Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis

Decision-making on systemic antibiotics in the management of periodontitis: A retrospective comparison of two concepts

AIM

To retrospectively compare two approaches for the adjunctive use of systemic antibiotics in non-surgical periodontal therapy: one based on the detection of Aggregatibacter actinomycetemcomitans (Aa) and the other on age and severity of periodontitis (Age & PPD). We also assessed the additional benefit of antibiotics in reducing the need for further surgical therapy in each group.

MATERIALS AND METHODS

Patients of the Department of Periodontology, Goethe University Frankfurt, Germany, were screened for microbiological testing between 2008 and 2018. Patients were categorized by their microbiological result (Aa+/-) and demographic/clinical data (Age & PPD+/-). Agreement on antibiotic indication was tested. The clinical evaluation focussed on teeth with probing pocket depths (PPDs) ≥ 6 mm.

RESULTS

Analysis of 425 patients revealed 30% categorized as Age & PPD+ and 34% as Aa+. Sixty-three percent had consistent antibiotic recommendations (phi coefficient 0.14, p = .004). Patients in the Age & PPD+ group receiving antibiotics showed the most substantial reduction in the number of teeth with PPD ≥ 6 mm after non-surgical periodontal therapy.

CONCLUSIONS

Both strategies resulted in a significant clinical improvement compared with those without antibiotic treatment and restricted antibiotic use similarly, but targeted different patient groups. Younger individuals with severe periodontitis benefited most from antibiotics, reducing the need for additional surgeries. The study was registered in an international trial register (German Clinical Trial Register number DRKS00028768, registration date 27 April 2022, https://drks.de/search/en/trial/DRKS00028768).

Oral Prevalence of Selenomonas noxia Differs among Orthodontic Patients Compared to Non-Orthodontic Controls: A Retrospective Biorepository Analysis

The oral microbial flora may be significantly altered by orthodontic therapy and the use of fixed orthodontic brackets. Most orthodontic research has focused on cariogenic pathogens, while some evidence has demonstrated an increase in many known periodontal pathogens. However, little is known about the prevalence of the Gram-negative periodontal pathogen Selenomonas noxia (SN) among these patients. Using an existing saliva biorepository, n = 208 samples from adult and pediatric orthodontic and non-orthodontic patients were identified and screened for the presence of SN using qPCR and validated primers. In the pediatric study sample (n = 89), 36% tested positive for the presence of SN, with orthodontic patients comprising more SN-positive samples (87.5%) than SN-negative samples (78.9%), p = 0.0271. In the adult study sample (n = 119), SN was found in 28.6%, with orthodontic patients comprising 58.8% of positive samples and only 28.2% of negative samples (p < 0.0001). These data demonstrated that both pediatric and adult orthodontic patients exhibited higher prevalence of SN compared with age-matched non-orthodontic controls. As this microorganism is associated not only with periodontal disease but also long-term health issues such as obesity, more research is needed regarding the factors that increase the prevalence of this microbe.

Enhancing tomato disease resistance through endogenous antifungal proteins and introduced nematode-targeting dsRNA of biocontrol agent Bacillus velezensis HS-3

BACKGROUND

As a type of biological control agent (BCA), Bacillus velezensis possesses the efficacy of inhibiting pathogenic microorganisms, promoting plant growth, and overcoming continuous cropping obstacles (CCOs). However, there is limited reporting on the optimization of the cultivation conditions for such biocontrol agents and their role as double-stranded RNA (dsRNA) delivery vectors.

RESULTS

In this study, a Bacillus velezensis strain HS-3 was isolated from the root zone of tomato plants with in vitro anti-Botrytis cinerea activity. The investigation into active compounds revealed that HS-3 predominantly employs proteins with molecular weights greater than 3 kDa for its antifungal activity. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified various proteases and chitosanase, further suggesting that HS-3 most likely employs these enzymes to degrade fungal cell walls for its antifungal effect. To optimize the production of extracellular proteins, fermentation parameters for HS-3 were systematically optimized, leading to an optimized medium (OP-M). HS-3 cultured in OP-M demonstrated enhanced capacity to assist tomato plants in withstanding CCOs. However, the presence of excessive nematodes in diseased soil resulted in the disease severity index (DSI) remaining high. An RNA interference mechanism was further introduced to HS-3, targeting the nematode tyrosine phosphatase (TP) gene. Ultimately, HS-3 expressing dsRNA of TP in OP-M effectively assisted tomatoes in mitigating CCOs, reducing DSI to 2.2% and 17.8% of the control after 45 and 90 days of growth, respectively.

