosis correlated positively with the severity of clinical inflammation measured by the sulcus bleeding index (SBI) in PM. Prevotella and protein processing in the endoplasmic reticulum also correlated positively with the SBI. Our study revealed PM's microbiological and functional traits and suggested the importance of certain functions in disease severity.IMPORTANCEPeri-implant mucositis is an early stage in the progression of peri-implantitis. The high prevalence of it has been a threat to the widespread use of implant prosthodontics. The link between the submucosal microbiome and peri-implant mucositis was demonstrated previously. Nevertheless, the taxonomic and functional composition of the peri-implant mucositis microbiome remains controversial. In this study, we comprehensively characterize the microbial signature of peri-implant mucositis and for the first time, we investigate the correlations between microbial dysbiosis, functional potential, and disease severity. With the help of metagenomic sequencing, we find the positive correlations between microbial dysbiosis, genus Prevotella, pathway of protein processing in the endoplasmic reticulum, and more severe mucosal bleeding in the peri-implant mucositis. Our studies offer insight into the pathogenesis of peri-implant mucositis by providing information on the relationships between community function and disease severity.

Biology of tongue coating in different disease stages of RA and its value in disease progression

OBJECTIVE

To assess and compare the composition of tongue coating microbiota among patients at different stages of rheumatoid arthritis (RA).

METHODS

A total of 47 patients diagnosed with RA, as per the American College of Rheumatology criteria, and 10 healthy individuals were enrolled in this study. The RA patients were stratified considering their Disease Activity Score 28 (DAS28), a composite measure based on the 28 tender and swollen joint count and erythrocyte sedimentation rate (ESR). The study population was further categorized into active phase group (LMH group) and inactive phase group (RE group) according to their DAS28 values. DNA extraction was extracted from tongue coating samples. Subsequently, the V3-V4 16S rDNA region was selectively amplified and sequenced through high-throughput 16S rDNA analysis. The resulting data were then utilized to ascertain the microbial contents.

RESULTS

Significant variations were observed in the tongue coating microbiota of patients with RA during active and inactive phases, in comparison to healthy individuals (p < 0.05). At the genus level, the presence of Prevotellan, Veillonella, Rothia, and Neisseria in RA patients was notably more evident than in the healthy control (HC) group. These disparities find support in existing research on gut and oral microbiota. During the active phase of RA, the relative abundance of Veillonella, Rothia, and Neisseria in the tongue coating microbiota of patients was significantly higher than in those with inactive RA. These findings underscore the need for further and in-depth research on the potential impact of these microorganisms on the progression of RA disease.

CONCLUSION

The results substantiate the hypothesis that tongue coating microbes actively contribute to the progression of RA.

Subgingival microbial changes in Down Syndrome adults with periodontitis after chlorhexidine adjunct non-surgical therapy and monthly recalls-A 12-month case series study

OBJECTIVES

Down Syndrome (DS) adults are at risk for periodontitis. Previous reports indicated difficulties in periodontopathogen reduction or eradication in DS individuals after periodontal treatment. This case series follows the subgingival microbial changes in adult DS individuals with periodontitis who received chlorhexidine adjunct non-surgical therapy plus 12-month recalls.

METHODS

Twenty periodontitis DS participants (7 females; 25.5 ± 5.6 years of age; 3 with generalized periodontitis) partook in a study involving non-surgical mechanical periodontal therapy, twice daily chlorhexidine gel toothbrushing, chlorhexidine mouthwash, and monthly recalls. The subgingival microbiota profile was followed at baseline, 6-, and 12-months post-operation.

RESULTS

Desulfobulbus, Saccharibacteria (TM7), Tannerella, and Porphyromonas were the major subgingival genera in this DS cohort. Favorable chlorhexidine adjunct non-surgical treatment outcomes were observed, with the relative abundance of Desulfobulbus sp. HMT 041, Saccharibacteria (TM7) [G-1] bacterium HMT 346 or 349, and Tannerella forsythia significantly reduced at the end of the study, but no significant reduction of Porphyromonas gingivalis or Aggregatibacter actinomycetemcomitans could be observed. Relative abundance of Desulfobulbus sp. HMT 041 and T. forsythia were also found to be significantly associated with plaque, bleeding on probing, and probing pocket depth (PPD, in mm) at a site level, while the relative abundance of Halomonas pacifica was negatively associated with PPD.

CONCLUSIONS

Successful chlorhexidine adjunct non-surgical treatment with hygiene care was accompanied by a subgingival microbial shift involving certain periodontopathogenic species, except P. gingivalis and A. actinomycetemcomitans. Further investigations are required to clarify the mechanism underpinning the unchanged relative abundance of the above two pathogens despite favorable clinical responses.

CLINICAL SIGNIFICANCE

DS adults face challenges achieving optimal home care or hygiene for periodontal healing and disease prevention. Chemical adjunct mechanical periodontal therapy plus regular recalls appeared promising clinically and microbiologically, with subgingival periodontopathogenic species reduction. The persistence of A. actinomycetemcomitans and P. gingivalis in subgingival niches post-treatment warrants further investigation.

Microbial composition of goat buck's ejaculates is modified by the process of preparing and storing refrigerated semen doses

Ejaculates present their own microbiota, and a link between ejaculates' microbiota and sperm quality and fertility exists. With the development of artificial insemination in animal breeding, ejaculates must be manipulated by diluting them with extenders and storing them at temperatures below body temperature. The effects that these processes have on the original semen microbiota have never been studied. This study explores the effects of the protocol for preparing refrigerated goat buck semen doses and storing on seminal microbiota. Semen from six adult goat bucks of the Murciano-Granadina breed (24 ejaculates) was used, cooled to 4 °C in a skimmed milk-based extender, and stored at this temperature for 24 h. Samples were taken in different steps: in the raw ejaculates (ejaculates), after dilution with the refrigeration extender (diluted), immediately after reaching 4 °C (chilled 0 h) and the samples refrigerated at 4 °C and stored at this temperature for 24 h (chilled 24 h). Sperm quality (motility and integrity of plasma and acrosomal membrane, and mitochondrial functionality) was also evaluated. Bacterial 16S rRNA sequencing was used to study the seminal microbiota. Our results indicated that both refrigeration and storage at 4 °C negatively affected sperm quality parameters. Preparing semen doses and their subsequent conservation caused a significant change in the bacterial community structure. Raw ejaculates showed a lower Pielou's evenness index than the other samples (diluted, chilled 0 h and chilled 24 h). Ejaculates also had a lower Shannon's diversity index (3.44) than the diluted semen (4.17) and the semen chilled for 24 h (4.43). Regarding beta diversity, significant differences were detected between ejaculates and the other treatments. Differences were also found in unweighted UniFrac distances between the semen chilled for 0 h and that chilled for 24 h. At the genus level, marked effects of preparing doses and their subsequent conservation were also evident: 199 genera that were absent in ejaculates were found in the semen chilled and stored for 24 h; 177 genera that were present in ejaculates disappeared after 24-h refrigeration. In conclusion, the extender and protocol for preparing refrigerated goat buck semen doses considerably modify microbial ejaculate composition.

Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis

In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes in the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.

Mucosal bleeding correlates with submucosal microbial dysbiosis in peri-implant mucositis of patients with periodontitis

OBJECTIVES

This study aimed to investigate the relationship between microbial communities and the severity of peri-implant mucosal bleeding in peri-implant mucositis.

MATERIALS AND METHODS

Submucosal plaque samples were collected from 54 implants divided into the healthy implant (HI) group, peri-implant mucositis (PM) group, and peri-implantitis (PI) group. Sequencing of 16S rRNA was performed using the Illumina MiSeq platform. Alpha diversity (i.e., Shannon and Chao index) and beta diversity were used to measure microbial diversity within and between microbial communities, respectively. Differences in microbial taxa between groups were assessed via linear discriminate analysis effect size. Correlation between the modified sulcus bleeding index (mSBI) and microbial dysbiosis index (MDI) was examined using Spearman correlation analysis and linear models.

RESULTS

The submucosal bacterial richness (Chao index) was positively correlated with the mean mSBI in the PM group. As the mean mSBI increased in the PM group, the beta diversity became closer to that of the PI group. In the PM group, the abundances of 47 genera were significantly correlated with the mean mSBI, and the MDI was positively associated with the mean mSBI. Fourteen of the forty-seven genera were discriminative taxa between the HI and PI groups, and the abundances of these biomarkers became closer to those in the PI group in the progression of peri-implant disease.

CONCLUSIONS

A higher mSBI value corresponded to a higher risk of microbial dysbiosis in peri-implant mucositis. The biomarkers identified may be useful for monitoring the progression of peri-implant disease.

Whole-genome metagenomic analysis of the oral microbiota in patients with obstructive sleep apnea

PURPOSE

The oral microbiota is closely associated with systemic health, but few studies have investigated the oral microbiota in patients with obstructive sleep apnea (OSA). This study aimed to identify the variation of oral microbiota among patients with severe OSA, and the change of oral microbiota after treatment with continuous positive airway pressure (CPAP).

