Subgingival microbial profiles of smokers with periodontitis

Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar

Physiological hormonal fluctuations exert endogenous pressures on the structure and function of the human microbiome. As such, the menstrual cycle may selectively disrupt the homeostasis of the resident oral microbiome, thus compromising oral health. Hence, the aim of the present study was to structurally and functionally profile the salivary microbiome of 103 women in reproductive age with regular menstrual cycle, while evaluating the modifying influences of hormonal contraceptives, sex hormones, diet, and smoking. Whole saliva was sampled during the menstrual, follicular, and luteal phases (n = 309) of the cycle, and the participants reported questionnaire-based data concerning their life habits and oral or systemic health. No significant differences in alpha-diversity or phase-specific clustering of the overall microbiome were observed. Nevertheless, the salivary abundances of genera Campylobacter, Haemophilus, Prevotella, and Oribacterium varied throughout the cycle, and a higher species-richness was observed during the luteal phase. While the overall community structure maintained relatively intact, its functional properties were drastically affected. In particular, 11 functional modules were differentially abundant throughout the menstrual cycle, including pentose phosphate metabolism, and biosynthesis of cobalamin and neurotransmitter gamma-aminobutyric acid. The menstrual cycle phase, but not oral contraceptive usage, was accountable for greater variations in the metabolic pathways of the salivary microbiome. Further co-risk factor analysis demonstrated that Prevotella and Veillonella were increased in current smokers, whereas high dietary sugar consumption modified the richness and diversity of the microbiome during the cycle. This is the first large study to systematically address dysbiotic variations of the oral microbiome during the course of menstrual cycle, and document the additive effect of smoking and sugar consumption as environmental risk factors. It reveals the structural resilience and functional adaptability of the oral microbiome to the endogenous hormonal pressures of the menstrual cycle, while revealing its vulnerability to the exogenous exposures of diet and smoking.

Looking beyond the smokescreen: can the oral microbiome be a tool or target in the management of tobacco-associated oral cancer?

A wide range of microbes inhabit the oral cavity, and bacterial and fungal communities most often exist as structured communities or biofilms. The use of tobacco alters the structure of the oral microbiome, including that of potentially malignant lesions, and the altered oral microbiome influences key microenvironmental changes such as chronic inflammation, secretion of carcinogenic toxins, cellular and tissue remodelling and suppression of apoptosis. Given this, it is clear that the bacterial and fungal biofilms in potentially malignant states are likely not passive entities, but could play a critical role in shaping potential malignant and carcinogenic conditions. This holds potential towards leveraging the oral microbiome for the management of tobacco-associated potentially malignant lesions and oral cancer. Here, we explore this line of investigation by reviewing the effects of tobacco in shaping the oral microbiome, and analyse the available evidence in the light of the microbiome of oral potentially malignant and cancerous lesions, and the role of dysbiosis in carcinogenesis. Finally, we discuss possible interventions and approaches using which the oral microbiome could be leveraged towards precision-based oral cancer therapeutics.

The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study

Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect of other tobacco types on the oral microbiome. This study investigates subgingival microbiome composition in smokers of different tobacco types and their effect on periodontal health. Subgingival plaques were collected from 40 individuals, including smokers of either cigarettes, medwakh, or shisha, and non-smokers seeking dental treatment at the University Dental Hospital in Sharjah, United Arab Emirates. The entire (~ 1500 bp) 16S rRNA bacterial gene was fully amplified and sequenced using Oxford Nanopore technology. Subjects were compared for the relative abundance and diversity of subgingival microbiota, considering smoking and periodontal condition. The relative abundances of several pathogens were significantly higher among smokers, such as Prevotella denticola and Treponema sp. OMZ 838 in medwakh smokers, Streptococcus mutans and Veillonella dispar in cigarette smokers, Streptococcus sanguinis and Tannerella forsythia in shisha smokers. Subgingival microbiome of smokers was altered even in subjects with no or mild periodontitis, probably making them more prone to severe periodontal diseases. Microbiome profiling can be a useful tool for periodontal risk assessment. Further studies are recommended to investigate the impact of tobacco cessation on periodontal disease progression and oral microbiome.

Association of bacterial vaginosis with periodontitis in a cross-sectional American nationwide survey

To explore the association between bacterial vaginosis (BV) and periodontitis (PD) and to determine whether PD and BV might be linked with systemic serum alterations. We used the National Health and Nutrition Examination Survey 2001-2004, with women aged 18-49 years old and diagnosed with or without BV according to Nugent's method. PD was defined according to the 2012 case definition. We compared serum counts according to the presence of PD and the presence of BV. Multivariable regression was used to explore and identify relevant variables towards the presence of BV. 961 women fulfilled the inclusion criteria. In women with BV, PD was associated with higher inflammation, characterized by increased white blood cells (p = 0.006) and lymphocyte (p = 0.009) counts. Predictive models presented a statistically significant association between PD and BV [Odds Ratio (OD) = 1.69, 95% Confidence Interval (CI): 1.09-2.61 for periodontitis; OD = 2.37, 95% CI: 1.30-4.29 for severe PD]. Fully adjusted models for age, smoking, body mass index, diabetes mellitus and number of systemic conditions reinforced this association [OD = 1.71, 95% CI: 1.06-2.76 for PD; OD = 2.21, 95% CI: 1.15-4.25 for severe PD]. An association between BV and PD is conceivable. PD was associated with higher systemic markers of inflammation in women with BV. Our data is novel and could serve as a foundation to guide future studies in the confirmation of this association and the underlying mechanisms.

Probing periodontal microbial dark matter using metataxonomics and metagenomics

Our view of the periodontal microbial community has been shaped by a century or more of cultivation-based and microscopic investigations. While these studies firmly established the infection-mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka described as the "great plate count anomaly", in that these culturable bacteria were only a minor part of what was visible under the microscope. For nearly a century, much effort has been devoted to finding the right tools to investigate this uncultivated majority, also known as "microbial dark matter". The discovery that DNA was an effective tool to "see" microbial dark matter was a significant breakthrough in environmental microbiology, and oral microbiologists were among the earliest to capitalize on these advances. By identifying the order in which nucleotides are arranged in a stretch of DNA (DNA sequencing) and creating a repository of these sequences, sequence databases were created. Computational tools that used probability-driven analysis of these sequences enabled the discovery of new and unsuspected species and ascribed novel functions to these species. This review will trace the development of DNA sequencing as a quantitative, open-ended, comprehensive approach to characterize microbial communities in their native environments, and explore how this technology has shifted traditional dogmas on how the oral microbiome promotes health and its role in disease causation and perpetuation.

Environmental factors and periodontal microbiome

Periodontal diseases are chronic inflammatory, multifactorial diseases where the major triggering factors for disease onset are bacteria and their toxins, but the major part of tissue destruction occurs as a result of host response towards the periodontal microbiome. Periodontal microbiome consists of a wide range of microorganisms including obligate and facultative anaerobes. In health, there is a dynamic balance between the host, environment, and the microbiome. Environmental factors, mainly tobacco smoking and psychological stress, disrupt the symbiotic relationship. Tobacco smoke and its components alter the bacterial surface and functions such as growth. Psychological stressors and stress hormones may affect the outcome of an infection by changing the virulence factors and/or host response. This review aims to provide currently available data on the effects of the major environmental factors on the periodontal microbiome.

Impact of systemic factors in shaping the periodontal microbiome

Since 2010, next-generation sequencing platforms have laid the foundation to an exciting phase of discovery in oral microbiology as it relates to oral and systemic health and disease. Next-generation sequencing has allowed large-scale oral microbial surveys, based on informative marker genes, such as 16S ribosomal RNA, community gene inventories (metagenomics), and functional analyses (metatranscriptomics), to be undertaken. More specifically, the availability of next-generation sequencing has also paved the way for studying, in greater depth and breadth, the effect of systemic factors on the periodontal microbiome. It was natural to investigate systemic diseases, such as diabetes, in such studies, along with systemic conditions or states, , pregnancy, menopause, stress, rheumatoid arthritis, and systemic lupus erythematosus. In addition, in recent years, the relevance of systemic "variables" (ie, factors that are not necessarily diseases or conditions, but may modulate the periodontal microbiome) has been explored in detail. These include ethnicity and genetics. In the present manuscript, we describe and elaborate on the new and confirmatory findings unveiled by next-generation sequencing as it pertains to systemic factors that may shape the periodontal microbiome. We also explore the systemic and mechanistic basis for such modulation and highlight the importance of those relationships in the management and treatment of patients.