CONCLUSION

The advantages of Bacillus velezensis in crop disease management and the mitigation of CCOs become even more pronounced when utilizing both optimized levels of endogenous enzymes and introduced nematode-targeting dsRNA. © 2024 Society of Chemical Industry.

Longitudinal Microbiome Changes in Supragingival Biofilm Transcriptomes Induced by Orthodontics

INTRODUCTION

Common oral diseases are known to be associated with dysbiotic shifts in the supragingival microbiome, yet most oral microbiome associations with clinical end points emanate from cross-sectional studies. Orthodontic treatment is an elective procedure that can be exploited to prospectively examine clinically relevant longitudinal changes in the composition and function of the supragingival microbiome.

METHODS

A longitudinal cohort study was conducted among 24 adolescent orthodontic patients who underwent saliva and plaque sampling and clinical examinations at time points: before fixed appliance bonding and at 1, 6, and 12 wk thereafter. Clinical indices included bleeding on probing (BOP), mean gingival index (GI), probing depths (PDs), and plaque index (PI). To study the biologically (i.e., transcriptionally) active microbial communities, RNA was extracted from plaque and saliva for RNA sequencing and microbiome bioinformatics analysis. Longitudinal changes in microbiome beta diversity were examined using PERMANOVA tests, and the relative abundance of microbial taxa was measured using Kruskal-Wallis tests, Wilcoxon rank-sum tests, and negative binomial and zero-inflated mixed models.

RESULTS

Clinical measures of oral health deteriorated over time-the proportion of sites with GI and PI ≥1 increased by over 70% between prebonding and 12 wk postbonding while the proportion of sites with PD ≥4 mm increased 2.5-fold. Streptococcus sanguinis, a health-associated species that antagonizes cariogenic pathogens, showed a lasting decrease in relative abundance during orthodontic treatment. Contrarily, caries- and periodontal disease-associated taxa, including Selenomonas sputigena, Leptotrichia wadei, and Lachnoanaerobaculum saburreum, increased in abundance after bonding. Relative abundances of Stomatobaculum longum and Mogibacterium diversum in prebonding saliva predicted elevated BOP 12 wk postbonding, whereas Neisseria subflava was associated with lower BOP.

CONCLUSIONS

This study offers insights into longitudinal community and species-specific changes in the supragingival microbiome transcriptome during fixed orthodontic treatment, advancing our understanding of microbial dysbioses and identifying targets of future health-promoting clinical investigations.

KNOWLEDGE TRANSFER STATEMENT

Bonding braces was associated with subsequent changes in the oral microbiome characterized by increases in disease-associated species, decreases in health-associated species, and worsened clinical measures of oral health.

Diversity Analysis of Intestinal Bifidobacteria in the Hohhot Population

(1) Background: Bifidobacterium plays a pivotal role within the gut microbiota, significantly affecting host health through its abundance and composition in the intestine. Factors such as age, gender, and living environment exert considerable influence on the gut microbiota, yet scant attention has been directed towards understanding the specific effects of these factors on the Bifidobacterium population. Therefore, this study focused on 98 adult fecal samples to conduct absolute and relative quantitative analyses of bifidobacteria. (2) Methods: Using droplet digital PCR and the PacBio Sequel II sequencing platform, this study sought to determine the influence of various factors, including living environment, age, and BMI, on the absolute content and biodiversity of intestinal bifidobacteria. (3) Results: Quantitative results indicated that the bifidobacteria content in the intestinal tract ranged from 106 to 109 CFU/g. Notably, the number of bifidobacteria in the intestinal tract of the school population surpassed that of the off-campus population significantly (p = 0.003). Additionally, the group of young people exhibited a significantly higher count of bifidobacteria than the middle-aged and elderly groups (p = 0.041). The normal-weight group displayed a significantly higher bifidobacteria count than the obese group (p = 0.027). Further analysis of the relative abundance of bifidobacteria under different influencing factors revealed that the living environment emerged as the primary factor affecting the intestinal bifidobacteria structure (p = 0.046, R2 = 2.411). Moreover, the diversity of bifidobacteria in the intestinal tract of college students surpassed that in the out-of-school population (p = 0.034). This was characterized by a notable increase in 11 strains, including B. longum, B. bifidum, and B. pseudolongum, in the intestinal tract of college students, forming a more intricate intestinal bifidobacteria interaction network. (4) Conclusions: In summary, this study elucidated the principal factors affecting intestinal bifidobacteria and delineated their characteristics of intestinal bifidobacteria in diverse populations. By enriching the theory surrounding gut microbiota and health, this study provides essential data support for further investigations into the intricate dynamics of the gut microbiota.

