Subgingival microbiota in health compared to periodontitis and the influence of smoking

Differences Between Vietnamese Living in Germany and German Periodontitis Patients in Periodontal Conditions and Subgingival Microbiota

INTRODUCTION AND AIMS

A number of studies have reported ethnic differences in the prevalence and severity of periodontitis. Such discrepancies could be attributed to disparities in periodontal risk factors, as well as variations in the composition of the subgingival microbiota. Given the substantial Vietnamese population residing in the former German Democratic Republic, the present study aimed to compare the clinical and microbial characteristics of periodontitis patients of Vietnamese Asian origin living in Germany with those of German Caucasian periodontitis patients.

METHODS

A total of 60 patients with a minimum stage II periodontitis diagnosis were included in the study. Of these, 30 were of Vietnamese origin, with an average age of 55 years and a male prevalence of 33.3%. The remaining 30 patients were of German origin, with an average age of 54.5 years and a male prevalence of 40%. The periodontal diagnosis was made in accordance with the recently revised classification of periodontal disease. The pooled subgingival plaque samples were subjected to next-generation sequencing on the MiSeq platform (Illumina).

RESULTS

The German patients were significantly more likely to be smokers (56.7% vs 13.3%), had significantly higher body mass index (26 vs 22.6 kg/m²), probing depth (4.1 vs 3.6 mm), and clinical attachment loss (5 vs 4.1 mm). In terms of microbiota, the Vietnamese patients exhibited significantly lower beta diversity compared to the German patients, and smokers demonstrated a significantly higher beta diversity compared to nonsmokers. The microbiota of both groups differed most significantly in the relative abundance of Porphyromonas gingivalis (Vietnamese) and Fusobacteriia (German).

CONCLUSIONS

German patients with periodontitis showed more severe periodontal symptoms and more pronounced periodontal risk factors compared to Vietnamese patients. Both patient groups also showed significant differences in the subgingival microbiota.

CLINICAL RELEVANCE

Compared to Vietnamese living in Germany, German patients have a higher need for periodontal treatment and at the same time the risk factors of smoking and obesity should be reduced. More research is needed before the differences in oral microbiota between the two groups can lead to individualised therapeutic approaches.

Anti-obesogenic effect of lupin-derived protein hydrolysate through modulation of adiposopathy, insulin resistance and gut dysbiosis in a diet-induced obese mouse

The prevalence of obesity is increasingly widespread, resembling a global epidemic. Lifestyle changes, such as consumption of high-energy-dense diets and physical inactivity, are major contributors to obesity. Common features of this metabolic pathology involve an imbalance in lipid and glucose homeostasis including dyslipidemia, insulin resistance and adipose tissue dysfunction. Moreover, the importance of the gut microbiota in the development and susceptibility to obesity has recently been highlighted. In recent years, new strategies based on the use of functional foods, in particular bioactive peptides, have been proposed to counteract obesity outcomes. In this context, the present study examines the effects of a lupin protein hydrolysate (LPH) on obesity, dyslipidemia and gut dysbiosis in mice fed a high-fat diet (HFD). After 12 weeks of LPH treatment, mice gained less weight and showed decreased adipose dysfunction compared to the HFD-fed group. HFD-induced dyslipidemia (increased triglycerides, cholesterol and LDL concentration) and insulin resistance were both counteracted by LPH consumption. Discriminant analysis differentially distributed LPH-treated mice compared to non-treated mice. HFD reduced gut ecological parameters, promoted the blooming of deleterious taxa and reduced the abundance of commensal members. Some of these changes were corrected in the LPH group. Finally, correlation analysis suggested that changes in this microbial population could be responsible for the improvement in obesity outcomes. In conclusion, this is the first study to show the effect of LPH on improving weight gain, adiposopathy and gut dysbiosis in the context of diet-induced obesity, pointing to the therapeutic potential of bioactive peptides in metabolic diseases.

Obesity and periodontitis: a comprehensive review of their interconnected pathophysiology and clinical implications

Obesity and periodontitis are significant health problems with a complex bidirectional relationship. Excess body fat is linked to systemic diseases and can lead to persistent inflammation, potentially harming periodontal health. Periodontitis, a chronic inflammatory condition affecting the supporting structures of teeth, poses substantial health risks. Both conditions share pathological processes such as inflammation and oxidative stress, which aggravate health status and make treatment more challenging. Understanding this interaction is crucial for developing effective management strategies for both diseases. This study explores the multifaceted aspects of obesity and periodontitis and their reciprocal relationship.

Resistant Starch-Encapsulated Probiotics Attenuate Colorectal Cancer Cachexia and 5-Fluorouracil-Induced Microbial Dysbiosis

5-Fluorouracil (5-FU) is commonly used as the primary chemotherapy for colorectal cancer (CRC). However, it can lead to unwanted chemoresistance. Resistant starch (RS), which functions similarly to fermentable dietary fiber, has the potential to reduce the risk of CRC. The effects of RS on improving CRC-associated cachectic symptoms and 5-FU chemotherapy-induced microbial dysbiosis remain unknown. Female BALB/cByJNarl mice were randomly divided into four groups: one tumor group (with CT26 colonic carcinoma but no treatment) and three CT26 colonic carcinoma-bearing groups that were administered 20 mg/kg 5-FU (T+5-FU group), a probiotic cocktail (4 × 108 CFUs) plus chemotherapy (T+5-FU+Pro), or resistant-starch-encapsulated probiotics plus chemotherapy (T+5-FU+RS-Pro). T+5-FU and T+5-FU+RS-Pro administration significantly suppressed tumor growth and activated apoptotic cell death in CT26-bearing mice. 5-FU-induced increases in inflammatory cytokines and NF-κB signaling were mitigated by the Pro or RS-Pro supplementation. A gut microbial composition comparison indicated that the abundance of intestinal bacteria in the T and T+5-FU groups decreased significantly, while the groups receiving Pro or RS-Pro maintained a greater abundance and healthy gut microbiota composition, suggesting that RS can reduce the microbial dysbiosis that occurs during 5-FU chemotherapy. The use of RS-Pro before chemotherapy should be considered for the regulation of chemotherapy-associated cachectic symptoms, inflammation, and chemotherapy-induced microbial dysbiosis.

Bacteria of healthy periodontal tissues as candidates of probiotics: a systematic review

OBJECTIVES

The use of probiotics could promote the balance of the subgingival microbiota to contribute to periodontal health. This study aimed to identify the potential of bacteria commonly associated with healthy periodontal tissues as probiotic candidates.

MATERIAL AND METHODS

A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines using the PubMed, Scopus, Science Direct, ProQuest, and Ovid databases as well as the combination of Medical Subject Headings (MeSH) and non-MeSH terms. Based on the selection criteria, original studies published in English and identifying the microorganisms present in the periodontium of healthy individuals and patients with periodontitis using the high-throughput 16S ribosomal gene sequencing technique were included.

RESULTS

Out of 659 articles, 12 met the criteria for this review. These articles were published from 2012 to 2020 and mainly originated from the United States, China, and Spain. Most of these studies reported adequate criteria for selecting participants, using standardized clinical criteria, and compliance with quality based on the tools used. In periodontal healthy tissue were identified species like Actinomyces viscosus, Actinomyces naeslundii, Haemophilus parainfluenzae, Rothia dentocariosa, Streptococcus sanguinis, Streptococcus mitis, Streptococcus oralis, Streptococcus gordonii, Streptococcus intermedius, and Prevotella nigrescens which have recognized strains with a capacity to inhibit periodontopathogens.

CONCLUSIONS

S. sanguinis, S. oralis, S. mitis, and S. gordonii are among the bacterial species proposed as potential probiotics because some strains can inhibit periodontopathogens and have been reported as safe for humans.

Tooth- and implant-related prognostic factors in treatment planning

Following a comprehensive patient examination, including the assessment of periodontal and peri-implant diseases as well as considering the patient's needs, a pretherapeutic prognosis for each tooth and implant is given. Teeth and implants with a secure pretherapeutic prognosis require simple procedures and may be regarded as secure abutments for function and with a doubtful pretherapeutic prognosis usually need a comprehensive therapy. Such teeth and implants must be brought into the category with a secure prognosis by means of additional therapy such as endodontic, restorative, and surgical procedures. Teeth and implants with a hopeless pretherapeutic prognosis should be extracted/explanted during the initial phase of cause-related therapy (i.e., infection control). For example, teeth with vertical root fracture or unrestorable caries and implants with mobility or unrestorable malposition fall into the category of hopeless units. The primary goal of periodontal and peri-implant therapy should be to arrest disease progression. The latest consensus statement highlights that periodontitis can be successfully controlled and treated teeth can be retained for life. Nevertheless, for patients with uncontrolled contributing factors, the endpoints might not always be achievable, and low disease activity may be an acceptable therapeutic goal. Similarly, the management of peri-implantitis frequently requires surgical intervention following nonsurgical therapy due to incomplete treatment outcomes. Different surgical modalities can be effective and lead to significant improvement; however, achieving complete resolution of peri-implantitis is challenging, not always predictable, and can depend on multiple baseline factors. Therefore, this review aims at summarising available evidence on the rationale for incorporating systemic, lifestyle-related, clinical, and radiographic prognostic factors into treatment planning of patients diagnosed with periodontal and peri-implant diseases.