METHODS

Participants were enrolled in the study from November 2020 to August 2021. Sleep parameters using full nocturnal polysomnography (PSG) were collected on healthy controls, patients with severe OSA, and patients with severe OSA after CPAP treatment for 3 months. Oral samples were also collected by rubbing disposable medical sterile swabs on the buccal mucosa. Routine blood tests and biochemical indicators were measured using the fully automated biochemical analyzer. Oral microbial composition of oral samples were determined using whole-genome metagenomic analysis in all participants. Correlations were analyzed between the oral microbiota and blood lipids.

RESULTS

Study enrollment included 14 participants, 7 healthy controls and 7 patients with severe OSA. At the species level, the relative abundances of Prevotella, Alloprevotella, Bacteroides, Veillonella_tobetsuensis, Candidatus saccharimonas, and Leptotrichia in the groups with severe OSA were significantly lower than those in the healthy controls (P both < 0.05). The abundances of Capnocytophaga, Veillonella, Bacillus_anthracis, Eikenella, and Kingella were significantly higher whereas the abundances of Gordonia and Streptococcus were significantly lower in the group with severe OSA compared to the severe OSA-CPAP group (P < 0.05 for both). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), 4 pathways changed in the group with severe OSA compared with healthy controls (P both < 0.05). Pathways related to Novobiocin biosynthesis, 2-Oxocarboxylic acid metabolism, and Histidine metabolism were enriched in the patients with severe OSA. Nine pathways showed significant differences with regard to the relative abundances of phenylalanine metabolism; alanine, aspartate, and glutamate metabolism; one carbon pool by folate; monobactam biosynthesis; 2-oxocarboxylic acid metabolism; arginine biosynthesis and vitamin B6 metabolism; novobiocin biosynthesis; and arginine and proline metabolism, which were significantly higher in the group with severe OSA compared to the severe OSA-CPAP group (P both < 0.05). The Spearman correlation analysis between blood lipid parameters and oral microbiota components showed that negative correlations were observed between total cholesterol and Streptomyces (r =  - 0.893, P = 0.007), and high-density lipoprotein cholesterol (HDL-C) and Gordonia (r = - 0.821, P = 0.023); positive correlations were observed between HDL-C and Candidatus saccharimonas (r = 0.929, P = 0.003), and low-density lipoprotein cholesterol (LDL-C) and Capnocytophaga (r = 0.893, P = 0.007).

CONCLUSION

There was an apparent discrepancy of the oral microbiota and metabolic pathways between the group with severe OSA and controls, and CPAP significantly changed oral microbial abundance and metabolic pathways in patients with severe OSA. Correlation analysis showed that these oral bacteria were strongly correlated with the blood lipids level.

The making of the oral microbiome in Agta hunter-gatherers

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analysed the oral microbiota of the Agta, a hunter-gatherer population where some members have adopted an agricultural diet. We show that age is the strongest factor modulating the microbiome, probably through immunosenescence since we identified an increase in the number of species classified as pathogens with age. We also characterised biological and cultural processes generating sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggest that shifting from a fish/meat diet to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All of these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial and shaped by various ecological and social factors that modify the oral environment.

Impact of 16S rRNA Gene Redundancy and Primer Pair Selection on the Quantification and Classification of Oral Microbiota in Next-Generation Sequencing

This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated. Next, 39 primer pairs were used to search for matches in the genomes and obtain amplicons. For each primer, we calculated the number of gene amplicons, variants, genomes, and species detected and the percentage of coverage at the species level with no MAs (SC-NMA). The results showed that 94.09% of oral bacteria and 52.59% of oral archaea had more than one intragenomic 16S rRNA gene. From 1.29% to 46.70% of bacterial species and from 4.65% to 38.89% of archaea detected by the primers had MAs. The best primers were the following (SC-NMA; region; position for Escherichia coli [GenBank version no. J01859.1]): KP_F048-OP_R030 for bacteria (93.55%; V3 to V7; 342 to 1079), KP_F018-KP_R063 for archaea (89.63%; V3 to V9; undefined to 1506), and OP_F114-OP_R121 for both domains (92.52%; V3 to V9; 340 to 1405). In addition to 16S rRNA gene redundancy, the presence of MAs must be controlled to ensure an accurate interpretation of microbial diversity data. The SC-NMA is a more useful parameter than the conventional coverage percentage for selecting the best primer pairs. The pairs used the most in the oral microbiome literature were not among the best performers. IMPORTANCE Hundreds of publications have studied the oral microbiome through 16S rRNA gene sequencing. However, none have assessed the number of 16S rRNA genes in the genomes of oral microbes, or how the use of primer pairs targeting different regions affects the detection of MAs from different taxa. Here, we found that almost all oral bacteria and more than half of oral archaea have more than one intragenomic 16S rRNA gene. The performance of the primer pairs in not detecting MAs increases as the length of the amplicon augments. As none of those most employed in the oral literature were among the best performers, we selected a series of primers to detect bacteria and/or archaea based on their percentage of species detected without MAs. The intragenomic 16S rRNA gene redundancy and the presence of MAs between distinct taxa need to be considered to ensure an accurate interpretation of microbial diversity data.

Periodontal disease severity is associated to pathogenic consortia comprising putative and candidate periodontal pathogens

BACKGROUND

Based on a holistic concept of polymicrobial etiology, we have hypothesized that putative and candidate periodontal pathogens are more frequently detected in consortia than alone in advanced forms of periodontal diseases (PD).

OBJECTIVE

To correlate specific consortia of periodontal pathogens with clinical periodontal status and severity of periodontitis.

METHODOLOGY

Subgingival biofilm was obtained from individuals with periodontal health (113, PH), gingivitis (91, G), and periodontitis (209, P). Genomic DNA was purified and the species Aggregatibacter actinomycetemcomitans (Aa), Aa JP2-like strain, Porphyromonas gingivalis (Pg), Dialister pneumosintes (Dp), and Filifactor alocis (Fa) were detected by PCR. Configural frequency and logistic regression analyses were performed to correlate microbial consortia and PD.

RESULTS

Aa + Pg in the presence of Dp (phi=0.240; χ2=11.9, p<0.01), as well as Aa JP2 + Dp + Fa (phi=0.186, χ2=4.6, p<0.05) were significantly more associated in advanced stages of P. The consortium Aa + Fa + Dp was strongly associated with deep pocketing and inflammation (p<0.001). The best predictors of disease severity (80% accuracy) included older age (OR 1.11 [95% CI 1.07 - 1.15], p<0.001), Black/African-American ancestry (OR 1.89 [95% CI 1.19 - 2.99], p=0.007), and high frequency of Aa + Pg + Dp (OR 3.04 [95% CI 1.49 - 6.22], p=0.002).

CONCLUSION

Specific microbial consortia of putative and novel periodontal pathogens, associated with demographic parameters, correlate with severe periodontitis, supporting the multifactorial nature of PD.

Tobacco smoke exacerbates Filifactor alocis pathogenicity

AIM

Filifactor alocis has recently emerged as a periodontal pathobiont that appears to thrive in the oral cavity of smokers. We hypothesized that identification of smoke-responsive F. alocis genes would provide insight into adaptive strategies and that cigarette smoke would enhance F. alocis pathogenesis in vivo.

MATERIALS AND METHODS

F. alocis was grown in vitro and cigarette smoke extract-responsive genes determined by RNAseq. Mice were exposed, or not, to mainstream 1R6F research cigarette smoke and infected with F. alocis, or not, in an acute ligature model of periodontitis. Key clinical, infectious, and immune data were collected.

RESULTS

In culture, F. alocis growth was unaffected by smoke conditioning and only a small number of genes were specifically regulated by smoke exposure. Reduced murine mass, differences in F. alocis-cognizant antibody production, and altered immune profiles as well as altered alveolar bone loss were all attributable to smoke exposure and/or F. alocis infection in vivo.

CONCLUSIONS

F. alocis is well-adapted to tobacco-rich conditions and its pathogenesis is enhanced by tobacco smoke exposure. A smoke-exposed ligature model of periodontitis shows promise as a tool with which to further unravel mechanisms underlying tobacco-enhanced, bacteria-induced disease.

Association of nine pathobionts with periodontitis in four South American and European countries

Aim

Our aim was to compare the prevalence and load of nine pathobionts in subgingival samples of healthy individuals and periodontitis patients from four different countries.

Methods

Five hundred and seven subgingival biofilm samples were collected from healthy subjects and periodontitis patients in Belgium, Chile, Peru and Spain. The prevalence and load of Eubacterium brachy, Filifactor alocis, Fretibacterium fastidiosum, Porphyromonas endodontalis, Porphyromonas gingivalis, Selenomonas sputigena, Treponema denticola, Tannerella forsythia and Treponema socranskii were measured by quantitative PCR.