Cefazolin versus ampicillin/sulbactam as an empiric antibiosis in severe odontogenic neck infection descending from the lower jaw-retrospective analysis of 350 cases

OBJECTIVES

Odontogenic infections descending from the lower jaw may lead to severe health conditions. Commonly, a biphasic treatment of surgical drainage and antibiotic therapy is conducted. The choice of the administered empiric antibiotic agent remains debatable.

MATERIAL AND METHODS

Retrospectively, we analyzed 350 medical records of patients who were consecutively treated with odontogenic infections descending from the lower jaw. All patients received surgical drainage and either cefazolin or ampicillin/sulbactam as empiric antibiosis. In particular, the number of secondary operations, infectious parameters, and length of in-hospital stay were investigated.

RESULTS

The most frequently infected space was the perimandibular/buccal space for both groups followed by the submandibular space. Number of revision procedures, early recurrence, and length of stay presented no significant difference between both groups (p > 0.05). Inflammatory parameters (c-reactive protein, leukocytes) similarly decreased in both groups.

CONCLUSION

Cefazolin targets the majority of the pathogens detected in severe odontogenic neck infections descending from the lower jaw and reveals comparable results to AMP/S in regard to the inflammatory parameters and in-hospital stay.

CLINICAL RELEVANCE

Cefazolin is a feasible empiric antibiosis for odontogenic neck infections descending from the lower jaw if surgical drainage is performed.

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

BACKGROUND

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

OBJECTIVE

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

DESIGN

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

RESULTS AND CONCLUSION

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

In vivo Microbial Diversity Analysis on Different Surfaces of Dental Restorative Materials via 16S rDNA Sequencing

Background

This study aimed to provide precise material selection guidance for proper clinical restoration and treatment of plaque-related oral diseases, such as dental caries and periodontal diseases.

Material/Methods

Four groups (n=24) of restorative material sheets (n=24) were prepared using 3M Z350 composite resin (ZR), zinc phosphate cement (ZPC), glass-ionomer (GI), and ICON permeable resin (IPR). Six volunteers wore a plaque-collection device equipped with the 4 restorative material sheets for 48 hours. Plaque samples were collected, and Miseq sequencing was applied to obtain template DNA fragments for microbial diversity analysis. The data were analyzed with nonparametric tests.

Results

The microbial diversity on the ZPC surface was significantly lower than that on GI and IPR surfaces. The abundance of Firmicutes and Streptococcus on the ZPC surface was significantly higher than on the surfaces of GI and IPR. In contrast, the abundance of Porphyromonas on the surface of ZPC was significantly lower than that on GI and IPR surfaces. (P<0.05).

Conclusions

The results of the present study might serve as a basis for material selection under different oral microbial conditions to provide more accurate treatments and restorative procedures in the oral cavity.

Gut microbiota of invasive bullfrog tadpoles responds more rapidly to temperature than a noninvasive congener

Environmental temperature can alter the composition, diversity, and function of ectothermic vertebrate gut microbial communities, which may result in negative consequences for host physiology, or conversely, increase phenotypic plasticity and persistence in harsh conditions. The magnitude of either of these effects will depend on the length of time animals are exposed to extreme temperatures, and how quickly the composition and function of the gut microbiota can respond to temperature change. However, the temporal effects of temperature on gut microbiota are currently unknown. Here, we investigated the length of time required for increased temperature to alter the composition of gut bacterial communities in tadpoles of two frog species, the green frog, Lithobates clamitans, and its congener, the globally invasive American bullfrog, L. catesbeianus. We also explored the potential functional consequences of these changes by comparing predicted metagenomic profiles across temperature treatments at the last experimental time point. Bullfrog-associated microbial communities were more plastic than those of the green frog. Specifically, bullfrog communities were altered by increased temperature within hours, while green frog communities took multiple days to exhibit significant changes. Further, over ten times more bullfrog bacterial functional pathways were temperature-dependent compared to the green frog. These results support our hypothesis that bullfrog gut microbial communities would respond more rapidly to temperature change, potentially bolstering their ability to exploit novel environments. More broadly, we have revealed that even short-term increases in environmental temperature, expected to occur frequently under global climate change, can alter the gut microbiota of ectothermic vertebrates.

Interplay between vitamin D receptor FokI polymorphism and smoking influences Porphyromonas gingivalis proportions in subgingival plaque

AIM

This cross-sectional study investigated the effect of the vitamin D receptor (VDR) FokI polymorphism and its interactions with smoking/drinking on the proportions of periodontal pathogens and periodontitis severity.

MATERIALS AND METHODS

FokI genotyping and bacterial quantification were performed using real-time polymerase chain reaction. Periodontitis severity was determined using mean clinical attachment level (CAL). Regression analyses examined the associations between the FokI polymorphism (rs2228570) and bacterial proportions or periodontitis severity. Effect modification by smoking or drinking was assessed.

RESULTS

The study population comprised 1,460 individuals, aged 39-66 years. After multivariable adjustment, the FokI risk genotypes (CC + CT) were associated with elevated Porphyromonas gingivalis proportions (regression coefficient (β) =0.294 ± 0.139; p = .034) and increased mean CAL (β = 0.130 ± 0.048; p = .007). The effect of the FokI polymorphism on P. gingivalis proportions was greater in smokers (β = 0.897 ± 0.328; p = .006) compared to non-smokers (β = 0.164 ± 0.153; p = .282) and in drinkers (β = 0.668 ± 0.242; p = .006) compared to non-drinkers (β = 0.114 ± 0.169; p = .500). The genotype*smoking interaction for P. gingivalis proportions was significant (p = .043), whereas the genotype*drinking interaction was not (p = .061). Similar results were found for the effect of the genotype*smoking/drinking interaction on mean CAL.

CONCLUSIONS

These findings suggest that the interplay between the host genotype and smoking is important in determining the subgingival microbial composition and periodontitis severity.

Gestation alters the gut microbiota of an oviparous lizard

Mammalian pregnancy can alter the diversity, membership and structure of the maternal gut microbiota, but it is unclear whether this phenomenon occurs in vertebrates with different reproductive strategies. We conducted 16S rRNA bacterial inventories to investigate whether oviparous lizards exhibit shifts in gut microbiota similar to those observed in mammals. Using wild-caught eastern fence lizards from Alabama, USA, we collected and extracted fecal DNA from gravid and non-gravid individuals over 54 days in captivity. We predicted that, like mammals, the alpha diversity of lizard gut microbiota would decrease over gestation, and that inter-individual variation in community composition would increase. Indeed, we found that individuals in late-gestation harbored lower gut bacterial richness compared to non-gravid females. Lizard gut microbial communities of late-gestational females exhibited higher pairwise distances for both community membership and community structure compared to earlier gestation stages, indicating a higher degree of inter-individual variation as gestation progressed. Additionally, we found that the relative abundance and prevalence of the candidate phylum Melainabacteria tended to decrease over the course of gestation. While the consequences of these specific alterations are unknown, our results suggest that a general restructuring of gut microbial communities over gestation may be widespread across vertebrate reproductive strategies.