Influence of gender on periodontal outcomes: A retrospective analysis of eight randomized clinical trials

AIMS

To explore the influence of gender on periodontal treatment outcomes in a dataset of eight RCTs conducted in Brazil, United States, and Germany.

METHODS

Clinical parameters were compared between men and women with stages III/IV grades B/C generalized periodontitis at baseline and 1-year post-therapy, including scaling and root planing with or without antibiotics.

RESULTS

Data from 1042 patients were analyzed. Men presented a tendency towards higher probing depth (p = .07, effect size = 0.11) and clinical attachment level (CAL) than women at baseline (p = .01, effect size = 0.16). Males also presented statistically significantly lower CAL gain at sites with CAL of 4-6 mm at 1-year post-therapy (p = .001, effect size = 0.20). Among patients with Grade B periodontitis who took antibiotics, a higher frequency of women achieved the endpoint for treatment (i.e., ≤4 sites PD ≥5 mm) at 1 year than men (p < .05, effect size = 0.12).

CONCLUSION

Men enrolled in RCTs showed a slightly inferior clinical response to periodontal therapy in a limited number of sub-analyses when compared to women. These small differences did not appear to be clinically relevant. Although gender did not dictate the clinical response to periodontal treatment in this population, our findings suggest that future research should continue to explore this topic.

Clinical Use of Paraprobiotics for Pregnant Women with Periodontitis: Randomized Clinical Trial

Periodontal disease is very common in pregnant women. Paraprobiotics are a subset of probiotics. They can be defined as inactivated microbial cells providing health benefits to the host and are considered particularly safe. The aim of this study was to compare the periodontal health of pregnant women and puerperae after 6 months of home use of paraprobiotics. A total of 30 pregnant women were enrolled and divided into two groups: the test group, who had to use a paraprobiotic-based toothpaste (Biorepair Peribioma Pro, Coswell S.p.A., Funo di Argelato, BO, Italy) and mousse (Mousse Mouthwash Biorepair Peribioma, Coswell S.p.A.) twice a day, and the control group, who had to use only the paraprobiotic-based toothpaste. The time frames of the study were: 1 month (T1), 3 months (T2) and 6 months (T3), and data were collected during pregnancy and in the period immediately following delivery. The following indices were evaluated at T0, T1, T2 and T3: clinical attachment loss (CAL), probing pocket depth (PPD), bleeding on probing (BOP), plaque control record (PCR), modified marginal gingival index (mMGI), papillary marginal gingival index (PMGI) and recessions (R). All data were subjected to statistical analysis. PCR decreased significantly from T0 to T1 in the control group and from T0 to T2 and from T0 to T3 in the test group. BOP tended to decrease in both groups, but a significant reduction was observed only in the test group. CAL, PPD, PMGI and mMGI tended to decrease gradually in both groups without significant differences between or within groups. The combination of the paraprobiotic-based toothpaste and the paraprobiotic-based mousse significantly reduced BoP and plaque control over time, although there were no significant differences with the use of the paraprobiotic-based toothpaste alone. In addition, the combination of the two products promoted a trend towards the better stabilization of recessions.

Nitrate reduction capacity of the oral microbiota is impaired in periodontitis: potential implications for systemic nitric oxide availability

The reduction of nitrate to nitrite by the oral microbiota has been proposed to be important for oral health and results in nitric oxide formation that can improve cardiometabolic conditions. Studies of bacterial composition in subgingival plaque suggest that nitrate-reducing bacteria are associated with periodontal health, but the impact of periodontitis on nitrate-reducing capacity (NRC) and, therefore, nitric oxide availability has not been evaluated. The current study aimed to evaluate how periodontitis affects the NRC of the oral microbiota. First, 16S rRNA sequencing data from five different countries were analyzed, revealing that nitrate-reducing bacteria were significantly lower in subgingival plaque of periodontitis patients compared with healthy individuals (P < 0.05 in all five datasets with n = 20-82 samples per dataset). Secondly, subgingival plaque, saliva, and plasma samples were obtained from 42 periodontitis patients before and after periodontal treatment. The oral NRC was determined in vitro by incubating saliva with 8 mmol/L nitrate (a concentration found in saliva after nitrate-rich vegetable intake) and compared with the NRC of 15 healthy individuals. Salivary NRC was found to be diminished in periodontal patients before treatment (P < 0.05) but recovered to healthy levels 90 days post-treatment. Additionally, the subgingival levels of nitrate-reducing bacteria increased after treatment and correlated negatively with periodontitis-associated bacteria (P < 0.01). No significant effect of periodontal treatment on the baseline saliva and plasma nitrate and nitrite levels was found, indicating that differences in the NRC may only be revealed after nitrate intake. Our results suggest that an impaired NRC in periodontitis could limit dietary nitrate-derived nitric oxide levels, and the effect on systemic health should be explored in future studies.

Sputum microbiome α-diversity is a key feature of the COPD frequent exacerbator phenotype

Background

The lung microbiome is an inflammatory stimulus whose role in COPD pathogenesis is incompletely understood. We hypothesised that the frequent exacerbator phenotype is associated with decreased α-diversity and increased lung inflammation. Our objective was to assess correlations between the frequent exacerbator phenotype, the microbiome and inflammation longitudinally during exacerbation-free periods.

Methods

We conducted a case-control longitudinal observational study of the frequent exacerbator phenotype and characteristics of the airway microbiome. 81 subjects (41 frequent and 40 infrequent exacerbators) provided nasal, oral and sputum microbiome samples at two visits over 2-4 months. Exacerbation phenotype, relevant clinical factors and sputum cytokine values were associated with microbiome findings.

Results

The frequent exacerbator phenotype was associated with lower sputum microbiome α-diversity (p=0.0031). This decrease in α-diversity among frequent exacerbators was enhanced when the sputum bacterial culture was positive (p<0.001). Older age was associated with decreased sputum microbiome α-diversity (p=0.0030). Between-visit β-diversity was increased among frequent exacerbators and those who experienced a COPD exacerbation between visits (p=0.025 and p=0.014, respectively). Sputum cytokine values did not differ based on exacerbation phenotype or other clinical characteristics. Interleukin (IL)-17A was negatively associated with α-diversity, while IL-6 and IL-8 were positively associated with α-diversity (p=0.012, p=0.012 and p=0.0496, respectively). IL-22, IL-17A and IL-5 levels were positively associated with Moraxella abundance (p=0.027, p=0.0014 and p=0.0020, respectively).

Conclusions

Even during exacerbation-free intervals, the COPD frequent exacerbator phenotype is associated with decreased sputum microbiome α-diversity and increased β-diversity. Decreased sputum microbiome α-diversity and Moraxella abundance are associated with lung inflammation.

Personalized antibiotic selection in periodontal treatment improves clinical and microbiological outputs

Introduction

Periodontitis is a biofilm-mediated disease that is usually treated by non-surgical biofilm elimination with or without antibiotics. Antibiotic treatment in periodontal patients is typically selected empirically or using qPCR or DNA hybridization methods. These approaches are directed towards establishing the levels of different periodontal pathogens in periodontal pockets to infer the antibiotic treatment. However, current methods are costly and do not consider the antibiotic susceptibility of the whole subgingival biofilm.

Methods

In the current manuscript, we have developed a method to culture subgingival samples ex vivo in a fast, label-free impedance-based system where biofilm growth is monitored in real-time under exposure to different antibiotics, producing results in 4 hours. To test its efficacy, we performed a double-blind, randomized clinical trial where patients were treated with an antibiotic either selected by the hybridization method (n=32) or by the one with the best effect in the ex vivo growth system (n=32).

Results

Antibiotic selection was different in over 80% of the cases. Clinical parameters such as periodontal pocket depth, attachment level, and bleeding upon probing improved in both groups. However, dental plaque was significantly reduced only in the group where antibiotics were selected according to the ex vivo growth. In addition, 16S rRNA sequencing showed a larger reduction in periodontal pathogens and a larger increase in health-associated bacteria in the ex vivo growth group.

Discussion

The results of clinical and microbiological parameters, together with the reduced cost and low analysis time, support the use of the impedance system for improved individualized antibiotic selection.