Results

The association with periodontitis of all species, except for T. socranskii, was confirmed in all countries but Peru, where only P. endodontalis, P. gingivalis and T. denticola were found to be significantly associated. Moreover, most species showed higher loads at greater CAL and PPD, but not where there was BOP. Through Principal Component Analysis, samples showed clearly different distributions by diagnosis, despite observing a smaller separation in Peruvian samples.

Conclusions

Unlike prevalence, relative load was found to be a reliable variable to discriminate the association of the species with periodontitis. Based on this, F. alocis, P. endodontalis, P. gingivalis, T. denticola and T. forsythia may be biomarkers of disease in Belgium, Chile and Spain, due to their significantly higher abundance in periodontitis patients.

A mouthwash formulated with o-cymen-5-ol and zinc chloride specifically targets potential pathogens without impairing the native oral microbiome in healthy individuals

Background

Many antimicrobial compounds in mouthwashes can have a negative impact on the oral microbiome. O-cymen-5-ol, a compound derived from a phytochemical, has a targeted mode of action and is being used as an alternative. However, its effect on the native oral microbiome is unknown.

Aim

To assess the effect of a mouthwash formulated with o-cymen-5-ol and zinc chloride on the oral microbiome of healthy individuals.

Methods

A mouthwash formulated with o-cymen-5-ol and zinc chloride was administered to a cohort of 51 volunteers for 14 days, while another cohort of 49 volunteers received a placebo. The evolution of the oral microbiome in both groups was analysed using a metataxonomic approach.

Results

Analysis of the oral microbiome showed that the mouthwash selectively targeted potential oral pathogens while maintaining the integrity of the rest of the microbiome. Specifically, the relative abundance of several potentially pathogenic bacterial taxa, namely Fusobacteriota, Prevotella, Actinomyces, Granulicatella, Abiotrophia, Lautropia, Lachnoanaerobaculum, Eubacterium (nodatum group) and Absconditabacteriales (SR1) decreased, while the growth of Rothia, a nitrate-reducing bacterium beneficial for blood pressure, was stimulated.

Conclusions

The use of o-cymen-5-ol and zinc chloride as antimicrobial agents in oral mouthwashes is a valuable alternative to classical antimicrobial agents.

An In Vivo Study on the Development of Bacterial Microbiome on Clear Orthodontic Retainer

OBJECTIVES

The objective of this study was to see how the bacterial composition changes on clear orthodontic retainer over a 14-day period.

METHODS

Saliva and plaque samples collected from a clear retainer surface were obtained from five healthy volunteers receiving retainer treatment. Prior to clear retainer delivery, patients had not been wearing any other appliances. Patients were instructed to wear their clear retainer for the 14-day period, taking them off to eat and to clean them with a soft-bristle toothbrush. The bacterial composition was determined via Illumina MiSeq sequencing of the bacterial 16S rRNA. After bioinformatics processing using the QIIME pipeline, the intra- and intergroup biodiversity of the sample was analyzed.

RESULTS

The bacterial composition changed over a 14-day period in the saliva and on the clear retainer. When comparing the different phylum levels between saliva and clear retainer' microbiota, the Firmicutes were significantly increased 1.26-fold (p = 0.0194) and 1.34-fold (p = 0.0123) after 7 and 14 days of retainer treatment when compared to saliva, respectively. The Campylobacteriota were significantly decreased 1.80-fold (p = 0.05) in the clear retainer when compared to saliva at 7 days. At the genus level, several microbiota were significantly increased in relative abundance in the clear retainer after the 14-day period.

CONCLUSION

These findings reveal that the presence of a clear retainer in the mouth might lead to enamel changes or periodontal tissue destruction, especially after 14 days of use.

Entamoeba gingivalis is associated with periodontal conditions in Chinese young patients: A cross-sectional study

Background

This study investigated the prevalence and relative abundance of Entamoeba gingivalis (E. gingivalis) in Chinese young patients with different periodontal conditions, and its association with subgingival microbial composition, periodontal parameters, and cytokines in gingival crevicular fluid.

Methods

Participants (age: 18–45 years) diagnosed with stage II–IV periodontitis, gingivitis, or periodontal health underwent periodontal examination and sampling. Subgingival plaque was analyzed by 16S+18S sequencing for E. gingivalis detection and microbial analysis. The distribution of E. gingivalis in subgingival plaque was illustrated by fluorescence in situ hybridization. Interleukin-1β, interleukin-8, and tumor necrosis factor-α in gingival crevicular fluid were measured by multiplexed flow cytometric assay.

Results

This cross-sectional study included 120 sites from 60 participants. The prevalence and relative abundance of E. gingivalis were significantly increased in periodontitis (p<0.05). The sites were classified into three subgroups according to the relative abundance of E. gingivalis: negative group (Eg0, n=56); low-abundance group (Eg1, n=32); and high-abundance group (Eg2, n=32). The subgingival microflora in the subgroups showed stepwise changes at both the phylum and genus levels. The microflora compositions were significantly altered from Eg0 to Eg2 (p<0.001). Co-occurrence network analysis showed that Porphyromonas, Treponema, Tannerella, Filifactor, TG5, and Desulfobulbus were highly correlated with E. gingivalis (r>0.6, p<0.001). Correlation analysis showed that E. gingivalis was closely associated with important periodontal parameters and cytokines (p<0.01).

Conclusion

E. gingivalis was enriched in periodontitis and closely associated with subgingival microbial dysbiosis, periodontal parameters and cytokines in gingival crevicular fluid. Thus, it may be an important pathogen in periodontal disease.

Differences in the subgingival microbiome according to stage of periodontitis: A comparison of two geographic regions

No microbiological criteria were included in the 2018 EFP-AAP classification of periodontal diseases that could be used to differentiate between stages and grades. Furthermore, differences in the subgingival microbiome depending on stage and grade have not been established. Sixty subgingival biofilm samples were collected in Spain (n = 30) and Colombia (n = 30) from three distinct patient categories: those with periodontal health/gingivitis (n = 20), those with stage I-II periodontitis (n = 20), and those with stage III-IV periodontitis (n = 20). Patients were evaluated by 16S rRNA gene amplification sequencing. Amplicon sequence variants were used to assign taxonomic categories compared to the Human Oral Microbiome Database (threshold ≥97% identity). Alpha diversity was established by Shannon and Simpson indices, and principal coordinate analysis, ANOSIM, and PERMANOVA of the UNIFRAC distances were performed using QIIME2. Although differences in the alpha diversity were observed between samples according to country, Filifactor alocis, Peptostreptococcaceae [XI][G-4] bacterium HMT 369, Fretibacterium fastidiosum, Lachnospiraceae [G-8] bacterium HMT 500, Peptostreptococcaceae [XI][G-5] [Eubacterium] saphenum, Peptostreptococcus stomatis, and Tannerella forsythia were associated with periodontitis sites in all stages. However, only F. alocis, Peptostreptococcaceae [XI][G-4] bacterium HMT 369, Peptostreptococcaceae [XI][G-9] [Eubacterium] brachy, Peptostreptococcaceae [XI][G-5] [Eubacterium] saphenum, and Desulfobulbus sp. HMT 041 were consistent in stage III-IV periodontitis in both countries. Porphyromonas gingivalis and Tannerella forsythia were differentially expressed in severe lesions in the countries studied. Although some non-cultivable microorganisms showed differential patterns between the different stages of periodontitis, they were not the same in the two countries evaluated. Further studies using larger samples with advanced next-generation techniques for high-throughput sequencing of phyla and non-cultivable bacteria within the subgingival microbiome could provide more insight into the differences between stages of periodontitis.

Impact of smoking on peri-implant bleeding on probing

BACKGROUND

Studies around natural dentition demonstrated that smoking can reduce the tendency of inflamed tissue to bleed upon probing after controlling for possible confounders. In addition, previous research suggested that smokers may present alterations of the peri-implant microbiome.

AIM

This study aimed at investigating the impact of smoking on: (1) peri-implant bleeding on probing (BOP; primary objective); (2) the association between BOP/bone loss and BOP/visible gingival inflammation; (3) peri-implant microbiome.

METHODS

Partially edentulous patients with implants restored with a single crowns were included in this study. Subjects were either smokers (≥1 cigarettes per day) or nonsmokers (never smokers). The primary outcome of this cross-sectional study was BOP and secondary outcomes included: Probing pocket depth (PPD), Modified gingival Index (mGI) and Progressive Marginal Bone Loss. In addition, microbial profiles of the subjects were assessed through sequencing of the 16S rRNA gene. Univariate and multilevel multivariate analyses by means of Generalized Estimating Equations were conducted to analyze the association between smoking and peri-implant BOP.