Significant Short-Term Shifts in the Microbiomes of Smokers With Periodontitis After Periodontal Therapy With Amoxicillin & Metronidazole as Revealed by 16S rDNA Amplicon Next Generation Sequencing

The aim of this follow-up study was, to compare the effects of mechanical periodontal therapy with or without adjunctive amoxicillin and metronidazole on the subgingival microbiome of smokers with periodontitis using 16S rDNA amplicon next generation sequencing. Fifty-four periodontitis patients that smoke received either non-surgical periodontal therapy with adjunctive amoxicillin and metronidazole (n = 27) or with placebos (n = 27). Subgingival plaque samples were taken before and two months after therapy. Bacterial genomic DNA was isolated and the V4 hypervariable region of the bacterial 16S rRNA genes was amplified. Up to 96 libraries were normalized and pooled for Illumina MiSeq paired-end sequencing with almost fully overlapping 250 base pairs reads. Exact ribosomal sequence variants (RSVs) were inferred with DADA2. Microbial diversity and changes on the genus and RSV level were analyzed with non-parametric tests and a negative binomial regression model, respectively. Before therapy, the demographic, clinical, and microbial parameters were not significantly different between the placebo and antibiotic groups. Two months after the therapy, clinical parameters improved and there was a significantly increased dissimilarity of microbiomes between the two groups. In the antibiotic group, there was a significant reduction of genera classified as Porphyromonas, Tannerella, and Treponema, and 22 other genera also decreased significantly, while Selenomonas, Capnocytophaga, Actinomycetes, and five other genera significantly increased. In the placebo group, however, there was not a significant decrease in periodontal pathogens after therapy and only five other genera decreased, while Veillonella and nine other genera increased. We conclude that in periodontitis patients who smoke, microbial shifts occurred two months after periodontal therapy with either antibiotics or placebo, but genera including periodontal pathogens decreased significantly only with adjunctive antibiotics.

Gingival health status in individuals using different types of toothpaste

OBJECTIVES

To examine the relationship between the medium term use (>1 year) of a toothpaste containing natural enzymes and proteins (Zendium™) upon gingival index, plaque index and bleeding index compared to medium term use of toothpastes without antimicrobial/antiinflammatory ingredients.

METHODS

A total of 305 participants eligible for inclusion were grouped according to their toothpaste use and matched with regard to gender and age (18-30, 31-55 and 56+ years of age). A total of 161 persons were using a toothpaste which contained enzymes and proteins (Zendium™, test group), and 144 persons were using a toothpaste without these ingredients (control group). The amount of dental plaque and the gingival condition were assessed at six sites of each tooth using the modified gingival index (MGI), plaque index (Modified Quigley and Hein plaque index, PI), and bleeding index (BI). Mean values of MGI, PI and BI were compared using analysis of covariance.

RESULTS

The test group had significantly less gingival inflammation than the control group (adjusted mean scores (SD); 1.80 (0.65) vs. 2.27 (0.63),p < 0.0001), as well as lower levels of plaque (2.03 (0.33) vs. 2.12 (0.33), p = 0.0168) and gingival bleeding (0.74 (0.45) vs. 1.08 (0.45), p < 0.0001). Females had significantly less gingival inflammation (p < 0.0001), plaque (p = 0.0005) and bleeding (p = 0.0118) than males. Participants aged 18-30 years had significantly higher levels of inflammation and bleeding than the older age groups (p < 0.001), and also higher plaque levels compared to participants aged 31-55 years (p = 0.0069). Potential confounding factors including oral hygiene practices and consistency of dental visits did not differ between groups.

CONCLUSIONS

Our findings indicate that medium term use of fluoride toothpaste containing enzymes and proteins (Zendium™) is associated with a better gingival health than the use of other types of fluoride toothpastes without antimicrobial active ingredients.

CLINICAL SIGNIFICANCE

Medium term (> 1 year) use of toothpaste containing naturally occurring enzymes and proteins (Zendium™) in an unsupervised home setting is associated with better gingival health compared to the unsupervised use of other commercially available toothpastes without antimicrobial/antiinflammatory active ingredients.

Prognostic Factors of Grade 2-3 Endo-Periodontal Lesions Treated Nonsurgically in Patients with Periodontitis: A Retrospective Case-Control Study

Background

Endo-periodontal lesions are bacterial infectious diseases involving both the periodontal and pulp tissues with poor outcomes. It is hard for clinicians to predict their prognosis. The aim of this study is to investigate the factors affecting the prognosis of endo-periodontal lesions.

Methods

A total of 140 teeth diagnosed with grade 2-3 endo-periodontal lesions in patients with periodontitis were recruited in this study. They were divided into high and low responder groups, according to the clinical symptoms and parameters of the teeth involved after nonsurgical treatment of both the endodontic and periodontal components. Clinical parameters and symptoms were compared before and after treatment, and gender, age, smoking, and all clinical parameters were compared between high and low responder groups using univariate analyses. Logistic regression was applied to evaluate the independent effects on endo-periodontal lesion prognosis.

Results

Compared with the clinical parameters at baseline, the values of tooth mobility (TM), periapical index (PAI), and discomfort when chewing were decreased after endodontic therapy, and the values of periodontal probing depth (PD), clinical attachment level (CAL), sulcus bleeding index (SBI), TM, simplified oral hygiene index (OHI-S), full-mouth periodontitis severity, PAI, and discomfort when chewing were decreased after periodontal therapy. Univariate analysis revealed that smoking, PD, CAL, TM, PAI, clinical crown-root ratio (CR), full-mouth periodontitis severities, and the number of root canals were significantly different between the high and low responder groups (P < 0.05). The logistic regression analysis showed that smoking, PD, CAL, full-mouth periodontitis severities, and the number of root canals remained significantly associated with grade 2-3 endo-periodontal lesions in patients with periodontitis (P < 0.05). The logistic regression analysis showed that smoking, PD, CAL, full-mouth periodontitis severities, and the number of root canals remained significantly associated with grade 2-3 endo-periodontal lesions in patients with periodontitis (

Conclusions

and Practical Implications. High PD and CAL, multirooted teeth, smoking, and serious full-mouth periodontitis indicated a poor prognosis for teeth with grade 2-3 endo-periodontal lesions.

The Impact of Smoking on Subgingival Microflora: From Periodontal Health to Disease

Periodontal disease is one of the most common diseases of the oral cavity affecting up to 90% of the worldwide population. Smoking has been identified as a major risk factor in the development and progression of periodontal disease. It is essential to assess the influence of smoking on subgingival microflora that is the principal etiological factor of the disease to clarify the contribution of smoking to periodontal disease. Therefore, this article reviews the current research findings regarding the impact of smoking on subgingival microflora and discusses several potential mechanisms. Cultivation-based and targeted molecular approaches yield controversial results in determining the presence or absence of smoking-induced differences in the prevalence or levels of certain periodontal pathogens, such as the “red complex.” However, substantial changes in the subgingival microflora of smokers, regardless of their periodontal condition (clinical health, gingivitis, or periodontitis), have been demonstrated in recent microbiome studies. Available literature suggests that smoking facilitates early acquisition and colonization of periodontal pathogens, resulting in an “at-risk-for-harm” subgingival microbial community in the healthy periodontium. In periodontal diseases, the subgingival microflora in smokers is characterized by a pathogen-enriched community with lower resilience compared to that in non-smokers, which increases the difficulty of treatment. Biological changes in key pathogens, such as Porphyromonas gingivalis, together with the ineffective host immune response for clearance, might contribute to alterations in the subgingival microflora in smokers. Nonetheless, further studies are necessary to provide solid evidence for the underlying mechanisms.

Transcriptome and methylome analysis of periodontitis and peri-implantitis with tobacco use

Peri-implantitis is similar to periodontitis in both symptoms and treatment; however, their level of similarity remains controversial. Here, we compared multiple cases of periodontitis and peri-implantitis through transcriptome and methylome profiling, and analyzed the effects of smoking as a typical risk factor. Human gingival tissues were obtained from 20 patients with periodontitis or peri-implantitis via periodontal surgical procedures. Total RNA and genomic DNA were isolated, and transcriptome and methylome datasets were generated. Comprehensive analysis of differential gene expression, DNA methylation, and protein-protein interactions indicated that periodontitis and peri-implantitis share biological similarities; however, hierarchical clustering between the two disease groups revealed distinct molecular characteristics. These differences might be related to structural differences in natural tooth-bone and implant-bone. Additionally, smoking differentially affected periodontitis and peri-implantitis in terms of host-defense mechanism impairment. Within the limitations of this study, the results provide evidence that peri-implantitis is distinct from periodontitis and that smoking potentially affects disease progression. Our study provides a foundation for the rational design of a large-scale study in the future for a more comprehensive analysis that includes microbiome and clinical data.