Salivary microbiomes vary among orthodontic appliances and associate with clinical periodontal parameters

OBJECTIVE

To investigate the salivary bacterial communities during the first 6-month orthodontic treatment with Clear Aligners (CA) and Fixed Appliances (FA), and its correlation with clinical periodontal parameters.

MATERIALS AND METHODS

Saliva and periodontal parameters were sampled from individuals wearing CA or FA before treatment (T0), and after 3- (T3) and 6-month (T6) treatments. Salivary bacterial communities characterized based on the 16S rRNA V3-V4 region were compared between FA and CA and correlated with clinical periodontal parameters.

RESULTS

Probing Depth (PD) significantly increased at T6 in the FA group versus T0, whereas it remained stable in the CA group. The Shannon and Pielou indices were significantly higher in the FA group and significantly positively correlated with periodontal inflammation parameters. β-diversity analysis revealed distinct communities between the FA group and CA group at T6. The relative abundances of 3 genera and 15 species were significantly higher in the FA group. Among the above appliance-type related taxa, bacterial genera Selenomonas, Stomatobaculum, Olsenella and Faecalicoccus and bacterial species Selenomonas_sputigena, Dialister_invisus, Olsenella_profus, Prevotella_buccae, Cryptobacterium_curtum and Clostridium_spiroforme were significantly positively associated with periodontal parameters.

CONCLUSIONS

Orthodontic treatments trigger appliance-related salivary bacterial communities, highlighting the importance of developing appliance-orientated periodontal strategies during orthodontic treatments. Salivary bacterial communities harboured by patients wearing FA possess higher bacterial parameters which were associated with increasing PD, PI and Gingival Index.

Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents

Background

Grade C (previously aggressive) periodontitis (GCP) in adolescents is prevalent in certain parts of Africa where it is associated with JP2 genotype, a highly virulent strain of Aggregatibacter actinomycetemcomitans. The aim of this study was to characterize the subgingival bacteriome in Moroccan subjects with GCP positive to A. actinomycetemcomitans JP2 genotype.

Methods

Subgingival plaque samples were collected from shallow and deep pockets of 8 subjects with GCP (17.2 ± 1.5 years) and from gingival sulci of 13 controls with no periodontitis (14.6 ± 1.1 years). Identification and genotyping of A. actinomycetemcomitans was performed using PCR analysis of the ltx operon, while bacteriome profiling was done by 16S rRNA gene sequencing (V1-V3 region). Groups were compared in terms of microbial diversity, abundances, and dysbiosis.

Results

The shallow and deep pocket sites from GCP cases had a significantly altered microbial composition compared to controls. Species associated with health included Haemophilus parainfluenzae, Lautropia mirabilis, Streptococcus spp., Gemella spp., and Rothia spp. While known periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema spp. and Fretibacterium spp., were significantly enriched in GCP, non-conventional taxa, including Pseudomonas oral taxon C61 and Enterobacter cloacae were more abundant and showed stronger association with the disease. Less significant differences in abundances of individual taxa were observed between shallow and deep pockets. Overall dysbiosis measured in terms of Subgingival Microbial Dysbiosis Index (SMDI) differentiated between GCP and no-periodontitis with 95% accuracy.

Conclusions

The results suggest that several periodontal pathogens involved in the adult-type periodontitis also play a role in JP2 genotype-associated GCP. The potential role of non-conventional taxa in the pathogenesis of GCP warrants further investigation.