Altered salivary microbiota profile in patients with abdominal aortic aneurysm

Evidence suggests that the DNA of oral pathogens is detectable in the dilated aortic tissue of abdominal aortic aneurysm (AAA), one of the most fatal cardiovascular diseases. However, the association between oral microbial homeostasis and aneurysm formation remains largely unknown. In this study, a cohort of individuals, including 53 AAA patients and 30 control participants (CTL), was recruited for salivary microbiota investigation by 16S rRNA gene sequencing and bioinformatics analysis. Salivary microbial diversity was decreased in AAA compared with CTL, and the microbial structures were significantly separated between the two groups. Additionally, significant taxonomic and functional changes in the salivary microbiota of AAA participants were observed. The genera Streptococcus and Gemella were remarkably enriched, while Selenomonas, Leptotrichia, Lautropia and Corynebacterium were significantly depleted in AAA. Co-occurrence network analysis showed decreased potential interactions among the differentially abundant microbial genera in AAA. A machine-learning model predicted AAA using the combination of 5 genera and 14 differentially enriched functional pathways, which could distinguish AAA from CTL with an area under the receiver-operating curve of 90.3 %. Finally, 16 genera were found to be significantly positively correlated with the morphological parameters of AAA. Our study is the first to show that AAA patients exhibit oral microbial dysbiosis, which has high predictive power for AAA, and the over-representation of specific salivary bacteria may be associated with AAA disease progression. Further studies are needed to better understand the function of putative oral bacteria in the etiopathogenesis of AAA.

Importance

Host microbial dysbiosis has recently been linked to AAA as a possible etiology. To our knowledge, studies of the oral microbiota and aneurysms remain scarce, although previous studies have indicated that the DNA of some oral pathogens is detectable in aneurysms by PCR method. We take this field one step further by investigating the oral microbiota composition of AAA patients against control participants via high-throughput sequencing technologies and unveiling the potential microbial biomarker associated with AAA formation. Our study will provide new insights into AAA etiology, treatment and prevention from a microecological perspective and highlight the effects of oral microbiota on vascular health.

Community dynamics of subgingival microbiome in periodontitis and targets for microbiome modulation therapy

The microbial aetiology for periodontitis has been widely studied and deciphered for more than a century. The evolving and changing concepts about periodontal microbiology can be attributed to continuously developing laboratory techniques. The current sequencing platforms have not only expanded the catalog of periodontal pathogens but have also facilitated the understanding of functional interactions of the ecological framework. However, the translation of this new knowledge to advance periodontal therapeutics is minimal. We contend that novel clinical interventions directed beyond conventional therapies need to be emphasized. A clear understanding of the structural and functional dynamics of subgingival microbiota is a pre-requisite for developing any microbiome-based interventions for applications in periodontal health care. In this review, we discuss the 16 s-rRNA gene sequencing-based knowledge of the subgingival microbial community structure, its interactions and functions, and our perspective on the potential to engineer it for periodontal therapeutics. Harnessing this next-generation sequencing-based knowledge, microbiome modulation therapies are poised to change microbiome therapeutics' face.

The homeostasis and therapeutic applications of innate and adaptive immune cells in periodontitis

OBJECTIVES

Periodontitis (PD) is one of the most common dental disorders. This chronic oral inflammation is caused by complicated interrelations between bacterial infections, dysregulated immune reactions, and environmental risk factors. A dysregulated immune response can lead to inflammatory bone resorption by allowing the recruitment of pro-inflammatory immune cells to the periodontal tissues.

SUBJECTS

The recruitment of innate and adaptive immune cells in PD initiates the acute and following chronic inflammatory processes. The inflamed tissues, on the other hand, can be restored if the anti-inflammatory lineages are predominantly established in the periodontal tissues. Therefore, we aimed to review the published literature to provide an overview of the existing knowledge about the role of immune cells in PD, as well as their possible therapeutic applications.

RESULTS

Experimental studies showed that drugs/systems that negatively regulate inflammatory cells in the body, as well as interventions aimed at increasing the number of anti-inflammatory cells such as Tregs and Bregs, can both help in the healing process of PD.

CONCLUSION

Targeting immune cells or their positive/negative manipulations has been demonstrated to be an effective therapeutic method. However, to use this sort of immunotherapy in humans, further pre-clinical investigations, as well as randomized clinical trials, are required.

New putative periodontopathogens and periodontal health-associated species: A systematic review and meta-analysis

To investigate the existence of any association between new putative periodontal pathogens and periodontitis. Two independent reviewers conducted electronic literature searches in the MEDLINE (PubMed), EMBASE, DOSS and Google Scholar databases as well as a manual search to identify eligible clinical studies prior to November 2022. Studies comparing the prevalence of microorganisms other than the already-known periodontal pathogens in subgingival plaque and/or saliva samples between subjects with periodontitis and subject with periodontal health were included. Meta-analyses were performed on data provided by the included studies. Fifty studies including a total of 2739 periodontitis subjects and 1747 subjects with periodontal health were included. The Archaea domain and 25 bacterial species (Anaeroglobus geminatus, Bacteroidales [G-2] bacterium HMT 274, Desulfobulbus sp. HMT 041, Dialister invisus, Dialister pneumosintes, Eubacterium brachy, Enterococcus faecalis, Eubacterium nodatum, Eubacterium saphenum, Filifactor alocis, Fretibacterium sp. HMT 360, Fretibacterium sp. HMT 362, Mogibacterium timidum, Peptoniphilaceae sp. HMT 113, Peptostreptococcus stomatis, Porphyromonas endodontalis, Slackia exigua, Streptococcus gordonii, Selenomonas sputigena, Treponema amylovorum, Treponema lecithinolyticum, Treponema maltophilum, Treponema medium, Treponema parvum and Treponema socranskii) were found to be statistically significantly associated with periodontitis. Network studies should be conducted to investigate the role of these newly identified periodontitis-associated microorganisms through interspecies interaction and host-microbe crosstalk analyses.

Longitudinal changes in subgingival biofilm composition following periodontal treatment

BACKGROUND

Current periodontal treatment involves instrumentation using hand and/or ultrasonic instruments, which are used either alone or in combination based on patient and clinician preference, with comparable clinical outcomes. This study sought to investigate early and later changes in the subgingival biofilm following periodontal treatment, to identify whether these changes were associated with treatment outcomes, and to investigate whether the biofilm responded differently to hand compared with ultrasonic instruments.

METHODS

This was a secondary-outcome analysis of a randomized-controlled trial. Thirty-eight periodontitis patients received full-mouth subgingival instrumentation using hand (n = 20) or ultrasonic instrumentation (n = 18). Subgingival plaque was sampled at baseline and 1, 7, and 90 days following treatment. Bacterial DNA was analyzed using 16S rRNA sequencing. Periodontal clinical parameters were evaluated before and after treatment.

RESULTS

Biofilm composition was comparable in both (hand and ultrasonics) treatment groups at all time points (all genera and species; p[adjusted] > 0.05). Large-scale changes were observed within groups across time points. At days 1 and 7, taxonomic diversity and dysbiosis were reduced, with an increase in health-associated genera including Streptococcus and Rothia equating to 30% to 40% of the relative abundance. When reassessed at day 90 a subset of samples reformed a microbiome more comparable with baseline, which was independent of instrumentation choice and residual disease.

CONCLUSIONS

Hand and ultrasonic instruments induced comparable impacts on the subgingival plaque microbiome. There were marked early changes in the subgingival biofilm composition, although there was limited evidence that community shifts associated with treatment outcomes.

Subgingival microbiome in periodontal health, gingivitis and different stages of periodontitis

AIM

To characterize the subgingival microbiome in subjects with different periodontal health statuses.

MATERIALS AND METHODS

In this cross-sectional observational study, subgingival samples were harvested from Spanish subjects with different periodontal health statuses, based on the 2018 Classification of Periodontal and Peri-Implant Diseases and Conditions. Samples were processed using high-throughput sequencing technologies (Illumina MiSeq). Taxa differentially abundant were identified using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). α- and β-diversity metrics were calculated using q2-diversity in QIIME2. The analyses were adjusted for age, gender and smoking status.

RESULTS

The identified subgingival microbiome showed statistically significant differences among subjects, categorized into periodontal health, gingivitis and stages I-II and III-IV periodontitis (p < .05). In patients with severe (stages III-IV) periodontitis, the genera Filifactor and Fretibacterium were detected 24 times more frequently than in periodontally healthy subjects. Similarly, the genera Porphyromonas, Prevotella and Tannerella were detected four times more frequently (p < .05). The genera Granulicatella, Streptococcus, Paracoccus, Pseudomonas, Haemophilus, Actinobacteria, Bergeyella and Capnocytophaga were significantly associated with healthier periodontal status (p < .05).

CONCLUSIONS

Significant differences were detected in the subgingival microbiome among periodontal health, gingivitis and stages I-II or III-IV periodontitis, suggesting overlapping, yet distinguishable microbial profiles.

The oral microbiome of implant-abutment screw holes compared with the peri-implant sulcus and natural supragingival plaque in healthy individuals

PURPOSE

An implant-supported prosthesis consists of an implant fixture, an abutment, an internal screw that connects the abutment to the implant fixture, and the upper prosthesis. Numerous studies have investigated the microorganisms present on the implant surface, surrounding tissues, and the subgingival microflora associated with peri-implantitis. However, there is limited information regarding the microbiome within the internal screw space. In this study, microbial samples were collected from the supragingival surfaces of natural teeth, the peri-implant sulcus, and the implant-abutment screw hole, in order to characterize the microbiome of the internal screw space in healthy subjects.