RESULTS

Overall, 27 nonsmokers and 27 smokers were included and 96.3% and 77.78% of patients presented peri-implant BOP in the nonsmoker and smoker group, respectively (p = 0.046). Smoking was inversely associated with BOP in the multivariate multilevel analysis (OR = 0.356; 95% CI: 0.193-0.660; p = 0.001) whereas a positive correlation was demonstrated for mGI > 0 (OR = 3.289; 95% CI: 2.014-5.371; p < 0.001); PPD (OR = 1.692; 95% CI: 0.263-0.883; p = 0.039) and gender (OR = 2.323; 95% CI: 1.310-4.120 p = 0.004). A decrease of BOP sensitivity in detecting visible gingival inflammation (mGI > 0) was observed in smokers. Besides, taxonomic and changes in diversity regarding the peri-implant microbiota were detected comparing the two groups. Significantly higher richness of the microbiota was demonstrated in the smoker group when implants affected by peri-implantitis were compared to either healthy implants or implants presenting mucositis.

CONCLUSIONS

Smoking is a potential modifier of BOP and peri-implant microbiota.

Microbiome profiles of non-responding and responding paired periodontitis sites within the same participants following non-surgical treatment

Aim

Periodontitis is a site-specific, chronic disease treated by non-surgical debridement of subgingival plaque. We aimed to determine the microbiome of sites that did not respond to this treatment (NR) compared with paired good responding (GR) sites before and after treatment.

Materials and methods

In a longitudinal cohort study, clinical parameters of disease and biological samples were taken prior to and 3 months after treatment. Twelve NR sites from six participants were paired with GR sites within the same participant. Subgingival plaque samples were subjected to bacterial community analysis using 16S rRNA gene sequencing.

Results

There were no significant differences in clinical parameters and microbial communities at baseline between GR and NR sites. Bacterial communities in deep pockets were dominated by a small number of species, notably Porphyromonas gingivalis and Treponema denticola. In NR sites three months after treatment there was no significant change in bacterial composition whilst there was a collapse in the abundance of pathobionts in GR sites.

Conclusion

NR sites were not identifiable prior to treatment by clinical or microbiological parameters. Treatment failed to disrupt pathogenic bacterial community in NR sites. Targeted suppression of particular species should be considered to initiate community collapse and aid disease resolution.

Patterns of subgingival microbiota in different periodontal phenotypes

OBJECTIVES

To compare the subgingival microbiota of patients with aggressive (AgP) or chronic periodontitis (CP) to healthy (H), non-periodontitis patients as well as to explore their relevant associations to different host genetic variants.

METHODS

Following clinical examination, blood and subgingival plaque sampling of 471 study participants (125 AgP, 121 CP, 225 H), subgingival community analysis was performed by next generation sequencing of the 16S rRNA. Microbial data from 266 participants (75 AgP, 95 CP, 98 H) were available for analysis. SNPs in the IL6, IL6R and FTO gene were selected for genetic marker analyses.

RESULTS

Combined periodontitis patients (AgP + CP), particularly those classified with AgP, exhibited lower alpha- and beta- diversity. Several genera (including Peptostreptococcaceae, Filifactor, Desulfobulbus, Tannerella and Lachnospiracee) and species were over-abundant in combined periodontitis vs. healthy individuals, while other genera such as Prevotella or Dialister were found to be more abundant in healthy cases. The only genus with difference in abundance between AgP and CP was Granulicatella. No associations between IL6, IL6RA and FTO genetic variants and microbial findings were detected.

CONCLUSION

This study suggests that limited microbial differences existed between AgP and CP and challenges the current notion that periodontitis is associated with increased subgingival microbial diversity compared with periodontal health.

CLINICAL SIGNIFICANCE

The findings of this study cast some doubts on the notion that the dysbiosis characteristic of periodontal disease is expressed as increased microbial diversity.

Microbiome differences in periodontal, peri-implant, and healthy sites: a cross-sectional pilot study

OBJECTIVES

To explore microbial communities associated with health and disease status around teeth and dental implants.

MATERIALS AND METHODS

A total of 10 healthy, 24 periodontitis, and 24 peri-implant sites from 24 patients were sequenced by next-generation sequencing. Microbial DNA was extracted and 16S rRNA gene was amplified. Bioinformatic analyses were performed using quantitative insights into microbial ecology (QIIME), linear discriminant analysis effect size (LEfSE), and STAMP.

RESULTS

Differences in microbial diversity across three types of sites were not statistically significant. Several genera and species were more prevalent in healthy compared with diseased sites, including Lautropia, Rothia and Capnocytophaga and Kingella. Among diseased sites, Peptostreptococcaceae, Dialister, Mongibacterium, Atopobium, and Filifactor were over-represented in peri-implantitis sites, while Bacteroidales was more abundant in periodontitis sites.

CONCLUSIONS

Diseased periodontal and peri-implant sites and corresponding healthy sites have distinct microbiological profiles. These findings suggest that microbial analyses could identify biomarkers for periodontal health and disease and lead to the development of new strategies to improve periodontal health and treat peri-implant and periodontal diseases.

CLINICAL RELEVANCE

The study contributes to improving our understanding of healthy, periodontally affected, and peri-implantitis sites which can improve our ability to diagnose, monitor, and manage these oral conditions.

Submucosal microbiome of peri-implant sites: A cross-sectional study

AIM

To study the peri-implant submucosal microbiome in relation to implant disease status, dentition status, smoking habit, gender, implant location, implant system, time of functional loading, probing pocket depth (PPD), and presence of bleeding on probing.

MATERIALS AND METHODS

Biofilm samples were collected from the deepest peri-implant site of 41 patients with paper points, and analysed using 16S rRNA gene pyrosequencing.

RESULTS

We observed differences in microbial profiles by PPD, implant disease status, and dentition status. Microbiota in deep pockets included higher proportions of the genera Fusobacterium, Prevotella, and Anaeroglobus compared with shallow pockets that harboured more Rothia, Neisseria, Haemophilus, and Streptococcus. Peri-implantitis (PI) sites were dominated by Fusobacterium and Treponema compared with healthy implants and peri-implant mucositis, which were mostly colonized by Rothia and Streptococcus. Partially edentulous (PE) individuals presented more Fusobacterium, Prevotella, and Rothia, whereas fully edentulous individuals presented more Veillonella and Streptococcus.

CONCLUSIONS

PPD, implant disease status, and dentition status may affect the submucosal ecology leading to variation in composition of the microbiome. Deep pockets, PI, and PE individuals were dominated by Gram-negative anaerobic taxa.

Low-Abundant Microorganisms: The Human Microbiome's Dark Matter, a Scoping Review

Research on the human microbiome has mainly been restricted to the identification of most abundant microbiota associated with health or disease. Their abundance may reflect their capacity to exploit their niche, however, metabolic functions exerted by low-abundant microrganisms can impact the dysbiotic signature of local microbial habitats. This scoping review aims to map the literature regarding the management of low-abundant microorganisms in studies investigating human microbiome samples. A systematic literature search was performed in 5 electronic databases, as well as grey literature. We selected clinical microbiome studies targeting human participants of any age, from any body site. We also included studies with secondary data which originated from human biofilm samples. All of the papers used next-generation sequencing (NGS) techniques in their methodology. A total of 826 manuscripts were retrieved, of which 42 were included in this review and 22 reported low-abundant bacteria (LB) in samples taken from 7 body sites (breast, gut, oral cavity, skin, stomach, upper respiratory tract (URT), and vagina). Four studies reported microbes at abundance levels between 5 and 20%, 8 studies reported between 1 and 5%, and 18 studies reported below 1%. Fifteen papers mentioned fungi and/or archaea, and from those only 4 (fungi) and 2 (archaea) produced data regarding the abundance of these domains. While most studies were directed towards describing the taxonomy, diversity and abundance of the highly abundant species, low-abundant species have largely been overlooked. Indeed, most studies select a cut-off value at <1% for low-abundant organisms to be excluded in their analyses. This practice may compromise the true diversity and influence of all members of the human microbiota. Despite their low abundance and signature in biofilms, they may generate important markers contributing to dysbiosis, in a sort of ‘butterfly effect’. A detailed snapshot of the physiological, biological mechanisms at play, including virulence determinants in the context of a dysbiotic community, may help better understand the health-disease transition.

Microbial signatures of health, gingivitis, and periodontitis

The subgingival crevice harbors diverse microbial communities. Shifts in the composition of these communities occur with the development of gingivitis and periodontitis, which are considered as successive stages of periodontal health deterioration. It is not clear, however, to what extent health- and gingivitis-associated microbiota are protective, or whether these communities facilitate the successive growth of periodontitis-associated taxa. To further our understanding of the dynamics of the microbial stimuli that trigger disruptions in periodontal homeostasis, we reviewed the available literature with the aim of defining specific microbial signatures associated with different stages of periodontal dysbiosis. Although several studies have evaluated the subgingival communities present in different periodontal conditions, we found limited evidence for the direct comparison of communities in health, gingivitis, and periodontitis. Therefore, we aimed to better define subgingival microbiome shifts by merging and reanalyzing, using unified bioinformatic processing strategies, publicly available 16S ribosomal RNA gene amplicon datasets of periodontal health, gingivitis, and periodontitis. Despite inherent methodological differences across studies, distinct community structures were found for health, gingivitis, and periodontitis, demonstrating the specific associations between gingival tissue status and the subgingival microbiome. Consistent with the concept that periodontal dysbiosis is the result of a process of microbial succession without replacement, more species were detected in disease than in health. However, gingivitis-associated communities were more diverse than those from subjects with periodontitis, suggesting that certain species ultimately become dominant as dysbiosis progresses. We identified the bacterial species associated with each periodontal condition and prevalent species that do not change in abundance from one state to another (core species), and we also outlined species co-occurrence patterns via network analysis. Most periodontitis-associated species were rarely detected in health but were frequently detected, albeit in low abundance, in gingivitis, which suggests that gingivitis and periodontitis are a continuum. Overall, we provide a framework of subgingival microbiome shifts, which can be used to generate hypotheses with respect to community assembly processes and the emergence of periodontal dysbiosis.