Oral microbiome and ischemic stroke risk among elderly Chinese women

Background

Stroke, a leading cause of disability worldwide, has been associated with periodontitis. However, whether stroke risk is related to oral microbiota remains unknown. This study aims to evaluate the associations between the oral microbiome and ischemic stroke risk.

Methods

In a case-control study of 134 case-control pairs nested within a prospective cohort study, we examined pre-diagnostic oral microbiome in association with stroke risk via shotgun metagenomic sequencing. The microbial sub-community and functional profiling were performed using Latent Dirichlet Allocation and HUMAnN2. Associations of microbial diversity, sub-community structure, and individual microbial features with ischemic stroke risk were evaluated via conditional logistic regression.

Results

Alpha and beta diversities differ significantly between cases and controls. One genus- and two species-level sub-communities were significantly associated with decreased ischemic stroke risk, with odds ratios (95% confidence intervals) of 0.52 (0.31-0.90), 0.51 (0.31-0.84), and 0.60 (0.36-0.99), respectively. These associations were potentially driven by the representative taxa in these sub-communities, i.e., genus Corynebacterium and Lautropia, and species Lautropia mirabilis and Neisseria elongate (p < 0.05). Additionally, 55 taxa, 1,237 gene families, and 90 metabolic pathways were associated with ischemic stroke risk at p < 0.05.

Conclusion

Our study highlights the role of oral microbiota in the etiology of ischemic stroke and calls for further research.

Efficacy of the additional use of subgingival air-polishing with erythritol powder in the treatment of periodontitis patients: a randomized controlled clinical trial. Part II: effect on sub-gingival microbiome

OBJECTIVES

To date, scarce evidence exists around the application of subgingival air-polishing during treatment of severe periodontitis. The aim of this study was to evaluate the effect on the health-related and periodontitis-related subgingival microbiome of air-polishing during non-surgical treatment of deep bleeding pockets in stage III-IV periodontitis patients.

MATERIALS AND METHODS

Forty patients with stage III-IV periodontitis were selected, and pockets with probing depth (PD) 5-9 mm and bleeding on probing were selected as experimental sites. All patients underwent a full-mouth session of erythritol powder supragingival air-polishing and ultrasonic instrumentation. Test group received additional subgingival air-polishing at experimental sites. Subgingival microbial samples were taken from the maxillary experimental site showing the deepest PD at baseline. Primary outcome of the first part of the present study was the 3-month change in the number of experimental sites. Additional analysis of periodontal pathogens and other sub-gingival plaque bacteria sampled at one experimental site at baseline and 3 months following treatment was performed through a real-time quantitative PCR microarray.

RESULTS

In the test group, a statistical increase of some health-related species was observed (Abiotropha defectiva, Capnocytophaga sputigena, and Lautropia mirabilis), together with the decrease of pathogens such as of Actinomyces israelii, Catonella morbi, Filifactor alocis, Porphyromonas endodontalis, Sele-nomonas sputigena, Tannerella forsythia, Treponema denticola, and Treponema socranskii. In the control group, statistical significance was found only in the decrease of Filifactor alocis, Tannerella forsythia, and Treponema socranskii.

CONCLUSIONS

The addition of erythritol-chlorhexidine powder seems to cause a shift of the periodontal micro-biome toward a more eubiotic condition compared to a conventional treatment. The study was registered on Clinical Trials.gov (NCT04264624).

CLINICAL RELEVANCE

Subgingival air-polishing could help re-establishing a eubiotic microbioma in deep bleeding periodontal pockets after initial non-surgical treatment.

Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries

Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.

Pursuing new periodontal pathogens with an improved RNA-oligonucleotide quantification technique (ROQT)

OBJECTIVE

The aim of this study was to optimize the sensitivity, specificity and cost-effectiveness of the RNA-Oligonucleotide Quantification Technique (ROQT) in order to identify periodontal pathogens that remain unrecognized or uncultured in the oral microbiome.

DESIGN

Total nucleic acids (TNA) were extracted from subgingival biofilm samples using an automated process. RNA, DNA and Locked Nucleic Acid (LNA) digoxigenin-labeled oligonucleotide probes targeting 5 cultivated/named species and 16 uncultivated or unnamed bacterial taxa were synthesized. Probe specificity was determined by targeting 96 oral bacterial species; sensitivity was assessed using serial dilutions of reference bacterial strains. Different stringency temperatures were compared and new standards were tested. The tested conditions were evaluated analyzing samples from periodontally healthy individuals, and patients with moderate or severe periodontitis.