METHODS

Samples were obtained from the supragingival region of natural teeth, the peri-implant sulcus, and the implant screw hole in 20 healthy subjects. DNA was extracted, and the V3-V4 region of the 16S ribosomal RNA was sequenced for microbiome analysis. Alpha diversity, beta diversity, linear discriminant analysis effect size (LEfSe), and network analysis were employed to compare the characteristics of the microbiomes.

RESULTS

We observed significant differences in beta diversity among the samples. Upon analyzing the significant taxa using LEfSe, the microbial composition of the implant-abutment screw hole's microbiome was found to be similar to that of the other sampling sites' microbiomes. Moreover, the microbiome network analysis revealed a unique network complexity in samples obtained from the implant screw hole compared to those from the other sampling sites.

CONCLUSIONS

The bacterial composition of the biofilm collected from the implant-abutment screw hole exhibited significant differences compared to the supra-structure of the implant. Therefore, long-term monitoring and management of not only the peri-implant tissue but also the implant screw are necessary.

Smoking-induced subgingival dysbiosis precedes clinical signs of periodontal disease

Smoking accelerates periodontal disease and alters the subgingival microbiome. However, the relationship between smoking-associated subgingival dysbiosis and progression of periodontal disease is not well understood. Here, we sampled 233 subgingival sites longitudinally from 8 smokers and 9 non-smokers over 6-12 months, analyzing 804 subgingival plaque samples using 16 rRNA sequencing. At equal probing depths, the microbial richness and diversity of the subgingival microbiome was higher in smokers compared to non-smokers, but these differences decreased as probing depths increased. The overall subgingival microbiome of smokers differed significantly from non-smokers at equal probing depths, which was characterized by colonization of novel minority microbes and a shift in abundant members of the microbiome to resemble periodontally diseased communities enriched with pathogenic bacteria. Temporal analysis showed that microbiome in shallow sites were less stable than deeper sites, but temporal stability of the microbiome was not significantly affected by smoking status or scaling and root planing. We identified 7 taxa-Olsenella sp., Streptococcus cristatus, Streptococcus pneumoniae, Streptococcus parasanguinis, Prevotella sp., Alloprevotella sp., and a Bacteroidales sp. that were significantly associated with progression of periodontal disease. Taken together, these results suggest that subgingival dysbiosis in smokers precedes clinical signs of periodontal disease, and support the hypothesis that smoking accelerates subgingival dysbiosis to facilitate periodontal disease progression.

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.

Oral microbial dysbiosis in patients with periodontitis and chronic obstructive pulmonary disease

Background

Oral microbiota is closely related to the homeostasis of the oral cavity and lungs. To provide potential information for the prediction, screening, and treatment strategies of individuals, this study compared and investigated the bacterial signatures in periodontitis and chronic obstructive pulmonary disease (COPD).

Materials and methods

We collected subgingival plaque and gingival crevicular fluid samples from 112 individuals (31 healthy controls, 24 patients with periodontitis, 28 patients with COPD, and 29 patients with both periodontitis and COPD). The oral microbiota was analyzed using 16S rRNA gene sequencing and diversity and functional prediction analysis were performed.

Results

We observed higher bacterial richness in individuals with periodontitis in both types of oral samples. Using LEfSe and DESeq2 analyses, we found differentially abundant genera that may be potential biomarkers for each group. Mogibacterium is the predominant genus in COPD. Ten genera, including Desulfovibrio, Filifactor, Fretibacterium, Moraxella, Odoribacter, Pseudoramibacter Pyramidobacter, Scardovia, Shuttleworthia and Treponema were predominant in periodontitis. Bergeyella, Lautropia, Rothia, Propionibacterium and Cardiobacterium were the signature of the healthy controls. The significantly different pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) between healthy controls and other groups were concentrated in genetic information processing, translation, replication and repair, and metabolism of cofactors and vitamins.

Conclusions

We found the significant differences in the bacterial community and functional characterization of oral microbiota in periodontitis, COPD and comorbid diseases. Compared to gingival crevicular fluid, subgingival plaque may be more appropriate for reflecting the difference of subgingival microbiota in periodontitis patients with COPD. These results may provide potentials for predicting, screening, and treatment strategies for individuals with periodontitis and COPD.

Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma

A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104^T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0-7.0). It contained anteiso-C_15 : 0 and C_15 : 0 as the major fatty acids. The genome size of strain 14-104^T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929^T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104^T and P. abscessus CCUG 55929^T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104^T represents a novel species in the genus Phocaeicola, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104^T (=BCRC 81305^T= NBRC 115041^T).

TRAF3IP2-IL-17 Axis Strengthens the Gingival Defense against Pathogens

Recent genome-wide association studies have suggested novel risk loci associated with periodontitis, which is initiated by dysbiosis in subgingival plaque and leads to destruction of teeth-supporting structures. One such genetic locus was the tumor necrosis factor receptor-associated factor 3 interacting protein 2 (TRAF3IP2), a gene encoding the gate-keeping interleukin (IL)-17 receptor adaptor. In this study, we first determined that carriers of the lead exonic variant rs13190932 within the TRAF3IP2 locus combined with a high plaque microbial burden was associated with more severe periodontitis than noncarriers. We then demonstrated that TRAF3IP2 is essential in the IL-17-mediated CCL2 and IL-8 chemokine production in primary gingival epithelial cells. Further analysis suggested that rs13190932 may serve a surrogate variant for a genuine loss-of-function variant rs33980500 within the same gene. Traf3ip2 null mice (Traf3ip2^-/-) were more susceptible than wild-type (WT) mice to the Porphyromonas gingivalis-induced periodontal alveolar bone loss. Such bone loss was associated with a delayed P. gingivalis clearance and an attenuated neutrophil recruitment in the gingiva of Traf3ip2^-/- mice. Transcriptomic data showed decreased expression of antimicrobial genes, including Lcn2, S100a8, and Defb1, in the Traf3ip2^-/- mouse gingiva in comparison to WT mice prior to or upon P. gingivalis oral challenge. Further 16S ribosomal RNA sequencing analysis identified a distinct microbial community in the Traf3ip2^-/- mouse oral plaque, which was featured by a reduced microbial diversity and an overabundance of Streptococcus genus bacteria. More P. gingivalis was observed in the Traf3ip2^-/- mouse gingiva than WT control animals in a ligature-promoted P. gingivalis invasion model. In agreement, neutrophil depletion resulted in more local gingival tissue invasion by P. gingivalis. Thus, we identified a homeostatic IL-17-TRAF3IP2-neutrophil axis underpinning host defense against a keystone periodontal pathogen.

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.

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity is even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

Changes in the oral and nasal microbiota in pediatric obstructive sleep apnea

Background

Several clinical studies have demonstrated that pediatric obstructive sleep apnea (OSA) is associated with dysbiosis of airway mucosal microbiota. However, how oral and nasal microbial diversity, composition, and structure are altered in pediatric OSA has not been systemically explored.

Methods

30 polysomnography-confirmed OSA patients with adenoid hypertrophy, and 30 controls who did not have adenoid hypertrophy, were enrolled. Swabs from four surface oral tissue sites (tongue base, soft palate, both palatine tonsils, and adenoid) and one nasal swab from both anterior nares were collected. The 16S ribosomal RNA (rRNA) V3-V4 region was sequenced to identify the microbial communities.

Results

The beta diversity and microbial profiles were significantly different between pediatric OSA patients and controls at the five upper airway sites. The abundances of Haemophilus, Fusobacterium, and Porphyromonas were higher at adenoid and tonsils sites of pediatric patients with OSA. Functional analysis revealed that the differential pathway between the pediatric OSA patients and controls involved glycerophospholipids and amino acid metabolism.

Conclusions

In this study, the oral and nasal microbiome of pediatric OSA patients exhibited certain differences in composition compared with the controls. However, the microbiota data could be useful as a reference for studies on the upper airway microbiome.

The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis

Intra-oral halitosis usually results from the production of volatile sulfur compounds, such as methyl mercaptan and hydrogen sulfide, by the tongue microbiota. There are currently no reports on the microbial gene-expression profiles of the tongue microbiota in halitosis. In this study, we performed RNAseq of tongue coating samples from individuals with and without halitosis. The activity of Streptococcus (including S. parasanguinis), Veillonella (including V. dispar) and Rothia (including R. mucilaginosa) was associated with halitosis-free individuals while Prevotella (including P. shahi), Fusobacterium (including F. nucleatum) and Leptotrichia were associated with halitosis. Interestingly, the metatranscriptome of patients that only had halitosis levels of methyl mercaptan was similar to that of halitosis-free individuals. Finally, gene expression profiles showed a significant over-expression of genes involved in L-cysteine and L-homocysteine synthesis, as well as nitrate reduction genes, in halitosis-free individuals and an over-expression of genes responsible for cysteine degradation into hydrogen sulfide in halitosis patients.