A Literature Review of Metagenomics and Culturomics of the Peri-implant Microbiome: Current Evidence and Future Perspectives

Background and objectives: In recent years, many different culture-independent molecular techniques have been developed with the aim of investigating the not yet cultivated part of the resident flora of the oral cavity and of analyzing the peri-implant and periodontal flora both in healthy and diseased sites. The most used technologies are Roche 454 pyrosequencing, Illumina HiSeq/MiSeq, ABI SOLiD and Ion Torrent. Due to these methods, two different approaches are available: Metagenomics and the 16S gene analysis. A complementary strategy was also recently developed: Culturomics. Culturomics consists of different culture conditions that allow a very rapid bacterial identification. The focused question of this review was developed in PICO format in order to investigate the role of metagenomics, 16S gene analysis and culturomics (interventions) in the differential study (comparison) of the peri-implant and periodontal microbiome (outcome) in humans (participants). The secondary aim was the characterization of currents limits and future applications of the three techniques. Methods: The authors performed a literature search on three databases (Web of Science, Scopus and PubMed) from 01/01/2003 to 31/06/2019. Date of last search was: 25/08/19. Any type of article dealing with the analysis of periodontal and peri-implant flora with metagenomic, culturomic or 16S gene analysis was included. No language restrictions were applied. Risk of bias for RCT was assessed using the Cochrane collaboration's tool whereas case-control and cohort studies were evaluated through the Newcastle-Ottawa scale. Results: The initial search resulted in 330 titles in total. After careful evaluation of all results no studies were found to satisfy the primary outcome of the present review. Hence a narrative review dealing with the secondary aim was performed. Conclusions: Metagenomic and 16S gene analysis approaches contributed in clarifying some crucial aspects of the oral microbiome. Based on the reported evidence some bacteria could be found around teeth and implants even in the absence of signs of inflammation and other species are more frequently found in supragingival peri-implant biofilm. Teeth and implants (even if adjacent) seem not to share the same microbiome and healthy teeth have a more diversified one. The same analyses also highlighted that the oral biofilm of smokers is composed by more periodontopathogen bacteria compared to non-smokers and that geographical location and ethnicity seem to play a role in bacterial composition. Culturomics, which has not yet been applied to the study of oral microbiota, consists of the use of different culture conditions and of the identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) with the aim of increasing the bacterial repertoire and avoiding the limits of molecular methods. In order to better evaluate perspectives and limits of the all presented approaches further studies comparing the different molecular techniques are encouraged. This review received no funding.

Smoking and microbiome in oral, airway, gut and some systemic diseases

The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn’s disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.

Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients

RATIONALE

Cigarette smoking is associated with increased risk of acute respiratory distress syndrome (ARDS) in patients after severe trauma; however, the mechanisms underlying this association are unknown.

OBJECTIVES

To determine whether cigarette smoking contributes to ARDS development after trauma by altering community composition of the lung microbiota.

METHODS

We studied the lung microbiota of mechanically ventilated patients admitted to the ICU after severe blunt trauma. To do so, we used 16S ribosomal RNA gene amplicon sequencing of endotracheal aspirate samples obtained on ICU admission (n = 74) and at 48 hours after admission (n = 30). Cigarette smoke exposure (quantified using plasma cotinine), ARDS development, and other clinical parameters were correlated with lung microbiota composition.

MEASUREMENTS AND MAIN RESULTS

Smoking status was significantly associated with lung bacterial community composition at ICU admission (P = 0.007 by permutational multivariate ANOVA [PERMANOVA]) and at 48 hours (P = 0.03 by PERMANOVA), as well as with significant enrichment of potential pathogens, including Streptococcus, Fusobacterium, Prevotella, Haemophilus, and Treponema. ARDS development was associated with lung community composition at 48 hours (P = 0.04 by PERMANOVA) and was characterized by relative enrichment of Enterobacteriaceae and of specific taxa enriched at baseline in smokers, including Prevotella and Fusobacterium.

CONCLUSIONS

After severe blunt trauma, a history of smoking is related to lung microbiota composition, both at the time of ICU admission and at 48 hours. ARDS development is also correlated with respiratory microbial community structure at 48 hours and with taxa that are relatively enriched in smokers at ICU admission. The data derived from this pilot study suggest that smoking-related changes in the lung microbiota could be related to ARDS development after severe trauma.

Bioaerosols in the waterpipe cafés: genera, levels, and factors influencing their concentrations

This study was conducted in order to assess the exposure to bacterial and fungal bioaerosols in the air of waterpipe cafés (AWPCs), in the hose of waterpipe (HWP), and in the water bowl of the waterpipe (WBWP) and to investigate the factors influence increasing the contamination levels in waterpipe cafés in Ardabil. From all the 50 cafés studied, the samples were taken from air and from water contained in water bowl and hose for bacterial and fungal analyses. The results demonstrated that the mean numbers of bacteria and fungi in the indoor air of café, hose, and water bowl were 33.90 ± 14.86 and 25.24 ± 1.99 CFU/m³, 72.16 ± 29.55 and 72.78 ± 42.45 CFU/plate, 53.7 ± 25.46 and 25.26 ± 13.94 CFU/ml, respectively. The predominant bacterial genera in waterpipe cafés were Pseudomonas and Bacillus in air, Staphylococcus and Pseudomonas in the hose, and Staphylococcus and Pseudomonas in the water bowl, respectively. The predominant fungal species in waterpipe cafés were Penicillium and Cladosporium in air, yeast and Fusarium in the hose, and Paecilomyces and yeast in the water bowl, respectively. The results of statistical analysis showed that there was a significant relationship between the mean concentrations of bacterial aerosol and qualitative variables such as type of heating system, materials of wall and ceiling, traditional restaurants, interior supermarkets, moisturized walls, the number of people, area of cafés, and temperature. But there was no significant relationship between these variables and the mean concentration of fungal aerosols. The results also showed that the levels of bioaerosols were high in the air, hose, and water bowl of the waterpipe. Therefore, cafés can be a potential source for the transmission of pathogenic agents and increase the risk of respiratory diseases among waterpipe smoking individuals.

Association between the oral microbiome and brain resting state connectivity in smokers

Recent studies have shown a critical role of the gastrointestinal microbiome in brain and behavior via the complex gut-microbiome-brain axis. However, the influence of the oral microbiome in neurological processes is much less studied, especially in response to the stimuli, such as smoking, within the oral microenvironment. Additionally, given the complex structural and functional networks in brain, our knowledge about the relationship between microbiome and brain function through specific brain circuits is still very limited. In this pilot study, we leveraged next generation sequencing for microbiome and functional neuroimaging technique to enable the delineation of microbiome-brain network links as well as their relationship to cigarette smoking. Thirty smokers and 30 age- and sex-matched nonsmokers were recruited for 16S sequencing of their oral microbial community. Among them, 56 subjects were scanned by resting-state functional magnetic resonance imaging to derive brain functional networks. Statistical analyses were performed to demonstrate the influence of smoking on the oral microbial composition, functional network connectivity, and the associations between microbial shifts and functional network connectivity alternations. Compared to nonsmokers, we found a significant decrease of beta diversity (P = 6 × 10^-3) in smokers and identified several classes (Betaproteobacteria, Spirochaetia, Synergistia, and Mollicutes) with significant alterations in microbial abundance. Pathway analysis on the predicted KEGG pathways shows that the microbiota with altered abundance are mainly involved in pathways related to cell processes, DNA repair, immune system, and neurotransmitters signaling. One brain functional network connectivity component was identified to have a significant difference between smokers and nonsmokers (P = 0.032), mainly including connectivity between brain default network and other task-positive networks. This brain functional component was also significantly associated with smoking related microbiota, suggesting a correlated cross-individual pattern between smoking-induced oral microbiome dysbiosis and brain functional connectivity alternation, possibly involving immunological and neurotransmitter signaling pathways. This work is the first attempt to link oral microbiome and brain functional networks, and provides support for future work in characterizing the role of oral microbiome in mediating smoking effects on brain activity.