RESULTS

The automated extraction method at 63⁰C along with LNA-oligunucleotides probes, and use of reverse RNA sequences for standards yielded stronger signals without cross-reactions. In the pilot clinical study, the most commonly detected uncultivated/unrecognized species were Selenomonas sp. HMT 134, Prevotella sp. HMT 306, Desulfobulbus sp. HMT 041, Synergistetes sp. HMT 360 and Bacteroidetes HMT 274. In the cultivated segment of the microbiota, the most abundant taxa were T. forsythia HMT 613 and Fretibacterium fastidiosum (formerly Synergistetes) HMT 363.

CONCLUSIONS

In general, samples from severe patients had the greatest levels of organisms. Classic (T. forsythia, P. gingivalis) and newly proposed (F. alocis and Desulfobulbus sp. HMT 041) pathogens were present in greater amounts in samples from severe periodontitis sites, followed by moderate periodontitis sites.

Decreased retronasal olfaction and taste perception in obesity are related to saliva biochemical and microbiota composition

Understanding the individual factors that modulate flavor perception is a central issue for the development of personalized diets strategies to fight obesity. This study aimed to investigate differences in flavor perception between adults with normal weight and those with obesity, as well as some potential biological factors related to these differences. To do that, liking and flavor perception intensity were measured against retronasal olfactory (pineapple, butter, tropical and chocolate) and taste attributes (sweetness, umami and bitter) in 77 individuals grouped as normalweight or obese, according to their body mass index (BMI). Unstimulated saliva was collected from all participants and characterized in terms of salivary flow, total protein content, total antioxidant capacity, total esterase activity and bacterial composition through 16S rDNA amplicon sequencing. The results showed that participants displayed differences in flavor perception according to their BMI group. Thus, the group with obesity showed significant lower liking and intensity scores for low calorie related food aroma (pineapple and tropical), lower taste intensity scores for sweet and umami, and a higher acceptability for umami than the group with normal weight. Significant differences between BMI groups were observed for salivary biochemical variables and specific bacterial taxa, some of which were significantly correlated to flavor intensity. This work suggests for the first time the existence of an oral-brain axis that might contribute to the development or perpetuation of obesity, which opens new and interesting avenues of research.

Exploratory studies of oral and fecal microbiome in healthy human aging

Growing evidence has linked an altered host fecal microbiome composition with health status, common chronic diseases, and institutionalization in vulnerable older adults. However, fewer studies have described microbiome changes in healthy older adults without major confounding diseases or conditions, and the impact of aging on the microbiome across different body sites remains unknown. Using 16S ribosomal RNA gene sequencing, we reconstructed the composition of oral and fecal microbiomes in young (23-32; mean = 25 years old) and older (69-94; mean = 77 years old) healthy community-dwelling research subjects. In both body sites, we identified changes in minor bacterial operational taxonomic units (OTUs) between young and older subjects. However, the composition of the predominant bacterial species of the healthy older group in both microbiomes was not significantly different from that of the young cohort, which suggests that dominant bacterial species are relatively stable with healthy aging. In addition, the relative abundance of potentially pathogenic genera, such as Rothia and Mycoplasma, was enriched in the oral microbiome of the healthy older group relative to the young cohort. We also identified several OTUs with a prevalence above 40% and some were more common in young and others in healthy older adults. Differences with aging varied for oral and fecal samples, which suggests that members of the microbiome may be differentially affected by aging in a tissue-specific fashion. This is the first study to investigate both oral and fecal microbiomes in the context of human aging, and provides new insights into interactions between aging and the microbiome within two different clinically relevant sites.

mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis

The analysis of microbiome data has several technical challenges. In particular, count matrices contain a large proportion of zeros, some of which are biological, whereas others are technical. Furthermore, the measurements suffer from unequal sequencing depth, overdispersion, and data redundancy. These nuisance factors introduce substantial noise. We propose an accurate and robust method, mbDenoise, for denoising microbiome data. Assuming a zero-inflated probabilistic PCA (ZIPPCA) model, mbDenoise uses variational approximation to learn the latent structure and recovers the true abundance levels using the posterior, borrowing information across samples and taxa. mbDenoise outperforms state-of-the-art methods to extract the signal for downstream analyses.