Influence of periodontal treatment on blood microbiotas: a clinical trial

Objective

To investigate the effects of periodontal treatment on the abundance and diversity of blood microbiota.

Methods and Materials

Twenty-seven periodontitis patients were randomly allocated to a control group (A) and two test groups (B1 and B2). Group A patients received full-mouth scaling and root planing (SRP), group B1 patients received subgingival glycine air polishing (GAP) right after SRP, and group B2 patients received subgingival glycine air polishing right before SRP. Peripheral blood samples were obtained at the baseline, the day after periodontal treatment, and 6 weeks after treatment and evaluated using nested polymerase chain reaction and 16SrRNA Gene Sequencing (Miseq platform).

Results

All participants exhibited significant improvements in the clinical parameters evaluated at the 6-week follow-up visit compared to the values at the baseline, but no significant differences were observed between the three groups. The total bacterial count was lowest in group B2. The bacterial species diversity (α-diversity) in group B1 was significantly higher (Chao-1 index, P = 0.03) and Porphyromonas and Pantoea were the dominant genera (linear discriminant analysis (LDA > 2)) in this group the day after treatment compared to the baseline. No significant difference was detected in the relative abundance and α-diversity of blood microbiota between the baseline and 6 weeks after treatment.

Conclusion

Local periodontal treatment merely disrupts the stability of blood microbiota in the short term. Periodontitis treatment using full-mouth SRP followed by adjunctive GAP is a promising approach to reduce the introduction of bacteria into the bloodstream during the procedure.

Removal of nonimpacted third molars alters the periodontal condition of their neighbors clinically, immunologically, and microbiologically

Considering the adverse effects of nonimpacted third molars (N-M3s) on the periodontal health of adjacent second molars (M2s), the removal of N-M3s may be beneficial to the periodontal health of their neighbors. This study aimed to investigate the clinical, immunological, and microbiological changes of the periodontal condition around M2s following removal of neighboring N-M3s across a 6-month period. Subjects with at least one quadrant containing an intact first molar (M1), M2, and N-M3 were screened and those who met the inclusion criteria and decided to receive N-M3 extraction were recruited in the following investigation. M2 periodontal condition was interrogated before M3 extraction (baseline) and at 3 and 6 months postoperatively. Improvements in clinical periodontal indexes of M2s in response to their adjacent N-M3 removal, along with changes in inflammatory biomarkers among gingival crevicular fluid (GCF) and the composition of subgingival plaque collected from the distal sites of the M2s of the targeted quadrant were parallelly analyzed. Complete data of 26 tooth extraction patients across the follow-up period were successfully obtained and subsequently applied for statistical analysis. Compared to the baseline, the periodontal condition of M2s was significantly changed 6 months after N-M3 removal; specifically, the probing depth of M2s significantly reduced (P < 0.001), the matrix metalloproteinase (MMP)-8 concentration involved in GCF significantly decreased (P = 0.025), and the abundance of the pathogenic genera unidentified Prevotellaceae and Streptococcus significantly decreased (P < 0.001 and P = 0.009, respectively). We concluded that N-M3 removal was associated with superior clinical indexes, decreased GCF inflammatory biomarkers, and reduced pathogenic microbiome distribution within the subgingival plaque. Although the retention or removal of N-M3s continues to be controversial, our findings provide additional evidence that medical decisions should be made as early as possible or at least before the neighboring teeth are irretrievably damaged.

Quantification of Bacterial Colonization in Dental Hard Tissues Using Optimized Molecular Biological Methods

Bacterial infections of root canals and the surrounding dental hard tissue are still a challenge due to biofilm formation as well as the complex root canal anatomy. However, current methods for analyzing biofilm formation, bacterial colonization of root canals and dental hard tissue [e.g., scanning electron microscopy, confocal laser scanning microscopy (CLSM) or determination of colony forming units (CFU)] are time-consuming and only offer a selective qualitative or semi-quantitative analysis. The aim of the present study is the establishment of optimized molecular biological methods for DNA-isolation and quantification of bacterial colonization via quantitative PCR (qPCR) from dental hard tissue. Root canals of human premolars were colonized with Enterococcus faecalis. For isolation of DNA, teeth were then grinded with a cryo mill. Since the hard tissues dentin and especially enamel belong to the hardest materials in the human organism, the isolation of bacterial DNA from root dentin is very challenging. Therefore, treatment steps for the isolation of DNA from grinded teeth were systematically analyzed to allow improved recovery of bacterial DNA from dental hard tissues. Starting with the disintegration of the peptidoglycan-layer of bacterial cells, different lysozyme solutions were tested for efficacy. Furthermore, incubation times and concentrations of chelating agents such as EDTA were optimized. These solutions are crucial for the disintegration of teeth and hence improve the accessibility of bacterial DNA. The final step was the determination of prior bacterial colonization of each root canal as determined by qPCR and comparing the results to alternative methods such as CFU. As a result of this study, optimized procedures for bacterial DNA-isolation from teeth were established, which result in an increased recovery rate of bacterial DNA. This method allows a non-selective and straightforward procedure to quantify bacterial colonization from dental hard tissue. It can be easily adapted for other study types such as microbiome studies and for comparable tissues like bones.

Changes in the Microbiome of the Inner Surface of Clear Aligners After Different Usage Periods

Clear aligners are removable orthodontic appliances that cover the tooth surface. The microbial composition and pH of the inner surface of aligners directly affect the enamel health. In this study, eight subjects who used the same type of clear aligners were instructed to brush their teeth normally and to not clean their aligners until sampling. Saliva and the contents of the inner surface of the aligners (liquid and plaque) were collected at 0 h (T0), 4 h (T4), 8 h (T8), 12 h (T12), and 24 h (T24) after usage, and pH values and microbial compositions were measured. The microbial composition was analyzed with 16S rRNA gene sequencing, and changes were assessed based on operational taxonomic unit abundance. The pH, alpha diversity values, and abundance of specific microbes on the inner surface of the aligners gradually decreased from T0 to T24 (P < 0.05). An insignificant increase in microbial community beta diversity was observed from T0 to T24. Principal component analysis revealed that the microbial composition at T0 was different from at T12 and T24. The relative abundances of phylum Firmicutes (P < 0.01), orders Lactobacillales and Bacteroidales (P < 0.05), and genus Streptococcus and species Streptococcus infantis increased significantly, while those of genera Actinomyces and Rothia and species Rothia aeria decreased significantly at T24 (P < 0.05). These findings reveal that uncleaned aligners might lead to enamel damage, especially after continuous usage for 12 h. Thus, clear aligners should be cleaned after 12 h of usage or at least within 24 h of usage.

A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen

Recent studies describe in detail the shifts in composition of human-associated polymicrobial communities from health to disease. However, the specific processes that drive the colonization and overgrowth of pathogens within these communities remain incompletely understood. We used in vitro culture systems and a disease-relevant mouse model to show that population size, which determines the availability of an endogenous diffusible small molecule, limits the growth, colonization, and in vivo virulence of the human oral pathogen Porphyromonas gingivalis. This bacterial pathogen overcomes the requirement for an endogenous cue by utilizing a cell-density dependent, growth-promoting, soluble molecule provided by the symbiotic early colonizer Veillonella parvula, but not produced by other commensals tested. Our work shows that exchange of cell-density-dependent diffusible cues between specific early and late colonizing species in a polymicrobial community drives microbial successions, pathogen colonization and disease development, representing a target process for manipulation of the microbiome towards the healthy state.

Dysbiosis of Oral Microbiota Associated with Palmoplantar Pustulosis

BACKGROUND

Dysbiosis of oral microbiota is implicated not only in oral inflammatory lesions, but also in a variety of extraoral diseases. The etiology of palmoplantar pustulosis (PPP) remains unclear; however, it has been suggested that chronic inflammation caused by periodontopathic bacterial infection may play a role.

OBJECTIVES/METHODS

To determine whether patients with PPP have altered diversity and composition of oral microbiota, we conducted the 16S rDNA analysis using saliva samples collected from 21 outpatients with PPP and 10 healthy individuals.

RESULTS

We found that the proportion of bacteria in the phylum Proteobacteria was significantly lower in PPP patients (p = 0.025). At the genus level, patients with PPP had a significantly lower abundance of Neisseria (p = 0.014), which best accounted for the observed decrease in Proteobacteria. We also identified multiple minor genera and species that were represented at a significantly higher level in the PPP group, several of which have been associated with periodontal diseases.