Smoking and periodontal microorganisms

Resolution of dysbiosis following treatment for periodontal disease and tobacco dependence has been reported in longitudinal intervention studies. In the present report, we evaluated the biological findings regarding the effect of smoking on the periodontal microbiome. A standardized electronic search was conducted using MEDLINE; overall, 1099 papers were extracted. Studies that addressed the relationship between tobacco and periodontal pathogens were included. Finally, 42 papers were deemed appropriate for the present review. Functional changes in periodontal pathogens exposed to nicotine and cigarette smoke extract support the clinical findings regarding dysbiosis of the subgingival microbiome. Dysbiosis of the periodontal microbiome was presented in smokers regardless of their periodontal condition (healthy, gingivitis, or periodontitis) and remained significant only in smokers even after the resolution of experimentally-induced gingivitis and following reduction of clinical signs of periodontitis with non-surgical periodontal treatment and over 3 months post-therapy. Based on these findings, smoking cessation in periodontitis patients is beneficial for promoting a health-compatible subgingival microbial community. To maximize the benefits of these interventions in dental settings, further studies on periodontal microbiome are needed to elucidate the impact of tobacco intervention on preventing recurrence of periodontal destruction in the susceptible subjects.

Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia

Gut bacteria that produce urease, the enzyme hydrolysing urea, contribute to nitrogen balance in diverse vertebrates, although the presence of this system of urea-nitrogen recycling in Amphibia is as yet unknown. Our studies of the wood frog (Rana sylvatica), a terrestrial species that accrues urea in winter, documented robust urease activity by enteric symbionts and hence potential to recoup nitrogen from the urea it produces. Ureolytic capacity in hibernating (non-feeding) frogs, whose guts hosted an approximately 33% smaller bacterial population, exceeded that of active (feeding) frogs, possibly due to an inductive effect of high urea on urease expression and/or remodelling of the microbial community. Furthermore, experimentally augmenting the host's plasma urea increased bacterial urease activity. Bacterial inventories constructed using 16S rRNA sequencing revealed that the assemblages hosted by hibernating and active frogs were equally diverse but markedly differed in community membership and structure. Hibernating frogs hosted a greater relative abundance and richer diversity of genera that possess urease-encoding genes and/or have member taxa that reportedly hydrolyse urea. Bacterial hydrolysis of host-synthesized urea probably permits conservation and repurposing of valuable nitrogen not only in hibernating R. sylvatica but, given urea's universal role in amphibian osmoregulation, also in virtually all Amphibia.

Exploring a temporal relationship between biofilm microbiota and inflammatory mediators during resolution of naturally occurring gingivitis

BACKGROUND

This study uses multiple, contemporary methodologies to expand our knowledge of the temporal relationship between host-microbial interactions and clinical signs of gingivitis.

METHODS

Subgingival plaque and crevicular fluid samples were collected from 31 systemically healthy adults with naturally occurring plaque-induced gingivitis. Professional prophylaxis was administered and participants were followed over 7 weeks. Microbial characterization was performed using a bead-based hybridization assay and cytokine analysis using bead-based flow cytometry.

RESULTS

The provision of sequential interventions, oral hygiene instruction, and subsequent professional prophylaxis brought about significant reduction of plaque and resolution of gingivitis at all post baseline time points (P < 0.0001). Candidate cytokines that increased significantly (95% level) were interleukin (IL)-1β, matrix metalloproteinases (MMP)-1, MMP-3, MMP-8, MMP-9, from baseline to week 2; regulated on activation, normal T cell expressed and secreted (RANTES) at week 4 and week 8; macrophage inflammatory protein (MIP)-1α and MIP-1β at week 8. Resolution of inflammation was accompanied by a shift in the microbiological flora toward those species associated with health.

CONCLUSIONS

This study provides further evidence of the dynamic relationships that exist between the overt clinical signs, the microbial biofilm, and the host response in gingivitis and upon resolution following clinical interventions. Understanding the interactions between the host immune system and subgingival microbial communities during the resolution of established gingivitis continues to evolve as additional knowledge is achieved through using new analytical technologies. The present study confirms a critical effect of oral hygiene measures on restoration of microbial eubiosis in subgingival communities, confirming the important role for home care and professional intervention in maintaining oral health.

A cross-sectional study on the periodontal status and prevalence of red complex periodontal pathogens in a Japanese population

This large-scale study cross-sectionally examined the periodontal status and prevalence of "red complex" bacteria (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) in Japanese adults. A total of 977 participants were enrolled in the study. Probing depth (PD), bleeding on probing (BOP), and bone crest level (BCL) were recorded, and the presence of red complex bacteria in the saliva was examined using polymerase chain reaction. The mean BCL value and the percentage of sites with a PD ≥4 mm or the presence of BOP were significantly higher in older participants. The detection rates of P. gingivalis, T. denticola, and T. forsythia were 46.3%, 76.4%, and 61.1%, respectively. The P. gingivalis detection rate significantly increased with age, while those of T. denticola and T. forsythia were comparably high for all age groups. A close correlation between P. gingivalis and the percentage of sites with PD ≥4 mm was indicated by nonlinear canonical correlation analysis. Current smokers exhibited a more advanced disease condition and a significantly higher P. gingivalis detection rate than non-smokers. In conclusion, periodontal condition worsens with age, and P. gingivalis appears to be the red complex bacterium most closely associated with periodontitis.

Microcosm biofilms cultured from different oral niches in periodontitis patients

Objective: Periodontal diseases are triggered by dysbiotic microbial biofilms. Therefore, it is essential to develop appropriate biofilm models. Aim of the present study was to culture microcosm biofilms inoculated from different niches in periodontitis patients and compare their microbial composition to those inoculated from subgingival plaque. Methods: Saliva, subgingival plaque, tongue and tonsils were sampled in five periodontitis patients to serve as inocula for culturing biofilms in vitro in an active attachment model. Biofilms were grown for 14 or 28 d and analyzed for their microbial composition by 16S rDNA sequencing. Results: As classified by HOMD, all biofilms were dominated by periodontitis-associated taxa, irrespective which niche had been used for inoculation. There was a low similarity between 14 d biofilms and their respective inocula (Bray-Curtis similarity 0.26), while biofilms cultured for 14 and 28 d shared high similarity (0.69). Principal components analysis showed much stronger clustering per patient than per niche indicating that the choice of patients may be more crucial than choice of the respective niches in these patients. Conclusion: Saliva, tongue scrapings or tonsil swabs may represent sufficient alternative inocula for growing microcosm biofilms resembling periodontitis-associated microbial communities in cases when sampling subgingival plaque is not possible.

Tobacco-induced suppression of the vascular response to dental plaque

Cigarette smoking presents oral health professionals with a clinical and research conundrum: reduced periodontal vascular responsiveness to the oral biofilm accompanied by increased susceptibility to destructive periodontal diseases. This presents a significant problem, hampering diagnosis and complicating treatment planning. The aim of this review is to summarize contemporary hypotheses that help to explain mechanistically the phenomenon of a suppressed bleeding response to dysbiotic plaque in the periodontia of smokers. The influence of smoke exposure on angiogenesis, innate cell function, the production of inflammatory mediators including cytokines and proteases, tobacco-bacteria interactions, and potential genetic predisposition are discussed.

Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study

Cigarette smoking alters the oral microbiome; however, the effect of alternative tobacco products remains unclear. Middle Eastern tobacco products like dokha and shisha, are becoming globally widespread. We tested for the first time in a Middle Eastern population the hypothesis that different tobacco products impact the oral microbiome. The oral microbiome of 330 subjects from the United Arab Emirates Healthy Future Study was assessed by amplifying the bacterial 16S rRNA gene from mouthwash samples. Tobacco consumption was assessed using a structured questionnaire and further validated by urine cotinine levels. Oral microbiome overall structure and specific taxon abundances were compared, using PERMANOVA and DESeq analyses respectively. Our results show that overall microbial composition differs between smokers and nonsmokers (p = 0.0001). Use of cigarettes (p = 0.001) and dokha (p = 0.042) were associated with overall microbiome structure, while shisha use was not (p = 0.62). The abundance of multiple genera were significantly altered (enriched/depleted) in cigarette smokers; however, only Actinobacillus, Porphyromonas, Lautropia and Bifidobacterium abundances were significantly changed in dokha users whereas no genera were significantly altered in shisha smokers. For the first time, we show that smoking dokha is associated to oral microbiome dysbiosis, suggesting that it could have similar effects as smoking cigarettes on oral health.

Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with clinical and immunologic variables of HIV infection

BACKGROUND

The effect of smoking on microbial dysbiosis and the potential consequence of such shift on markers of HIV disease is unknown. Here we assessed the relationship of microbial dysbiosis with smoking and markers of HIV disease.

METHODS

Oral wash was collected from: (1) HIV-infected smokers (HIV-SM, n = 48), (2) HIV-infected non-smokers (HIV-NS, n = 24), or (3) HIV-uninfected smokers (UI-SM, n = 24). Microbial DNA was extracted and their bacterial and fungal microbiota (bacteriome and mycobiome, respectively) were characterized using Ion-Torrent sequencing platform. Sequencing data were compared using clustering, diversity, abundance and inter-kingdom correlations analyses.

RESULTS

Bacteriome was more widely dispersed than mycobiome, there was no noticeable difference in clustering between groups. Richness of oral bacteriome in HIV-SM was significantly lower than that of UI-SM (P ≤ .03). Diversity of HIV-NS was significantly lower than that of HIV-SM or UI-SM at phylum level (P ≤ .02). Abundance of Phylum Firmicutes was significantly decreased in HIV-NS compared to HIV-SM and UI-SM (P = .007 and .027, respectively), while abundance of Proteobacteria was significantly increased in HIV-NS compared to HIV-SM and UI-SM (P = .0005 and .011, respectively). Fungal phyla did not differ significantly between the three cohorts. Cumulative smoking was positively correlated with Facklamia but negatively with Enhydrobacter, and current alcohol use was negatively correlated with Geniculata. Bacteria Facklamia exhibited weakly positive correlation with longer PI duration (r = 0.094, P = 0.012), and a negative correlation with nadir CD4 count (r = -0.345; P = 0.004), while Granulicatella was negatively correlated with nadir CD4 count (r = -0.329; P = 0.007). Fungus Stemphylium correlated negatively with nadir CD4 (r = -0.323; P = 0.008).

CONCLUSIONS

Dysbiosis of the oral microbiota is associated with clinical and immunologic variables in HIV-infected patients.

Streptococcus sanguinis biofilm formation & interaction with oral pathogens

Caries and periodontitis are the two most common human dental diseases and are caused by dysbiosis of oral flora. Although commensal microorganisms have been demonstrated to protect against pathogens and promote oral health, most previous studies have addressed pathogenesis rather than commensalism. Streptococcus sanguinis is a commensal bacterium that is abundant in the oral biofilm and whose presence is correlated with health. Here, we focus on the mechanism of biofilm formation in S. sanguinis and the interaction of S. sanguinis with caries- and periodontitis-associated pathogens. In addition, since S. sanguinis is well known as a cause of infective endocarditis, we discuss the relationship between S. sanguinis biofilm formation and its pathogenicity in endocarditis.

Effect of Smoking on Periodontitis: A Systematic Review and Meta-regression

CONTEXT

The study systematically reviewed articles on the association between tobacco smoking and periodontitis, as it has been hypothesized that smoking affects the course of periodontitis through impairment of immunological and vascular mechanisms.

EVIDENCE ACQUISITION

Searches of articles indexed in PubMed, Scopus, and Embase were performed up to and including May 2017. Search strategy included MeSH and free terms: periodontitis, periodontal diseases, smoking, tobacco use, tobacco, tobacco products, cigarette, pipe, and cigar. Only original prospective longitudinal studies that investigated the association between smoking and periodontitis incidence or progression were included. Results were shown as combined risk ratio. Meta-regression and subgroup analyses were used to explore potential sources of heterogeneity. Analyses were conducted in August 2017.

EVIDENCE SYNTHESIS

Twenty-eight studies were included in the review; of these, only 14 presented data that could be included in the meta-analysis. Pooled adjusted risk ratios estimate that smoking increases the risk of periodontitis by 85% (risk ratio=1.85, 95% CI=1.5, 2.2). Meta-regression demonstrated that age explained 54.2% of the variability between studies, time of follow-up explained 13.5%, loss to follow-up 10.7%, criteria used to assess the periodontal status explained 2.1%, and severity of periodontitis explained 16.9%.

CONCLUSIONS

Smoking has a detrimental effect on the incidence and progression of periodontitis. Tobacco smoking, therefore, is important information that should be assessed along with other risk factors for periodontitis.

Gut microbes limit growth in house sparrow nestlings (Passer domesticus) but not through limitations in digestive capacity

Recent research often lauds the services and beneficial effects of host‐associated microbes on animals. However, hosting these microbes may come at a cost. For example, germ‐free and antibiotic‐treated birds generally grow faster than their conventional counterparts. In the wild, juvenile body size is correlated with survival, so hosting a microbiota may incur a fitness cost. Avian altricial nestlings represent an interesting study system in which to investigate these interactions, given that they exhibit the fastest growth rates among vertebrates, and growth is limited by their digestive capacity. We investigated whether reduction and restructuring of the microbiota by antibiotic treatment would: (i) increase growth and food conversion efficiency in nestling house sparrows (Passer domesticus); (ii) alter aspects of gut anatomy or function (particularly activities of digestive carbohydrases and their regulation in response to dietary change); and (iii) whether there were correlations between relative abundances of microbial taxa, digestive function and nestling growth. Antibiotic treatment significantly increased growth and food conversion efficiency in nestlings. Antibiotics did not alter aspects of gut anatomy that we considered but depressed intestinal maltase activity. There were no significant correlations between abundances of microbial taxa and aspects of host physiology. Overall, we conclude that microbial‐induced growth limitation in developing birds is not driven by interactions with digestive capacity. Rather, decreased energetic and material costs of immune function or beneficial effects from microbes enriched under antibiotic treatment may underlie these effects. Understanding the costs and tradeoffs of hosting gut microbial communities represents an avenue of future research.

Role of prebiotics and probiotics in oral health

Purpose

This paper aims to focus on the utilisation of pre- and probiotics for oral care and the state of knowledge at this time.

Design/methodology/approach

Pre- and probiotics describe beneficial carbohydrates and microbiota, respectively, for optimal gut health. Carbohydrates provide energy selectively for the gut-friendly bacteria. The use of both carbohydrates and bacteria is, however, being expanded into other areas of the body – including the skin, vagina and oral cavity – for health-related applications.

Findings

There is increased interest in both pre- and probiotics for oral care products. The importance of oral microflora and their selective substrates is discussed against a background of contemporary oral care approaches. The issues and benefits are discussed in this review.

Originality/value

It is clear that consumption of prebiotics and probiotics may play a role as potential prophylactic or therapeutic agents for reducing the presence of organisms in the mouth associated with tooth decay. To confirm a beneficial effect of pre- and probiotics further in vivo studies involving healthy human volunteers should be considered.

Alterations in oral microbial flora induced by waterpipe tobacco smoking

Background

Waterpipe smoking is a global health problem and a serious public concern. Little is known about the effects of waterpipe smoking on oral health. In the current study, we examined the alterations of oral microbial flora by waterpipe smoking.

Methods

One hundred adult healthy subjects (59 waterpipe smokers and 41 non-smokers) were recruited into the study. Swabs were taken from the oral cavity and subgingival regions. Standard culturing techniques were used to identify types, frequency, and mean number of microorganisms in cultures obtained from the subjects.

Results

It was notable that waterpipe smokers were significantly associated with a history of oral infections. In subgingiva, Acinetobacter and Moraxella species were present only in waterpipe smokers. In addition, the frequency of Candida albicans was higher in the subgingiva of waterpipe smokers (p = 0.023) while the frequency of Fusobacterium nucleatum was significantly lower in the subgingiva of waterpipe smokers (p = 0.036). However, no change was observed in other tested bacteria, such as Campylobacter species; Viridans group streptococci, Enterobacteriaceae, and Staphylococcus aureus. In oral cavity and when colony-forming units were considered, the only bacterial species that showed significant difference were the black-pigmented bacteria (p < 0.001).

Conclusion

This study provides evidence indicating that some of the oral microflora is significantly altered by waterpipe smoking.