Overexpression of proinflammatory cytokines in dental pulp tissue and distinct bacterial microbiota in carious teeth of Mexican Individuals

The prevalence of dental caries in the Mexican adult population aged 20 to 85 years is around 93.3%, and 50% in Mexican children and adolescents. Worldwide, it is the most common non-communicable disease. One of the main etiological factors for dental caries is the oral microbiome and changes in its structure and function, with an expansion of pathogenic bacteria like Streptococcus mutans. The exposed dental pulp tissue triggers an innate immune response to counteract this bacterial invasion. The relation between oral dysbiosis and innate immune responses remains unclear. We aimed to understand the relationship between innate immune response and the oral microbiota by quantifying the expression of Toll-like receptors (TLRs) and proinflammatory markers (cytokines and a chemokine) in dental pulp tissue, either exposed or not to carious dentin, and to correlate this information with the oral microbiome found in healthy teeth and those with moderate caries. RNA was purified from pulp tissue, subjected to RT-qPCR and analysed with the ^ΔΔCt method. Supragingival dental plaque of non-carious teeth and dentin of carious teeth were subjected to 16S targeted sequencing. Principal coordinate analysis, permutational multivariate ANOVA, and linear discriminant analysis were used to assess differences between non-carious and carious teeth. Correlations were assessed with Spearman´s test and corrected for multiple comparisons using the FDR method. The relative abundance (RA) of Lactobacillus, Actinomyces, Prevotella, and Mitsuokella was increased in carious teeth; while the RA of Haemophilus and Porphyromonas decreased. Olsenella and Parascardovia were only detected in carious teeth. Significant overexpression of interleukin 1 beta (IL1 β), IL6, and CXCL8 was detected in pulp tissue exposed to carious dentin. IL1β correlated positively with TLR2 and Actinomyces; yet negatively with Porphyromonas. These findings suggest that immune response of pulp tissue chronically exposed to cariogenic microbiome is triggered by proinflammatory cytokines IL1β and IL6 and the chemokine CXCL8.

Human microbiome and microbiota identification for preventing and controlling healthcare-associated infections: A systematic review

Objective

This systematic review describes the role of the human microbiome and microbiota in healthcare-associated infections (HAIs). Studies on the microbiota of patients, healthcare environment (HE), medical equipment, or healthcare workers (HCW) and how it could be transmitted among the different subjects will be described in order to define alarming risk factors for HAIs spreading and to identify strategies for HAIs control or prevention.

Methods

This review was performed in adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. After retrieval in databases, identification, and screening of available records, 36 published studies were considered eligible and included in the review.

Results

A multifaceted approach is required and the analyses of the many factors related to human microbiota, which can influence HAIs onset, could be of paramount importance in their prevention and control. In this review, we will focus mainly on the localization, transmission, and prevention of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) bacteria and Clostridium difficile which are the most common pathogens causing HAIs.

Conclusions

Healthcare workers' microbiota, patient's microbiota, environmental and medical equipment microbiota, ecosystem characteristics, ways of transmission, cleaning strategies, and the microbial resistome should be taken into account for future studies on more effective preventive and therapeutic strategies against HAIs.

Interdisciplinary Approaches to Deal with Alzheimer's Disease-From Bench to Bedside: What Feasible Options Do Already Exist Today?

Alzheimer's disease is one of the most common neurodegenerative diseases in the western population. The incidence of this disease increases with age. Rising life expectancy and the resulting increase in the ratio of elderly in the population are likely to exacerbate socioeconomic problems. Alzheimer's disease is a multifactorial disease. In addition to amyloidogenic processing leading to plaques, and tau pathology, but also other molecular causes such as oxidative stress or inflammation play a crucial role. We summarize the molecular mechanisms leading to Alzheimer's disease and which potential interventions are known to interfere with these mechanisms, focusing on nutritional approaches and physical activity but also the beneficial effects of cognition-oriented treatments with a focus on language and communication. Interestingly, recent findings also suggest a causal link between oral conditions, such as periodontitis or edentulism, and Alzheimer's disease, raising the question of whether dental intervention in Alzheimer's patients can be beneficial as well. Unfortunately, all previous single-domain interventions have been shown to have limited benefit to patients. However, the latest studies indicate that combining these efforts into multidomain approaches may have increased preventive or therapeutic potential. Therefore, as another emphasis in this review, we provide an overview of current literature dealing with studies combining the above-mentioned approaches and discuss potential advantages compared to monotherapies. Considering current literature and intervention options, we also propose a multidomain interdisciplinary approach for the treatment of Alzheimer's disease patients that synergistically links the individual approaches. In conclusion, this review highlights the need to combine different approaches in an interdisciplinary manner, to address the future challenges of Alzheimer's disease.

Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study

BACKGROUND

Tooth decay is one of the most prevalent diseases worldwide, and efficient tooth brushing with a fluoride-containing dentifrice is considered fundamental to caries prevention. Fluoride-containing dentifrices have been extensively studied in relation to enamel resistance to demineralization. Arginine (Arg) has also been proposed as a promising prebiotic to promote pH buffering through ammonia production. Here, we present the first metagenomic (DNA sequencing of the whole microbial community) and metatranscriptomic (RNAseq of the same community) analyses of human dental plaque to evaluate the effect of brushing with fluoride (Fl) and a Fl+Arg containing dentifrices on oral microbial composition and activity. Fifty-three patients were enrolled in a longitudinal clinical intervention study with two arms, including 26 caries-active and 27 caries-free adults. After a minimum 1-week washout period, dental plaque samples were collected at this post-washout baseline, 3 months after the use of a 1450-ppm fluoride dentifrice, and after 6 months of using a 1450-ppm fluoride with 1.5% arginine dentifrice.

RESULTS

There was a shift in both the composition and activity of the plaque microbiome after 3 months of brushing with the fluoride-containing toothpaste compared to the samples collected at the 1-week post-washout period, both for caries-active and caries-free sites. Although several caries-associated bacteria were reduced, there was also an increase in several health- and periodontitis-associated bacteria. Over 400 genes changed proportion in the metagenome, and between 180 and 300 genes changed their expression level depending on whether caries-free or caries-active sites were analyzed. The metagenome and metatranscriptome also changed after the subjects brushed with the Fl+Arg dentifrice. There was a further decrease of both caries- and periodontitis-associated organisms. In both caries-free and caries-active sites, a decrease of genes from the arginine biosynthesis pathway was also observed, in addition to an increase in the expression of genes associated with the arginine deiminase pathway, which catabolizes arginine into ammonia, thereby buffering acidic pH. Bacterial richness and diversity were not affected by either of the two treatments in the two arms of the study.

CONCLUSIONS

Our data demonstrate that long-term use of both assayed dentifrices changes the bacterial composition and functional profiles of human dental plaque towards a healthier microbial community, both in caries-free and caries-active sites. This observation was especially apparent for the Fl+Arg dentifrice. Thus, we conclude that the preventive benefits of tooth brushing go beyond the physical removal of dental plaque and that the active ingredients formulated within dentifrices have a positive effect not only on enamel chemistry but also on the metabolism of oral microbial populations. Video Abstract.

A potential oral microbiome signature associated with coronary artery disease in Tunisia

The coronary artery disease (CAD) is a chronic inflammatory disease involving genetic as well as environmental factors. Recent evidence suggests that the oral microbiome has a significant role in triggering atherosclerosis. The present study assessed the oral microbiome composition variation between coronary patients and healthy subjects in order to identify a potential pathogenic signature associated with CAD. We performed metagenomic profiling of salivary microbiomes by 16S ribosomal RNA (rRNA) next-generation sequencing. Oral microbiota profiling was performed for 30 individuals including 20 patients with CAD and ten healthy individuals without carotid plaques or previous stroke or myocardial infarction. We found that oral microbial communities in patients and healthy controls are represented by similar global core oral microbiome. The predominant taxa belonged to Firmicutes (genus Streptococcus, Veillonella, Granulicatella, Selenomonas), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Rothia), Bacteroidetes (genus Prevotella, Porphyromonas), and Fusobacteria (genus Fusobacterium, Leptotrichia). More than 60% relative abundance of each sample for both CAD patients and controls is represented by three major genera including Streptococcus (24.97 and 26.33%), Veillonella (21.43 and 19.91%), and Neisseria (14.23 and 15.33%). Using penalized regression analysis, the bacterial genus Eikenella was involved as the major discriminant genus for both status and Syntax score of CAD. We also reported a significant negative correlation between Syntax score and Eikenella abundance in coronary patients' group (Spearman rho = -0.68, P=0.00094). In conclusion, the abundance of Eikenella in oral coronary patient samples compared with controls could be a prominent pathological indicator for the development of CAD.

Effects of the increased protein level in small intestine on the colonic microbiota, inflammation and barrier function in growing pigs

Background

An increased level of the dietary protein alters the colonic microbial community and metabolic profile of pigs, but it remains unclear whether this leads to colonic inflammation and impairs barrier function in growing pigs.