CONCLUSION

Our results suggest a possible link between PPP and dysbiosis of oral microbiota, particularly the lower abundance of Neisseria, the most predominant genus of Proteobacteria in healthy oral microbiota. Probiotics that improves oral dysbiosis may be beneficial for patients with PPP as an adjunctive therapy.

Omics and interspecies interaction

Interspecies interactions are key determinants in biofilm behavior, ecology, and architecture. The cellular responses of microorganisms to each other at transcriptional, proteomic, and metabolomic levels ultimately determine the characteristics of biofilm and the corresponding implications for health and disease. Advances in omics technologies have revolutionized our understanding of microbial community composition and their activities as a whole. Large-scale analyses of the complex interaction between the many microbial species residing within a biofilm, however, are currently still hampered by technical and bioinformatics challenges. Thus, studies of interspecies interactions have largely focused on the transcriptional and proteomic changes that occur during the contact of a few prominent species, such as Porphyromonas gingivalis, Streptococcus mutans, Candida albicans, and a few others, with selected partner species. Expansion of available tools is necessary to grow the revealing, albeit limited, insight these studies have provided into a profound understanding of the nature of individual microbial responses to the presence of others. This will allow us to answer important questions including: Which intermicrobial interactions orchestrate the myriad of cooperative, synergistic, antagonistic, manipulative, and other types of relationships and activities in the complex biofilm environment, and what are the implications for oral health and disease?

Screening for prevalence and abundance of Capnocytophaga spp by analyzing NGS data: A scoping review

BACKGROUND

Capnocytophaga spp. are commensal bacteria of the oral cavity and constitute a genus of the core microbiome.

OBJECTIVE

This genus is responsible for many local and systemic conditions in both the immunocompetent and immunocompromised patients, but its beneficial or deleterious role in the microbiota has been little explored.

DESIGN

Online databases were used to identify papers published from 1999 to 2019 based on next-generation sequencing (NGS) data to study comparative trials. Work using other identification methods, case reports, reviews, and non-comparative clinical trials was excluded.

RESULTS AND CONCLUSION

We selected 42 papers from among 668 publications. They showed a link between the abundance of Capnocytophaga spp. in the oral microbiota and various local pathologies (higher for gingivitis and halitosis; lower in active smokers, etc.) or systemic diseases (higher for cancer and carcinomas, IgA nephropathy, etc.). After discussing the limits inherent to the NGS techniques, we present several technical and biological hypotheses to explain the diversity of results observed between studies, as well as the links between the higher or lower abundance of Capnocytophaga spp and the appearance of local or systemic conditions and diseases.

Differences in the periodontal microbiome of successfully treated and persistent aggressive periodontitis

AIMS

The primary aim of this investigation was to analyse the periodontal microbiome in patients with aggressive periodontitis (AgP) following treatment.

METHODS

Sixty-six AgP patients were recalled on average 7 years after completion of active periodontal treatment and had subgingival plaque samples collected and processed for 16S rRNA gene sequencing analyses.

RESULTS

Of 66 participants, 52 showed persistent periodontal disease, while 13 participants were considered as "successfully treated AgP" (no probing pocket depths >4 mm) and 1 was fully edentulous. Genera associated with persistent generalized disease included Actinomyces, Alloprevotella, Capnocytophaga, Filifactor, Fretibacterium, Fusobacterium, Leptotrichia, Mogibacterium, Saccharibacteria [G-1], Selenomonas and Treponema. "Successfully treated" patients harboured higher proportions of Haemophilus, Rothia, and Lautropia and of Corynebacterium, Streptococcus and Peptidiphaga genera. Overall, patients with persistent generalized AgP (GAgP) revealed higher alpha diversity compared to persistent localized AgP (LAgP) and stable patients (p < .001). Beta diversity analyses revealed significant differences only between stable and persistent GAgP groups (p = .004).

CONCLUSION

Patients with persistent AgP showed a more dysbiotic subgingival biofilm than those who have been successfully treated. It remains to be established whether such differences were predisposing to disease activity or were a result of a dysbiotic change associated with disease recurrence in the presence of sub-standard supportive periodontal therapy or other patient-related factors.

The neovaginal microbiome of transgender women post-gender reassignment surgery

BACKGROUND

Gender reassignment surgery is a procedure some transgender women (TW) undergo for gender-affirming purposes. This often includes the construction of a neovagina using existing penile and scrotal tissue and/or a sigmoid colon graft. There are limited data regarding the composition and function of the neovaginal microbiome representing a major gap in knowledge in neovaginal health.

RESULTS

Metaproteomics was performed on secretions collected from the neovaginas (n = 5) and rectums (n = 7) of TW surgically reassigned via penile inversion/scrotal graft with (n = 1) or without (n = 4) a sigmoid colon graft extension and compared with secretions from cis vaginas (n = 32). We identified 541 unique bacterial proteins from 38 taxa. The most abundant taxa in the neovaginas were Porphyromonas (30.2%), Peptostreptococcus (9.2%), Prevotella (9.0%), Mobiluncus (8.0%), and Jonquetella (7.2%), while cis vaginas were primarily Lactobacillus and Gardnerella. Rectal samples were mainly composed of Prevotella and Roseburia. Neovaginas (median Shannon's H index = 1.33) had higher alpha diversity compared to cis vaginas (Shannon's H = 0.35) (p = 7.2E-3, Mann-Whitney U test) and were more similar to the non-Lactobacillus dominant/polymicrobial cis vaginas based on beta diversity (perMANOVA, p = 0.001, r2 = 0.342). In comparison to cis vaginas, toll-like receptor response, amino acid, and short-chain fatty acid metabolic pathways were increased (p < 0.01), while keratinization and cornification proteins were decreased (p < 0.001) in the neovaginal proteome.

CONCLUSIONS

Penile skin-lined neovaginas have diverse, polymicrobial communities that show similarities in composition to uncircumcised penises and host responses to cis vaginas with bacterial vaginosis (BV) including increased immune activation pathways and decreased epithelial barrier function. Developing a better understanding of microbiome-associated inflammation in the neovaginal environment will be important for improving our knowledge of neovaginal health. Video Abstract.

Persistence of Tannerella forsythia and Fusobacterium nucleatum in dental plaque: a strategic alliance

PURPOSE OF REVIEW

The Gram-negative oral pathogen Tannerella forsythia is implicated in the pathogenesis of periodontitis, an inflammatory disease characterized by progressive destruction of the tooth supporting structures affecting over 700 million people worldwide. This review highlights the basis of why and how T. forsythia interacts with Fusobacterium nucleatum, a bacterium considered to be a bridge between the early and late colonizing bacteria of the dental plaque.

RECENT FINDINGS

The recent findings indicate that these two organisms have a strong mutualistic relationship that involves foraging by T. forsythia on F. nucleatum peptidoglycan and utilization of glucose, released by the hydrolytic activity of T. forsythia glucanase, as a nutrient by F. nucleatum. In addition, T. forsythia has the unique ability to generate a toxic and inflammogenic compound, methylglyoxal, from glucose. This compound can induce inflammation, leading to the degradation of periodontal tissues and release of host components as nutrients for bacteria to further exacerbate the disease.

SUMMARY

In summary, this article will present our current understanding of mechanisms underpinning T. forsythia-F. nucleatum mutualism, and how this mutualism might impact periodontal disease progression.

A Potential Role of Phospholipase 2 Group IIA (PLA2-IIA) in P. gingivalis-Induced Oral Dysbiosis

Porphyromonas gingivalis is an oral pathogen with the ability to induce oral dysbiosis and periodontal disease. Nevertheless, the mechanisms by which P. gingivalis could abrogate the host-microbe symbiotic relationship leading to oral dysbiosis remain unclear. We have recently demonstrated that P. gingivalis specifically increased the antimicrobial properties of oral epithelial cells, through a strong induction of the expression of PLA₂-IIA in a mechanism that involves activation of the Notch-1 receptor. Moreover, gingival expression of PLA₂-IIA was significantly increased during initiation and progression of periodontal disease in non-human primates and interestingly, those PLA₂-IIA expression changes were concurrent with oral dysbiosis. In this chapter, we present an innovative hypothesis of a potential mechanism involved in P. gingivalis-induced oral dysbiosis and inflammation based on our previous observations and a robust body of literature that supports the antimicrobial and proinflammatory properties of PLA₂-IIA as well as its role in other chronic inflammatory diseases.

Oral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic Activities

Dental caries is a highly prevalent oral disease that can lead to severe dental damage and may greatly compromise the quality of life of the affected individuals. Previous studies, including those based on 16S rRNA gene, have revealed that the oral microbiota plays a prominent role in development of the disease. But the approach of those studies was limited in analyzing several key microbiome traits, including species- or strain-level composition and functional profile. Here, we performed metagenomic analyses for a cohort of preschool children with or without caries. Our results showed that caries was associated with extensive microbiota differences at various taxonomic and functional levels. Some caries-associated species had not been previously reported, some of which may have significant clinical implications. A microbiome gene catalogue from children with caries was constructed for the first time. The results demonstrated that caries is associated with alterations of the oral microbiome, including changes in microbial composition and metabolic functional profile.

Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to investigate the relationship between the oral microbiome and caries in preschool children. A total of 25 preschoolers, aged 3 to 5 years old with severe early childhood caries (ECC), and 19 age-matched, caries-free children as controls were recruited. Saliva samples were collected from the participants and were subjected to metagenomic analyses, whereby the oral microbial communities were investigated. The metagenomic analyses revealed substantial microbiota differences between the two groups, indicating apparent shifts of the oral microbiome present in the ECC group. At the species level, the ECC-enriched microbes included Prevotella amnii, Shuttleworthia satelles, Olsenella uli, and Anaeroglobus geminatus. Interestingly, Actinomyces odontolyticus and Actinomyces graevenitzii exhibited apparent differences at the strain level but not the species level between the ECC and control groups. Functional examination showed that the ECC group displayed extensive alterations in metabolic genes/pathways/modules, including enriched functions in sugar metabolism. Finally, an SVM (support vector machine) classifier comprising seven species was developed and generated a moderately good performance in predicting caries onset (area under the receiver operating characteristic curve [AUC] = 78.33%). Together, these findings indicate that caries is associated with considerable changes in the oral microbiome, some of which can potentially be exploited as therapeutic targets or diagnostic markers. (This study has been registered at ClinicalTrials.gov under registration no. NCT02341352.)

IMPORTANCE Dental caries is a highly prevalent oral disease that can lead to severe dental damage and may greatly compromise the quality of life of the affected individuals. Previous studies, including those based on 16S rRNA gene, have revealed that the oral microbiota plays a prominent role in development of the disease. But the approach of those studies was limited in analyzing several key microbiome traits, including species- or strain-level composition and functional profile. Here, we performed metagenomic analyses for a cohort of preschool children with or without caries. Our results showed that caries was associated with extensive microbiota differences at various taxonomic and functional levels. Some caries-associated species had not been previously reported, some of which may have significant clinical implications. A microbiome gene catalogue from children with caries was constructed for the first time. The results demonstrated that caries is associated with alterations of the oral microbiome, including changes in microbial composition and metabolic functional profile.

Species-Level Salivary Microbial Indicators of Well-Resolved Periodontitis: A Preliminary Investigation

Objective: To profile the salivary microbiomes of a Hong Kong Chinese cohort at a species-level resolution and determine species that discriminated clinically resolved periodontitis from periodontally healthy cases. Methods: Salivary microbiomes of 35 Hong Kong Chinese subjects' under routine supportive dental care were analyzed. All subjects had been treated for any dental caries or periodontal disease with all restorative treatment completed at least 1 year ago and had ≤3 residual pockets. They were categorized based on a past diagnosis of chronic periodontitis into "healthy" (H) or "periodontitis" (P) categories. Unstimulated whole saliva was collected, genomic DNA was isolated, and high throughput Illumina MiSeq sequencing of 16S rRNA (V3-V4) gene amplicons was performed. The sequences were assigned taxonomy at the species level by using a BLASTN based algorithm that used a combined reference database of HOMD RefSeqV14.51, HOMD RefSeqExtended V1.1 and GreenGeneGold. Species-level OTUs were subjected to downstream analysis in QIIME and R. For P and H group comparisons, community diversity measures were compared, differentially abundant species were determined using DESeq2, and disease indicator species were determined using multi-level pattern analysis within the R package "indicspecies." Results: P subjects were significantly older than H subjects (p = 0.003) but not significantly different in their BOP scores (p = 0.82). No significant differences were noted in alpha diversity measures after adjusting for age, gender, and BOP or in the beta diversity estimates. Four species; Treponema sp. oral taxon 237, TM7 sp. Oral Taxon A56, Prevotella sp. oral taxon 314, Prevotella sp. oral taxon 304, and Capnocytophaga leadbetteri were significantly more abundant in P than in the H group. Indicator species analysis showed 7 significant indicators species of P group. Fusobacterium sp oral taxon 370 was the sole positive indicator of P group (positive predictive value = 0.9, p = 0.04). Significant indicators of the H category were Leptotrichia buccalis, Corynebacterium matruchotii, Leptotrichia hofstadii, and Streptococcus intermedius. Conclusion: This exploratory study showed salivary microbial species could discriminate treated, well-maintained chronic periodontitis from healthy controls with similar gingival inflammation levels. The findings suggest that certain salivary microbiome features may identify periodontitis-susceptible individuals despite clinical disease resolution.

Microbiota in Human Periodontal Abscess Revealed by 16S rDNA Sequencing

Periodontal abscess is an oral infective disease caused by various kinds of bacteria. We aimed to characterize the microbiota composition of periodontal abscesses by metagenomic methods and compare it to that of the corresponding pocket and healthy gingival crevice to investigate the specific bacteria associated with this disease. Samples from abscess pus (AB), periodontal pocket coronally above the abscess (PO), and the gingival crevice of the periodontal healthy tooth were obtained from 20 periodontal abscess patients. Furthermore, healthy gingival crevice samples were obtained from 25 healthy individuals. Bacterial DNA was extracted and 16S rRNA gene fragments were sequenced to characterize the microbiota and determine taxonomic classification. The beta-diversity analysis results showed that the AB and PO groups had similar compositions. Porphyromonas gingivalis, Prevotella intermedia, and other Prevotella spp. were the predominant bacteria of human periodontal abscesses. The abundances of Filifactor alocis and Atopobium rimae were significantly higher in periodontal abscesses than in the periodontal pocket, suggesting their association with periodontal abscess formation. In conclusion, we characterized the microbiota in periodontal abscess and identified some species that are positively associated with this disease. This provides a better understanding of the components of periodontal abscesses, which will help facilitate the development of antibiotic therapy strategies.

Regulation of IL-24 in human oral keratinocytes stimulated with Tannerella forsythia

Interleukin-24 is a pleiotropic immunoregulatory cytokine and a member of the IL-20R subfamily of the IL-10 family. The aim of this study was to investigate the regulation of IL-24 in the human oral keratinocyte cell line HOK-16B following infection with Tannerella forsythia, a major periodontal pathogen. T. forsythia induced the expression of IL-24 mRNA and the secretion of glycosylated IL-24 in HOK-16B cells. Glycosylation of IL-24 is linked to its solubility and bioavailability. T. forsythia-stimulated reactive oxygen species (ROS) induced the expression of IL-24, which was regulated by IL-6. The ROS inhibitor N-acetylcysteine and MAPK inhibitors significantly reduced the expression of IL-6 and IL-24 induced by T. forsythia. Recombinant human IL-24 significantly enhanced the expression of IL-1α, IL-8, CXCL10, and MCP-1 in HOK-16B cells. Together, these results indicate that ROS, MAPKs, and IL-6 comprise the axis of IL-24 expression in HOK-16B cells stimulated with T. forsythia. Thus, IL-24 may be involved in inflammation in oral keratinocytes.

Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients

Although periodontal diseases during fixed appliance treatment are a common issue, few studies have focused on the clinical and microbial factors associated with orthodontic appliances. Hence, we investigated changes in the subgingival microbial community and their association with periodontal changes at the early stage of fixed appliance treatment. Subgingival plaques from ten female patients with fixed appliances were obtained at three time points: before, 1 month and 3 months after the placement of the brackets (T0, T1 and T2). The 16S rRNA gene sequencing was used to analyze the microbial community of the subgingival plaque. The Plaque Index (PI) and Gingival Bleeding Index (GBI) were also recorded. The GBI significantly increased at T2, and the PI showed a temporary increase without a significant difference. The alpha diversity indices were stable. However, the beta diversity was significantly higher at T2 compared to T0 and T1. The relative abundance of core microbiomes at the genus level was relatively stable. Four periodontal pathogens at the species level, including Prevotella intermedia (Pi), Campylobacer rectus (Cr), Fusobacterium nucleatum (Fn), and Treponema denticola (Td), increased without significant differences. The subgingival microbial community affected by fixed appliance treatment might cause transient mild gingival inflammation.

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis

Genetic haemochromatosis (GH) is responsible for iron overload. Increased transferrin saturation (TSAT) has been associated with severe periodontitis, which is a chronic inflammatory disease affecting tissues surrounding the teeth and is related to dysbiosis of the subgingival microbiota. Because iron is essential for bacterial pathogens, alterations in iron homeostasis can drive dysbiosis. To unravel the relationships between serum iron biomarkers and the subgingival microbiota, we analysed samples from 66 GH patients. The co-occurrence analysis of the microbiota showed very different patterns according to TSAT. Healthy and periopathogenic bacterial clusters were found to compete in patients with normal TSAT (≤45%). However, significant correlations were found between TSAT and the proportions of Porphyromonas and Treponema, which are two genera that contain well-known periopathogenic species. In patients with high TSAT, the bacterial clusters exhibited no mutual exclusion. Increased iron bioavailability worsened periodontitis and promoted periopathogenic bacteria, such as Treponema. The radical changes in host-bacteria relationships and bacterial co-occurrence patterns according to the TSAT level also suggested a shift in the bacterial iron supply from transferrin to NTBI when TSAT exceeded 45%. Taken together, these results indicate that iron bioavailability in biological fluids is part of the equilibrium between the host and its microbiota.