Exploring the microbiome in health and disease

The analysis of human microbiome is an exciting and rapidly expanding field of research. In the past decade, the biological relevance of the microbiome for human health has become evident. Microbiome comprises a complex collection of microorganisms, with their genes and metabolites, colonizing different body niches. It is now well known that the microbiome interacts with its host, assisting in the bioconversion of nutrients and detoxification, supporting immunity, protecting against pathogenic microbes, and maintaining health. Remarkable new findings showed that our microbiome not only primarily affects the health and function of the gastrointestinal tract but also has a strong influence on general body health through its close interaction with the nervous system and the lung. Therefore, a perfect and sensitive balanced interaction of microbes with the host is required for a healthy body. In fact, growing evidence suggests that the dynamics and function of the indigenous microbiota can be influenced by many factors, including genetics, diet, age, and toxicological agents like cigarette smoke, environmental contaminants, and drugs. The disruption of this balance, that is called dysbiosis, is associated with a plethora of diseases, including metabolic diseases, inflammatory bowel disease, chronic obstructive pulmonary disease, periodontitis, skin diseases, and neurological disorders. The importance of the host microbiome for the human health has also led to the emergence of novel therapeutic approaches focused on the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful roles. In the present review, we outline recent studies devoted to elucidate not only the role of microbiome in health conditions and the possible link with various types of diseases but also the influence of various toxicological factors on the microbial composition and function.

Do host-associated gut microbiota mediate the effect of an herbicide on disease risk in frogs?

Environmental stressors, such as pollutants, can increase disease risk in wildlife. For example, the herbicide atrazine affects host defences (e.g. resistance and tolerance) of the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), but the mechanisms for these associations are not entirely clear. Given that pollutants can alter the gut microbiota of hosts, which in turn can affect their health and immune systems, one potential mechanism by which pollutants could increase infection risk is by influencing host-associated microbiota. Here, we test whether early-life exposure to the estimated environmental concentration (EEC; 200 μg/L) of atrazine affects the gut bacterial composition of Cuban tree frog (Osteopilus septentrionalis) tadpoles and adults and whether any atrazine-induced change in community composition might affect host defences against Bd. We also determine whether early-life changes in the stress hormone corticosterone affect gut microbiota by experimentally inhibiting corticosterone synthesis with metyrapone. With the exception of changing the relative abundances of two bacterial genera in adulthood, atrazine did not affect gut bacterial diversity or community composition of tadpoles (in vivo or in vitro) or adults. Metyrapone did not significantly affect bacterial diversity of tadpoles, but significantly increased bacterial diversity of adults. Gut bacterial diversity during Bd exposure did not predict host tolerance or resistance to Bd intensity in tadpoles or adults. However, early-life bacterial diversity negatively predicted Bd intensity as adult frogs. Specifically, Bd intensity as adults was associated negatively with the relative abundance of phylum Fusobacteria in the guts of tadpoles. Our results suggest that the effect of atrazine on Bd infection risk is not mediated by host-associated microbiota because atrazine does not affect microbiota of tadpoles or adults. However, host-associated microbes seem important in host resistance to Bd because the early-life microbiota, during immune system development, predicted later-life infection risk with Bd. Overall, our study suggests that increasing gut bacterial diversity and relative abundances of Fusobacteria might have lasting positive effects on amphibian health.

The making of a miscreant: tobacco smoke and the creation of pathogen-rich biofilms

We have previously reported that oral biofilms in clinically healthy smokers are pathogen-rich, and that this enrichment occurs within 24 h of biofilm formation. The present investigation aimed to identify a mechanism by which smoking creates this altered community structure. By combining in vitro microbial–mucosal interface models of commensal (consisting of Streptococcus oralis, Streptococcus sanguis, Streptococcus mitis, Actinomyces naeslundii, Neisseria mucosa and Veillonella parvula) and pathogen-rich (comprising S.oralis, S.sanguis, S.mitis, A.naeslundii, N.mucosa and V.parvula, Fusobacterium nucleatum, Porphyromonas gingivalis, Filifactor alocis, Dialister pneumosintes, Selenonomas sputigena, Selenominas noxia, Catonella morbi, Parvimonas micra and Tannerella forsythia) communities with metatranscriptomics, targeted proteomics and fluorescent microscopy, we demonstrate that smoke exposure significantly downregulates essential metabolic functions within commensal biofilms, while significantly increasing expression of virulence genes, notably lipopolysaccharide (LPS), flagella and capsule synthesis. By contrast, in pathogen-rich biofilms several metabolic pathways were over-expressed in response to smoke exposure. Under smoke-rich conditions, epithelial cells mounted an early and amplified pro-inflammatory and oxidative stress response to these virulence-enhanced commensal biofilms, and a muted early response to pathogen-rich biofilms. Commensal biofilms also demonstrated early and widespread cell death. Similar results were observed when smoke-free epithelial cells were challenged with smoke-conditioned biofilms, but not vice versa. In conclusion, our data suggest that smoke-induced transcriptional shifts in commensal biofilms triggers a florid pro-inflammatory response, leading to early commensal death, which may preclude niche saturation by these beneficial organisms. The cytokine-rich, pro-oxidant, anaerobic environment sustains inflammophilic bacteria, and, in the absence of commensal antagonism, may promote the creation of pathogen-rich biofilms in smokers.

Tobacco smoke inhibits the metabolism of beneficial bacteria in biofilms, while activating specific genes in pathogenic bacteria. This suggests a mechanism to explain how smoking quickly leads to the formation of damaging biofilms in the mouth and respiratory tract. Purnima Kumar and colleagues at Ohio State University, USA studied the effect of tobacco smoke on cultured biofilms used to model those that form on mucous membranes. They detected specific and varied changes in the activity of genes, proteins and metabolism that allowed pathogenic bacteria to displace beneficial “commensal” bacteria. The research suggests the transition toward pathogen-rich biofilms may contribute to the health effects of smoking by causing increased inflammation of mucous membranes and the production of damaging oxidant chemicals. Further research should investigate the chemical constituents of smoke responsible for these effects.

Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs

Food resources can affect the health of organisms by altering their symbiotic microbiota and affecting energy reserves for host defenses against parasites. Different diets can vary in their macronutrient content and therefore they might favor certain bacterial communities of the host and affect the development and maintenance of the immune system, such as the inflammatory or antibody responses. Thus, testing the effect of diet, especially for animals with wide diet breadths, on host-associated microbiota and defenses against parasites might be important in determining infection and disease risk. Here, we test whether the early-life diet of Cuban tree frogs (Osteopilus septentrionalis) affects early- and later-life microbiota as well as later-life defenses against skin-penetrating, gut worms (Aplectana hamatospicula). We fed tadpoles two ecologically common diets: a diet of conspecifics or a diet of algae (Arthrospira sp.). We then: (1) characterized the gut microbiota of tadpoles and adults; and (2) challenged adult frogs with parasitic worms and measured host resistance (including the antibody-mediated immune response) and tolerance of infections. Tadpole diet affected bacterial communities in the guts of tadpoles but did not have enduring effects on the bacterial communities of adults. In contrast, tadpole diet had enduring effects on host resistance and tolerance of infections in adult frogs. Frogs that were fed a conspecific-based diet as tadpoles were more resistant to worm penetration compared with frogs that were fed an alga-based diet as tadpoles, but less resistant to worm establishment, which may be related to their suppressed antibody response during worm establishment. Furthermore, frogs that were fed a conspecific-based diet as tadpoles were more tolerant to the effect of parasite abundance on host mass during worm establishment. Overall, our study demonstrates that the diet of Cuban tree frog tadpoles affects the gut microbiota and defenses against parasitic gut worms of frogs, but these effects depend on the stage of the host and infection, respectively.

Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard

While herbivory is a common feeding strategy in a number of vertebrate classes, less than 4% of squamate reptiles feed primarily on plant material. It has been hypothesized that physiological or microbial limitations may constrain the evolution of herbivory in lizards. Herbivorous lizards exhibit adaptations in digestive morphology and function that allow them to better assimilate plant material. However, it is unknown whether these traits are fixed or perhaps phenotypically flexible as a result of diet. Here, we maintained a naturally omnivorous lizard, Liolaemus ruibali, on a mixed diet of 50% insects and 50% plant material, or a plant-rich diet of 90% plant material. We compared parameters of digestive performance, gut morphology and function, and gut microbial community structure between the two groups. We found that lizards fed the plant-rich diet maintained nitrogen balance and exhibited low minimum nitrogen requirements. Additionally, lizards fed the plant-rich diet exhibited significantly longer small intestines and larger hindguts, demonstrating that gut morphology is phenotypically flexible. Lizards fed the plant-rich diet harbored small intestinal communities that were more diverse and enriched in Melainabacteria and Oscillospira compared with mixed diet-fed lizards. Additionally, the relative abundance of sulfate-reducing bacteria in the small intestine significantly correlated with whole-animal fiber digestibility. Thus, we suggest that physiological and microbial limitations do not sensu stricto constrain the evolution of herbivory in lizards. Rather, ecological context and fitness consequences may be more important in driving the evolution of this feeding strategy.