Results

Sixteen pigs (35.2 ± 0.3 kg) were infused with sterile saline (control) or soy protein hydrolysate (SPH) (70 g/day) through a duodenal fistula twice daily during a 15-day experimental period. The SPH treatment did not affect their average daily feed intake and daily weight gain (P > 0.05), but reduced colon index and length (P < 0.05). Illumina MiSeq sequencing revealed that species richness was increased following SPH intervention (P < 0.05). Furthermore, SPH reduced the abundance of butyrate- and propionate-producing bacteria—such as Lachnospiraceae NK4A136 group, Lachnospiraceae_uncultured, Coprococcus 3, Lachnospiraceae UCG-002, and Anaerovibrio—and increased the abundance of potentially pathogenic bacteria and protein-fermenting bacteria, such as Escherichia-Shigella, Dialister, Veillonella, Prevotella, Candidatus Saccharimonas, Erysipelotrichaceae UCG-006, Prevotellaceae_uncultured, and Prevotellaceae UCG-003 (P < 0.05). In addition, a lower content of total short-chain fatty acids, propionate, and butyrate and a higher concentration of cadaverine, putrescine, total biogenic amines, ammonia, and isovalerate were observed following SPH infusion (P < 0.05). Further analysis revealed that SPH increased the concentration of tumour necrosis factor-α, interleukin (IL)-1β, IL-6, and IL-8 in the colonic mucosa (P < 0.05). Interestingly, SPH intervention increased the expression of occludin, zonula occludens (ZO)-1, and claudin-1 in colonic mucosa (P < 0.05). Correlation analysis showed that different genera were significantly related to the production of metabolites and the concentrations of pro-inflammatory cytokines.

Conclusion

An increased soy protein level in the small intestine altered the colonic microbial composition and metabolic profile, which resulted in the secretion of colonic proinflammatory cytokines and the increased expression of tight junction proteins.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02498-x.

Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors

The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and circulatory systems, the composition of the oral microbiome is relevant beyond just oral health, impacting systemic processes across the body. However, we still have a very limited understanding about intrinsic and extrinsic factors that shape the composition of the healthy oral microbiome. Here, we followed a citizen-science approach to assess the relative impact on the oral microbiome of selected biological, social, and lifestyle factors in 1648 Spanish individuals. We found that the oral microbiome changes across age, with middle ages showing a more homogeneous composition, and older ages showing more diverse microbiomes with increased representation of typically low abundance taxa. By measuring differences within and between groups of individuals sharing a given parameter, we were able to assess the relative impact of different factors in driving specific microbial compositions. Chronic health disorders present in the analyzed population were the most impactful factors, followed by smoking and the presence of yeasts in the oral cavity. Finally, we corroborate findings in the literature that relatives tend to have more similar oral microbiomes, and show for the first time a similar effect for classmates. Multiple intrinsic and extrinsic factors jointly shape the oral microbiome. Comparative analysis of metabarcoding data from a large sample set allows us to disentangle the individual effects.

Smoking has disruptive effects on the small bowel luminal microbiome

Tobacco use is the leading preventable cause of cancer, and affects the respiratory, oral, fecal, and duodenal mucosa-associated microbiota. However, the effects of smoking on the duodenal luminal microbiome have not been studied directly. We aimed to compare the duodenal luminal microbiome in never-smokers, current smokers, and ex-smokers who quit ≥ 10 years ago. In a cross-sectional study, current smokers (CS, n = 24) were identified and matched to never-smokers (NS, n = 27) and ex-smokers (XS, n = 27) by age (± 5 years), body mass index (BMI, ± 3 kg/m²), and sex. Current antibiotic users were excluded. The duodenal luminal microbiome was analysed in 1 aspirate sample per subject by 16S rRNA gene sequencing. Relative abundances (RA) of families associated with increased duodenal microbial diversity, Prevotellaceae, Neisseriaceae, and Porphyromonadaceae, were significantly lower in CS vs. NS. This was driven by lower RA of unknown Prevotella and Porphyromonas species, and Neisseria subflava and N. cinerea, in CS. In contrast, RA of Enterobacteriaceae and Lactobacillaceae (associated with decreased diversity), were significantly higher in CS, due to higher RA of Escherichia-Shigella, Klebsiella and Lactobacillus species. Many of these changes were absent or less pronounced in XS, who exhibited a duodenal luminal microbiome more similar to NS. RA of taxa previously found to be increased in the oral and respiratory microbiota of smokers were also higher in the duodenal luminal microbiome, including Bulledia extructa and an unknown Filifactor species. In conclusion, smoking is associated with an altered duodenal luminal microbiome. However, ex-smokers have a duodenal luminal microbiome that is similar to never-smokers.

Microbiome Analysis and Pharmacovigilance After Inhaled Glucocorticoid: Oral Dysbiosis With the Isolation of Three Rothia Species and Subsequent Sjögren's Syndrome

Background: Treatment of respiratory tract diseases with inhaled glucocorticoids is a form of therapy that has been used for many years. It shows lower potency of side effects; nevertheless, microbiome change, sinopulmonary dysbiosis, secondary immunodeficiency, and immunomodulatory effects are underestimated. The latest guideline recommendations introduce the use of empirical antibiotic and/or multiplying inhaled glucocorticoids in therapeutic intervention of asthma and chronic pulmonary obstructive disease. Aims and objectives: The aim of the study was to describe a simple, universal, and cost-effective method of microbiome analysis for clinical trials. Such a general method for monitoring pharmacovigilance should be widely available and reliable. Methods: The study material included two kinds of swabs, taken from the same mouth ulcerations of patients with asthma treated with a temporary quadruple dose of fluticasone. The microbiological investigation was performed, and identification of the isolates was carried out using the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) Biotyper. Results: The analysis of dry swab demonstrated the presence of typical oral bacteria (Neisseria spp. and Streptococcus spp.), alongside with the potentially pathogenic Actinomyces spp. and three different Rothia species, identified simultaneously: R. aeria, R. dentocariosa, and R. mucilaginosa. Although quadrupled dose of corticoids was discontinued and ulcer healing was observed, the patients required topical therapy for maintained xerostomia. Progressive systemic autoimmunity (seronegative Sjögren's syndrome with major organ involvement) was observed later. Conclusion: Topical steroids (especially in quadruple dose) require attention to safety, immunomodulation, and microbiological outcome. They showed systemic side effects: microbiome alteration, humoral (IgG) immunodeficiency, and systemic autoimmunity. Isolation of three species of Rothia from a patient with mouth ulcers after steroid therapy suggests their participation in infectious and inflammatory processes. The proposed a methodology using MALDI-TOF-MS may be a prototype approach for microbial diagnostics in clinical trials of immunomodulatory drugs.

SMDI: An Index for Measuring Subgingival Microbial Dysbiosis

An intuitive, clinically relevant index of microbial dysbiosis as a summary statistic of subgingival microbiome profiles is needed. Here, we describe a subgingival microbial dysbiosis index (SMDI) based on machine learning analysis of published periodontitis/health 16S microbiome data. The raw sequencing data, split into training and test sets, were quality filtered, taxonomically assigned to the species level, and centered log-ratio transformed. The training data set was subject to random forest analysis to identify discriminating species (DS) between periodontitis and health. DS lists, compiled by various "Gini" importance score cutoffs, were used to compute the SMDI for samples in the training and test data sets as the mean centered log-ratio abundance of periodontitis-associated species subtracted by that of health-associated ones. Diagnostic accuracy was assessed with receiver operating characteristic analysis. An SMDI based on 49 DS provided the highest accuracy with areas under the curve of 0.96 and 0.92 in the training and test data sets, respectively, and ranged from -6 (most normobiotic) to 5 (most dysbiotic) with a value around zero discriminating most of the periodontitis and healthy samples. The top periodontitis-associated DS were Treponema denticola, Mogibacterium timidum, Fretibacterium spp., and Tannerella forsythia, while Actinomyces naeslundii and Streptococcus sanguinis were the top health-associated DS. The index was highly reproducible by hypervariable region. Applying the index to additional test data sets in which nitrate had been used to modulate the microbiome demonstrated that nitrate has dysbiosis-lowering properties in vitro and in vivo. Finally, 3 genera (Treponema, Fretibacterium, and Actinomyces) were identified that could be used for calculation of a simplified SMDI with comparable accuracy. In conclusion, we have developed a nonbiased, reproducible, and easy-to-interpret index that can be used to identify patients/sites at risk of periodontitis, to assess the microbial response to treatment, and, importantly, as a quantitative tool in microbiome modulation studies.