In situ substrate-formed biofilms using IDODS mimic supragingival tooth-formed biofilms

This study aimed to compare the bacterial viability and diversity of a substrate-formed biofilm (SF-biofilm) in situ to a supragingival tooth-formed biofilm (TF-biofilm) in the same group of individuals. The impact of the device/disc position and toothbrushing during the formation of SF-biofilm was also assessed. Two tests were run. In test 1, 15 volunteers wore two hemi-splints carrying six discs of human enamel, glass, and hydroxyapatite for 2 days, and were instructed to not perform any oral hygiene measure. Biofilm samples were collected from the substrates and the contralateral tooth and were analysed using CLSM. In five volunteers, half of the biofilm present on the discs and their contralateral teeth were scraped and analysed using 16S  pyrosequencing. In test 2, the microscopic analysis was repeated only on the SF-biofilm samples, and the volunteers were allowed to brush their teeth. Multivariate analyses revealed that the donors had a significant effect on the composition of the biofilm, confirming its subject-dependent character. The bacterial composition of the SF-biofilm was similar to the TF-biofilm, with significant differential abundance detected in very few taxa of low abundance. The toothbrushing during the formation of SF-biofilm was the only factor that conditioned the thickness or bacterial viability.

Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity

Diabetes is a risk factor for periodontitis, an inflammatory bone disorder and the greatest cause of tooth loss in adults. Diabetes has a significant impact on the gut microbiota; however, studies in the oral cavity have been inconclusive. By 16S rRNA sequencing, we show here that diabetes causes a shift in oral bacterial composition and, by transfer to germ-free mice, that the oral microbiota of diabetic mice is more pathogenic. Furthermore, treatment with IL-17 antibody decreases the pathogenicity of the oral microbiota in diabetic mice; when transferred to recipient germ-free mice, oral microbiota from IL-17-treated donors induced reduced neutrophil recruitment, reduced IL-6 and RANKL, and less bone resorption. Thus, diabetes-enhanced IL-17 alters the oral microbiota and renders it more pathogenic. Our findings provide a mechanistic basis to better understand how diabetes can increase the risk and severity of tooth loss.

Capnocytophaga keratitis in dogs: clinical, histopathologic, and microbiologic features of seven cases

OBJECTIVE

To describe the clinical, microbiologic, and histopathologic features of Capnocytophaga keratitis in dogs.

ANIMALS STUDIED

Seven dogs with naturally acquired Capnocytophaga keratitis.

PROCEDURES

Medical records of dogs with a clinical diagnosis of keratitis and corneal cultures positive for Capnocytophaga spp. were reviewed. Dog signalment, medical history, clinical findings, and diagnostic assay results were recorded.

RESULTS

Breeds included Boston terrier (n = 3 dogs), Rat terrier (n = 2), and single cases of mixed breed and Pug. All dogs examined had expansive corneal ulceration involving the majority of the corneal surface. Marked corneal infiltrates, keratomalacia, and hypopyon were present. Progression of corneal disease was rapid with extensive dissolution of the corneal stroma. Corneal lesions progressed to catastrophic perforations within 24 h of the initial examination in three dogs, requiring enucleation. One globe was enucleated after failure to resolve with long-term medical therapy. Globes and vision were retained in three dogs following aggressive medical therapy (two dogs) or 360° conjunctival graft surgery (one dog). Capnocytophaga cynodegmi, Capnocytophaga canimorsus, or unspeciated Capnocytophaga spp. were cultured from corneal samples of all dogs. Long, thin, gram-negative rods were present during cytological evaluation of the cornea in some dogs. Histopathologic evaluation of enucleated globes revealed severe and diffuse neutrophilic and collagenolytic keratitis.

CONCLUSIONS

Capnocytophaga keratitis is a severe, rapidly progressive corneal infection in dogs that is associated with diffuse corneal involvement, extensive keratomalacia, and a relatively poor prognosis. Clinical features of canine Capnocytophaga keratitis are similar to human cases of this infection.

Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study

Background

Clear aligners are well known for facilitating oral hygiene maintenance and decreasing susceptibility to periodontal diseases as compared to conventional fixed appliances. However, few research studies focus on the subgingival microbial community during clear aligner treatment (CAT). Hence, this study investigates changes of the subgingival microbial community and its association with clinical characteristics during the first three months of CAT.

Methods

Ten female patients with clear aligners were enrolled in this study. Subgingival plaque samples were obtained at three time points: before orthodontic treatment (T0), one month after orthodontic treatment (T1) and three months after orthodontic treatment (T2). DNA was then extracted from plaque samples and analyzed by 16S rRNA gene sequencing. Periodontal examinations, including plaque index (PI) and gingival bleeding index (GBI) measurements were also recorded.

Results

The plaque indices (PIs) and gingival bleeding indices (GBIs) were slightly increased at T1 and T2, but no statistically significant difference was found. The alpha diversity indices, including the ACE, Chao1, Shannon indices, all showed a declining trend without significance, and a rising trend in the Simpson diversity index was observed. The weighted UniFrac distance was significantly higher at T1 and T2 compared with T0. Principal Coordinates Analysis (PCoA) demonstrated that the communities at T0 tended to cluster apart from the communities at T1 and T2. The relative abundance of the phylum Firmicutes and genus Mycoplasma was significantly increased at T0 compared with T2. There was no significant difference in the relative abundance of periodontal pathogens at the genus and species levels or core microorganisms at the genus level.

Conclusion

A slightly decreasing microbial diversity with a significant change of microbial structure was found during the first three-month clear aligner treatment (CAT). However, subjects receiving clear aligner treatment were free from periodontal diseases with relatively stable levels of periodontal microorganisms and core microorganisms. Thus, our preliminary findings indicated that clear aligners induced nonpathogenic changes of the subgingival microbiome in the first three-month treatment.

Blood lactose after dairy product intake in healthy men

The absence of a dedicated transport for disaccharides in the intestine implicates that the metabolic use of dietary lactose relies on its prior hydrolysis at the intestinal brush border. Consequently, lactose in blood or urine has mostly been associated with specific cases in which the gastrointestinal barrier is damaged. On the other hand, lactose appears in the blood of lactating women and has been detected in the blood and urine of healthy men, indicating that the presence of lactose in the circulation of healthy subjects is not incompatible with normal physiology. In this cross-over study we have characterised the postprandial kinetics of lactose, and its major constituent, galactose, in the serum of fourteen healthy men who consumed a unique dose of 800 g milk or yogurt. Genetic testing for lactase persistence and microbiota profiling of the subjects were also performed. Data revealed that lactose does appear in serum after dairy intake, although with delayed kinetics compared with galactose. Median serum concentrations of approximately 0·02 mmol/l lactose and approximately 0·2 mmol/l galactose were observed after the ingestion of milk and yogurt respectively. The serum concentrations of lactose were inversely correlated with the concentrations of galactose, and the variability observed between the subjects’ responses could not be explained by the presence of the lactase persistence allele. Finally, lactose levels have been associated with the abundance of theVeillonellagenus in faecal microbiota. The measurement of systemic lactose following dietary intake could provide information about lactose metabolism and nutrient transport processes under normal or pathological conditions.

Exploring the microbiome of healthy and diseased peri-implant sites using Illumina sequencing

AIM

To compare the microbiome of healthy (H) and diseased (P) peri-implant sites and determine the core peri-implant microbiome.

MATERIALS AND METHODS

Submucosal biofilms from 32 H and 35 P sites were analysed using 16S rRNA sequencing (MiSeq, Illumina), QIIME and HOMINGS. Differences between groups were determined using principal coordinate analysis (PCoA), t tests and Wilcoxon rank sum test and FDR-adjusted. The peri-implant core microbiome was determined.

RESULTS

PCoA showed partitioning between H and P at all taxonomic levels. Bacteroidetes, Spirochetes and Synergistetes were higher in P, while Actinobacteria prevailed in H (p < .05). Porphyromonas and Treponema were more abundant in P while Rothia and Neisseria were higher in H (p < .05). The core peri-implant microbiome contained Fusobacterium, Parvimonas and Campylobacter sp. T. denticola, and P. gingivalis levels were higher in P, as well as F. alocis, F. fastidiosum and T. maltophilum (p < .05).

CONCLUSION

The peri-implantitis microbiome is commensal-depleted and pathogen-enriched, harbouring traditional and new pathogens. The core peri-implant microbiome harbours taxa from genera often associated with periodontal inflammation.