Smoking May Lead to Marginal Bone Loss Around Non-Submerged Implants During Bone Healing by Altering Salivary Microbiome: A Prospective Study

BACKGROUND

This prospective and controlled study elucidates the impact of smoking on the salivary microbiome and its further influence on marginal bone loss (MBL) around an implant during a 3-month bone-healing period.

METHODS

Saliva samples were collected preoperatively from 20 periodontally healthy patients with single-tooth replacement in the posterior mandible (smokers [n = 10] and non-smokers [n = 10]). Sequencing of 16S recombinant RNA gene amplicons was used to characterize the salivary microbiome. Each patient received implant surgery after oral clinical assessment, and MBL around the implant was measured during a 3-month healing period.

RESULTS

In total, 871,389 sequences were compared against the Human Oral Microbiome Database for bacterial identification. Microbial signatures of smokers exhibited lower diversity and richness, with a significant decrease in uncultured species. The phyla Gracilibacteria and Saccharibacteria showed a significant decrease in smokers. The genera Streptococcus, Lachnoanaerobaculum, Stomatobaculum, and Eubacterium were significantly increased in smokers, whereas Selenomonas, Selenomonas [G-3], and Catonella were significantly decreased. Specifically, Porphyromonas gingivalis was significantly more abundant in smokers, which was positively related to the severity of MBL during bone healing.

CONCLUSIONS

Smoking shapes the salivary microbiome in states of clinical health, and further may influence MBL during bone healing by creating high at-risk-for-harm communities. Understanding of the distinctly divergent oral microbiome in smokers and non-smokers is a base for personalized therapeutics for this high-risk cohort and also a base for further study on the pathologic mechanisms.

Genetic influences on the human oral microbiome

BACKGROUND

The human oral microbiome is formed early in development. Its composition is influenced by environmental factors including diet, substance use, oral health, and overall health and disease. The influence of human genes on the composition and stability of the oral microbiome is still poorly understood. We studied both environmental and genetic characteristics on the oral microbiome in a large twin sample as well as in a large cohort of unrelated individuals. We identify several significantly heritable features of the oral microbiome. The heritability persists in twins even when their cohabitation changes. The heritability of these traits correlates with the cumulative genetic contributions of over half a million single nucleotide sequence variants measured in a different population of unrelated individuals. Comparison of same-sex and opposite sex cotwins showed no significant differences. We show that two new loci on chromosomes 7 and 12 are associated with the most heritable traits.

RESULTS

An analysis of 752 twin pairs from the Colorado Twin Registry, shows that the beta-diversity of monozygotic twins is significantly lower than for dizygotic or unrelated individuals. This is independent of cohabitation status. Intraclass correlation coefficients of nearly all taxa examined were higher for MZ than DZ twin pairs. A comparison of individuals sampled over 2-7 years confirmed previous reports that the oral microbiome remains relatively more stable in individuals over that time than to unrelated people. Twin modeling shows that a number of microbiome phenotypes were more than 50% heritable consistent with the hypothesis that human genes influence microbial populations. To identify loci that could influence microbiome phenotypes, we carried out an unbiased GWAS analysis which identified one locus on chromosome 7 near the gene IMMPL2 that reached genome-wide significance after correcting for multiple testing. Another locus on chromosome 12 near the non-coding RNA gene INHBA-AS1 achieved genome-wide significance when analyzed using KGG4 that sums SNP significance across coding genes.

DISCUSSION

Using multiple methods, we have demonstrated that some aspects of the human oral microbiome are heritable and that with a relatively small sample we were able to identify two previously unidentified loci that may be involved.

Transcriptomics and methylomics in chronic periodontitis with tobacco use: a pilot study

Background

Accumulating evidence suggests that tobacco smoking affects the susceptibility to and severity of chronic periodontitis. Epigenetics may explain the role of smoking in the development and progress of periodontal disease. In this study, we performed transcriptomic and methylomic analyses of non-periodontitis and periodontitis-affected gingival tissues according to smoking status.

Methods

Human gingival tissues were obtained from 20 patients, including non-smokers with and without periodontitis (n = 5 per group) and smokers with and without periodontitis (n = 5 per group). Total RNA and genomic DNA were isolated, and their quality was validated according to strict standards. The Illumina NextSeq500 sequencing system was used to generate transcriptome and methylome datasets.

Results

Comprehensive analysis, including between-group correlation, differential gene expression, DNA methylation, gene set enrichment, and protein-protein interaction, indicated that smoking may change the transcription and methylation states of extracellular matrix (ECM) organization-related genes, which exacerbated the periodontal condition.

Conclusions

Our results suggest that smoking-related changes in DNA methylation patterns and subsequent alterations in the expression of genes coding for ECM components may be causally related to the increased susceptibility to periodontitis in smokers as they could influence ECM organization, which in turn may have an effect on disease characteristics.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-017-0381-z) contains supplementary material, which is available to authorized users.

Early-life disruption of amphibian microbiota decreases later-life resistance to parasites

Changes in the early-life microbiota of hosts might affect infectious disease risk throughout life, if such disruptions during formative times alter immune system development. Here, we test whether an early-life disruption of host-associated microbiota affects later-life resistance to infections by manipulating the microbiota of tadpoles and challenging them with parasitic gut worms as adults. We find that tadpole bacterial diversity is negatively correlated with parasite establishment in adult frogs: adult frogs that had reduced bacterial diversity as tadpoles have three times more worms than adults without their microbiota manipulated as tadpoles. In contrast, adult bacterial diversity during parasite exposure is not correlated with parasite establishment in adult frogs. Thus, in this experimental setup, an early-life disruption of the microbiota has lasting reductions on host resistance to infections, which is possibly mediated by its effects on immune system development. Our results support the idea that preventing early-life disruption of host-associated microbiota might confer protection against diseases later in life.

Early-life microbiota alterations can affect infection susceptibility later in life, in animal models. Here, Knutie et al. show that manipulating the microbiota of tadpoles leads to increased susceptibility to parasitic infection in adult frogs, in the absence of substantial changes in the adults’ microbiota.

Furcation Therapy With Enamel Matrix Derivative: Effects on the Subgingival Microbiome

BACKGROUND

Although enamel matrix derivative (EMD) has been used to promote periodontal regeneration, little is known of its effect on the microbiome. Therefore, this investigation aims to identify changes in periodontal microbiome after treatment with EMD using a deep-sequencing approach.

METHODS

Thirty-nine patients with mandibular Class II buccal furcation defects were randomized to beta-tricalcium-phosphate/hydroxyapatite graft (BONE group), EMD+BONE, or EMD alone. Plaque was collected from furcation defects at baseline and 3 and 6 months post-treatment. Bacterial DNA was analyzed using terminal restriction fragment length polymorphism and 16S pyrotag sequencing, resulting in 169,000 classifiable sequences being compared with the Human Oral Microbiome Database. Statistical comparisons were made using parametric tests.

RESULTS

At baseline, a total of 422 species were identified from the 39 defects, belonging to Fusobacterium, Pseudomonas, Streptococcus, Filifactor, and Parvimonas. All three regenerative procedures predictably altered the disease-associated microbiome, with a restitution of health-compatible species. However, EMD and BONE+EMD groups demonstrated more long-term reductions in a higher number of species than the BONE group (P <0.05), especially disease-associated species, e.g., Selenomonas noxia, F. alocis, and Fusobacterium.

CONCLUSIONS

EMD treatment predictably alters a dysbiotic subgingival microbiome, decreasing pathogen richness and increasing commensal abundance. Further investigations are needed to investigate how this impacts regenerative outcomes.