Electronic Cigarette Use Promotes a Unique Periodontal Microbiome

Electronic cigarettes (e-cigs) have become prevalent as an alternative to conventional cigarette smoking, particularly in youth. E-cig aerosols contain unique chemicals which alter the oral microbiome and promote dysbiosis in ways we are just beginning to investigate. We conducted a 6-month longitudinal study involving 84 subjects who were either e-cig users, conventional smokers, or nonsmokers. Periodontal condition, cytokine levels, and subgingival microbial community composition were assessed, with periodontal, clinical, and cytokine measures reflecting cohort habit and positively correlating with pathogenic taxa (e.g., Treponema, Saccharibacteria, and Porphyromonas). α-Diversity increased similarly across cohorts longitudinally, yet each cohort maintained a unique microbiome. The e-cig microbiome shared many characteristics with the microbiome of conventional smokers and some with nonsmokers, yet it maintained a unique subgingival microbial community enriched in Fusobacterium and Bacteroidales (G-2). Our data suggest that e-cig use promotes a unique periodontal microbiome, existing as a stable heterogeneous state between those of conventional smokers and nonsmokers and presenting unique oral health challenges. IMPORTANCE Electronic cigarette (e-cig) use is gaining in popularity and is often perceived as a healthier alternative to conventional smoking. Yet there is little evidence of the effects of long-term use of e-cigs on oral health. Conventional cigarette smoking is a prominent risk factor for the development of periodontitis, an oral disease affecting nearly half of adults over 30 years of age in the United States. Periodontitis is initiated through a disturbance in the microbial biofilm communities inhabiting the unique space between teeth and gingival tissues. This disturbance instigates host inflammatory and immune responses and, if left untreated, leads to tooth and bone loss and systemic diseases. We found that the e-cig user's periodontal microbiome is unique, eliciting unique host responses. Yet some similarities to the microbiomes of both conventional smokers and nonsmokers exist, with strikingly more in common with that of cigarette smokers, suggesting that there is a unique periodontal risk associated with e-cig use.

Oral microbiota and periodontitis severity among Hispanic adults

Background

Periodontitis, one of the most common bacterial infections characterized by chronic inflammation, is also known to be a risk factor for chronic conditions, including cardiovascular disease and cancer. This inflammation is driven by an altered microbiota with an increase in pathogenic bacteria. We evaluated the association between oral microbiota and periodontitis severity in high-risk Hispanics.

Method

This cross-sectional study recruited 134 sexually active participants aged 21 to 49 years old from STI Clinics in Puerto Rico. A periodontal examination, saliva collection, and an interviewer-administered questionnaire were performed. Periodontal severity was categorized as: having no disease, mild, and moderate/severe and BOP and tooth loos was noted. Saliva samples were collected for genomic DNA extraction, downstream 16S rDNA amplification sequencing, and bioinformatics analyses.

Results

The structure, composition, and diversity of bacterial communities differed significantly according to periodontal severity. The richness and overall diversity also differed between participants without periodontitis and participants with some level of periodontal disease. A higher abundance of Prevotella, Veillonella, or Treponema was attributed to periodontal disease and Aggregatibacter to severe bleeding on probing, while Neisseria was found in higher abundance in healthy participants, decreasing its levels with drinking, smoking, and oral sex practices.

Conclusions

Our findings indicate that dysbiosis occurs as periodontal disease progresses, and both alcohol consumption and smoking habits pose risk factors for oral dysbiosis. These results are of public health and clinical impact, as several bacteria identified could serve in the future as biomarkers for periodontitis and oral cancer risk.

Microbiota analysis of peri-implant mucositis in patients with periodontitis history

OBJECTIVES

To investigate the bacterial diversity in peri-implant plaques and the effect of periodontitis history on the occurrence of peri-implant mucositis.

MATERIALS AND METHODS

Three groups of subgingival plaques were collected from peri-implant sulci in the first molar area. The three groups included healthy implants in patients without periodontitis (NH implant), healthy implants in patients with periodontitis history (PH implant), and peri-implant mucositis implants in patients with periodontitis history (PM implant). Subgingival plaques in periodontal pockets of contralateral natural first molars were also collected. Bacterial DNA was extracted and the V4 region of the 16S rDNA sequence was amplified and sequenced on an Illumina HiSeq platform. The operational taxonomic units obtained from amplicon sequencing were used to analyze the prevalence and identity of bacteria based on public databases and advanced techniques.

RESULTS

Analysis of similarities indicated a significant difference in bacterial structures between the NH implant and PM implant groups. Additionally, a significantly higher relative abundance of the genera Actinomyces and Streptococcus was found in the samples of the NH implant group. The genera Fusobacterium and Prevotella could be considered as potential biomarkers for peri-implant mucositis. Moreover, more gram-negative anaerobic bacteria (Porphyromonas and Prevotella) were detected in the samples from patients with periodontitis history.

CONCLUSIONS

The increased accumulation of Fusobacterium and Prevotella is associated with a higher risk of peri-implant mucositis. In addition, patients with periodontal history may be more likely to develop peri-implant mucositis.

CLINICAL RELEVANCE

The increase in periodontal pathogens and the decrease in health-associated bacteria in patients with periodontitis history may be more likely to develop peri-implant mucositis. These results provide a bacteriological basis for the prevention and treatment of peri-implant mucositis in patients with periodontitis history.

Associations of sex, oral hygiene and smoking with oral species in distinct habitats at age 32 years

The oral microbiome is ecologically diverse, complex, dynamic, and little understood. We describe the microbiota of four oral habitats in a birth cohort at age 32 and examine differences by sex, oral hygiene, and current smoking status, dental caries, and periodontal health. Oral biofilm samples collected from anterior labial supragingival, posterior lingual supragingival, subgingival, and tongue sites of 841 Dunedin Multidisciplinary Health and Development Study members were analysed using checkerboard DNA-DNA hybridization; focusing on 30 ecologically important bacterial species. The four habitats exhibited distinct microbial profiles that differed by sex. Streptococcus gordonii was more dominant in supragingival and tongue biofilms of males; Porphyromonas gingivalis exhibited higher relative abundance in subgingival biofilm of females. Males had higher scores than females for periodontal pathogens at supragingival sites. The relative abundance of several putative caries and periodontal pathogens differed in smokers and non-smokers. With poor oral hygiene significantly higher proportions of Gram-negative facultative anaerobes were present in subgingival biofilm and there were higher scores for the principal components characterised by putative cariogenic and periodontal pathogens at each site. Distinctive microenvironments shape oral biofilms and systematic differences exist by sex, oral hygiene, and smoking status.

Current Concepts in the Management of Periodontitis

Periodontitis is a common disorder affecting >40% of adults in the United States. Globally, the severe form of the disease has a prevalence of 11%. In advanced cases, periodontitis leads to tooth loss and reduced quality of life. The aetiology of periodontitis is multifactorial. Subgingival dental biofilm elicits a host inflammatory and immune response, ultimately leading to irreversible destruction of the periodontium (i.e. alveolar bone and periodontal ligament) in a susceptible host. In order to successfully manage periodontitis, dental professionals must understand the pathogenesis, primary aetiology, risk factors, contributing factors and treatment protocols. Careful diagnosis, elimination of the causes and reduction of modifiable risk factors are paramount for successful prevention and treatment of periodontitis. Initial non-surgical periodontal therapy primarily consists of home care review and scaling and root planing. For residual sites with active periodontitis at periodontal re-evaluation, a contemporary regenerative or traditional resective surgical therapy can be utilised. Thereafter, periodontal maintenance therapy at a regular interval and long-term follow-ups are also crucial to the success of the treatment and long-term retention of teeth. The aim of this review is to provide current concepts of diagnosis, prevention and treatment of periodontitis. Both clinical and biological rationales will be discussed.

Influence of cigarette smoking on oral microbiota in patients with recurrent aphthous stomatitis

Recurrent aphthous stomatitis (RAS) is a common recurrent ulcerative disease of the oral mucosa which is closely related to oral microbial composition. However, the specific effect and the mechanism of smoking in RAS are unclear. In this study, 16S rRNA sequencing technology was used to compare the differences in saliva microbial community between 28 non-smoking healthy controls (NSctrl), 31 non-smoking RAS patients (NSras), and 19 smoking RAS patients (Sras). The results showed that the bacterial community diversity in patients with RAS (NSras and Sras) was lower than that of NSctrl. The microbial community in smoking-associated RAS is less diverse and distinct from that of non-smokers. The RAS groups have higher abundance of Veillonella, Rothia, and Sneathia and lower abundance of Bacteroidales, Bacteroides, Wolinella, Moryella, Pyramidobacter, and Christensenellaceae at the genera level. A significantly different abundance of Anaerovorax, Candidatus Endomicrobium, Lactococcus, Sneathia, Veillonella, and Cloacibacterium was observed between the Sras and the NSras group. Notably, there was a significant difference in many species from the genus Prevotella and Treponema between the NSras and the Sras group. Further, the relative abundance of several taxa is correlated with smoking age or frequency, including Megasphaera, Haemophilus, Leptotrichia, and Rothia at the genera level, and Prevotella melaninogenica, Prevotella salivae, Megasphaera micronuciformis, Haemophilus parainfluenzae, Alloprevotella tannerae, Actinomyces naeslundii, Lautropia mirabilis, and Capnocytophaga sputigena at the species level. Among patients with RAS, smoking aggravated the pathways of respiration and human pathogens. Our results suggest that smoking is closely related to changes in the oral microbiota, which may contribute an opposite effect to the pathogenesis of RAS. This study provides new insight and theoretical basis for the cause and pathogenesis of RAS and better prevention and treatment.

Subgingival Microbiota and Cytokines Profile Changes in Patients with Periodontitis: A Pilot Study Comparing Healthy and Diseased Sites in the Same Oral Cavities

Periodontitis is a common condition characterized by an exacerbated pro-inflammatory response, which leads to tissue destruction and, ultimately, alveolar bone loss. In this pilot study, we assess the microbiota composition and cytokine profile changes in patients with stage III/IV, grade B/C periodontitis, specifically by comparing healthy and diseased sites in the same oral cavity. Overall, we found that microbiota architecture was significantly disrupted between diseased and healthy sites, and that the clustering was driven, in part, by the increased relative abundances of Synergistetes in diseased sites, as well as the increased abundances of Firmicutes in healthy sites. We also observed that diseased sites were enriched in Synergistetes, TM7, SR1, Spirochaetes, Bacteroidetes and Fusobacteria, and depleted in Firmicutes, Proteobacteria, Tenericutes and Actinobacteria compared to healthy sites. We found that Interleukin-1b, Interleukin-4, Interleukin-10, and Interleukin-17A were significantly overexpressed in diseased sites, whereas Interleukin-6 and TNF-alpha do not differ significantly between healthy and diseased sites. Here, we observed concomitant changes in the subgingival plaque microbiota and cytokines profile, suggesting that this combined alteration could contribute to the pathobiology of periodontitis.

Periodontal Diseases: Major Exacerbators of Pulmonary Diseases?

Periodontal diseases are a range of polymicrobial infectious disorders, such as gingivitis and periodontitis, which affect tooth-supporting tissues and are linked to playing a role in the exacerbation of several pulmonary diseases. Pulmonary diseases, such as pneumonia, chronic obstructive pulmonary disease (COPD), asthma, tuberculosis, COVID-19, and bronchiectasis, significantly contribute to poor quality of life and mortality. The association between periodontal disease and pulmonary outcomes is an important topic and requires further attention. Numerous resident microorganisms coexist in the oral cavity and lungs. However, changes in the normal microflora due to oral disease, old age, lifestyle habits, or dental intervention may contribute to altered aspiration of oral periodontopathic bacteria into the lungs and changing inflammatory responses. Equally, periodontal diseases are associated with the longitudinal decline in spirometry lung volume. Several studies suggest a possible beneficial effect of periodontal therapy in improving lung function with a decreased frequency of exacerbations and reduced risk of adverse respiratory events and morbidity. Here, we review the current literature outlining the link between the oral cavity and pulmonary outcomes and focus on the microflora of the oral cavity, environmental and genetic factors, and preexisting conditions that can impact oral and pulmonary outcomes.

Associations of decayed and filled teeth with localized stage II/III periodontitis in young adults: The CHIEF oral health study

Background/purpose

To investigate the associations between treated and untreated dental caries and periodontitis in young adults.

Materials and methods

The study enrolled 1289 participants aged 18–45 years in Taiwan. Localized periodontitis was categorized into healthy and stage II/III (n = 936 and n = 353, respectively) based on the 2017 criteria of the World Workshop. Multivariable logistic regression analysis with adjustments for sex, age, tobacco smoking status, betel nut consumption status, metabolic syndrome, and total white blood cell count was used to determine the associations.

Results

Decayed tooth numbers were positively associated with localized stage II/III periodontitis [odds ratio (OR): 1.15 (95% confidence intervals (CI): 1.06–2.25)], while filled tooth numbers were inversely associated with localized stage II/III periodontitis in young adults [OR: 0.96 (95% CI: 0.92–0.99)].

Conclusion

Our study confirms the relationship between dental caries and periodontitis by direct evidence that the more decayed teeth there are, the higher the risk of periodontitis and by indirect evidence that the more treated decayed teeth there are, the lower the risk of periodontitis in young adults.

Characterization of Oral Bacterial Composition of Adult Smokeless Tobacco Users from Healthy Indians Using 16S rDNA Analysis

The present investigation is aiming to report the oral bacterial composition of smokeless tobacco (SLT) users and to determine the influence of SLT products on the healthy Indian population. With the aid of the V3 hypervariable region of the 16S rRNA gene, a total of 8,080,889 high-quality reads were clustered into 15 phyla and 180 genera in the oral cavity of the SLT users. Comparative analysis revealed a more diverse microbiome where two phyla and sixteen genera were significantly different among the SLT users as compared to the control group (p-value < 0.05). The prevalence of Fusobacteria-, Porphyromonas-, Desulfobulbus-, Enterococcus-, and Parvimonas-like genera among SLT users indicates altered bacterial communities among SLT users. Besides, the depletion of health-compatible bacteria such as Lactobacillus and Haemophilus also suggests poor oral health. Here, the majority of the altered genera belong to Gram-negative anaerobes that have been reported for assisting biofilm formation that leads in the progression of several oral diseases. The PICRUSt analysis further supports the hypothesis where a significant increase in the count of the genes involved in the metabolism of nitrogen, amino acids, and nicotinate/nicotinamide was observed among tobacco chewers. Moreover, this study has a high significance in Indian prospects where the SLT consumers are prevalent but we are deficient in information on their oral microbiome.

The Impact of Smoking on Subgingival Plaque and the Development of Periodontitis: A Literature Review

Smoking seriously affects oral health and causes a variety of oral diseases. Numerous clinical data show that smoking significantly increases the risk of periodontitis, and the duration and amount of smoking are positively correlated with the severity of periodontitis. In fact, smoking creates an environment conducive to the colonization of periodontopathogens, which affects the process of periodontitis. Since subgingival plaque which harbors periodontopathogens is the initiation factor of periodontitis, it is critical to study the impact of smoking on subgingival microbiota for understanding the relationship between smoking and periodontitis. Continuous advances have been made on the understanding of effects of smoking on subgingival plaque and the development of periodontitis. Smoking is observed to enhance the pathogenicity of periodontopathogens, especially the red complex microorganisms, via promoting their colonization and infection, and regulating the expression and function of multiple virulence factors. Furthermore, smoking has a negative impact on periodontal microecological homeostasis, which is reflected in the decrease of commensal bacteria and the increase of periodontopathogens, as well as the changes in the interaction between periodontopathogens and their commensal microbes in subgingival biofilm, thus influencing the pathogenicity of the subgingival plaque. In summary, the mechanism of smoking on subgingival plaque microorganisms represented by the red complex and its effect on the periodontal microecology still need to be further explored. The relevant research results are of great significance for guiding the periodontal clinical treatment of smoking population. This review summarizes the effects and relevant mechanisms of smoking on subgingival plaque and the development of periodontitis.

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies

The advent of high-throughput sequencing techniques has recently provided an astonishing insight into the composition and function of the human microbiome. Next-generation sequencing (NGS) has become the gold standard for advanced microbiome analysis; however, 3rd generation real-time sequencing, such as Oxford Nanopore Technologies (ONT), enables rapid sequencing from several kilobases to >2 Mb with high resolution. Despite the wide availability and the enormous potential for clinical and translational applications, ONT is poorly standardized in terms of sampling and storage conditions, DNA extraction, library creation, and bioinformatic classification. Here, we present a comprehensive analysis pipeline with sampling, storage, DNA extraction, library preparation, and bioinformatic evaluation for complex microbiomes sequenced with ONT. Our findings from buccal and rectal swabs and DNA extraction experiments indicate that methods that were approved for NGS microbiome analysis cannot be simply adapted to ONT. We recommend using swabs and DNA extractions protocols with extended washing steps. Both 16S rRNA and metagenomic sequencing achieved reliable and reproducible results. Our benchmarking experiments reveal thresholds for analysis parameters that achieved excellent precision, recall, and area under the precision recall values and is superior to existing classifiers (Kraken2, Kaiju, and MetaMaps). Hence, our workflow provides an experimental and bioinformatic pipeline to perform a highly accurate analysis of complex microbial structures from buccal and rectal swabs.

IMPORTANCE Advanced microbiome analysis relies on sequencing of short DNA fragments from microorganisms like bacteria, fungi, and viruses. More recently, long fragment DNA sequencing of 3rd generation sequencing has gained increasing importance and can be rapidly conducted within a few hours due to its potential real-time sequencing. However, the analysis and correct identification of the microbiome relies on a multitude of factors, such as the method of sampling, DNA extraction, sequencing, and bioinformatic analysis. Scientists have used different protocols in the past that do not allow us to compare results across different studies and research fields. Here, we provide a comprehensive workflow from DNA extraction, sequencing, and bioinformatic workflow that allows rapid and accurate analysis of human buccal and rectal swabs with reproducible protocols. This workflow can be readily applied by many scientists from various research fields that aim to use long-fragment microbiome sequencing.