Identification, Characterization, and Efficacy Evaluation of Bacillus velezensis for Shot-Hole Disease Biocontrol in Flowering Cherry

Though information exists regarding the pathogenesis of the shot-hole disease (SH) in flowering cherry (FC), there has been a lack of research focusing on SH management. Therefore, here, we investigated the inhibitory activities of antagonistic bacteria against SH pathogens both in vitro and in vivo as well as their biochemical characteristics and bioactive compounds. Two biosurfactant-producing bacterial antagonists, identified as Bacillus velezensis strains JCK-1618 and JCK-1696, exhibited the best effects against the growth of both bacterial and fungal SH pathogens in vitro through their cell-free culture filtrates (CFCFs). These two strains also strongly inhibited the growth of the pathogens via the action of their antimicrobial diffusible compounds and antimicrobial volatile organic compounds (VOCs). Crude enzymes, solvent extracts, and biosurfactants of the two strains exhibited antimicrobial activities. Liquid chromatography/electrospray ionization time-of-flight mass spectrometric analysis of the partially purified active fractions revealed that the two antagonists produced three cyclic lipopeptides, including iturin A, fengycin A, and surfactin, and a polyketide, oxydifficidin. In a detached leaf assay, pre-treatment and co-treatment of FC leaves with the CFCFs led to a large reduction in the severity of the leaf spots caused by Epicoccum tobaicum and Bukholderia contaminans, respectively. In addition, the two antagonists produced indole-3-acetic acid, siderophore, and a series of hydrolytic enzymes, along with the formation of a substantial biofilm. To our knowledge, this is the first report of the antimicrobial activities of the diffusible compounds and VOCs of B. velezensis against the SH pathogens and their efficiency in the biocontrol of SH.

First Report of Shot-Hole on Flowering Cherry Caused by Burkholderia contaminans and Pseudomonas syringae pv. syringae

Shot-hole disease (SH) is one of the most common and important diseases affecting flowering cherry (FC; Prunus × yedoensis Matsumura; Somei-yoshino) trees in South Korea every year, resulting in premature defoliation and reduced flowering in the following year. However, pathogens associated with the disease remain unknown, which has rendered disease management challenging. Here, the pathogens associated with SH, their biochemical characteristics, and their host range were elucidated. Detached-leaf and in planta assays revealed that two biofilm-forming bacteria-namely, Burkholderia contaminans and Pseudomonas syringae pv. syringae-caused SH of FC trees. These pathogens were recorded for the first time as the causes of SH of FC trees in South Korea. Additionally, the two pathogens induced similar disease symptoms in several stone fruit belonging to the genus Prunus, including peach (Prunus persica), plum (P. salicina), and apricot (P. mume), with peach being the most susceptible. These results indicate that B. contaminans and P. syringae pv. syringae caused SH on FC trees and presented a broad spectrum of hosts. Furthermore, Xanthomonas arboricola pv. pruni, the causative agent of leaf spot on stone fruit, incited brown spots and shot holes on FC leaves. Therefore, FC trees are susceptible to infections by various pathogenic bacteria, including B. contaminans, P. syringae pv. syringae, and X. arboricola pv. pruni. These findings will be of great importance as a reference for effective management of SH in the face of possible cross-infection between Prunus spp. in the future.

Oral microbial diversity analysis among atrophic glossitis patients and healthy individuals

Atrophic glossitis is a common disease in oral mucosal diseases. The Current studies have found the human oral cavity contains numerous and diverse microorganisms, their composition and diversity can be changed by various oral diseases. To understand the composition and diversity of oral microbiome in atrophic glossitis is better to explore the cause and mechanism of atrophic glossitis. The salivary microbiome is comprised of indigenous oral microorganisms that are specific to each person, exhibits long-term stability. We used llumina MiSeq high-throughput sequencing based on the V3-V4 region of the bacterial 16S rRNA gene and the internal transcribed spacer (ITS) region of fungal rRNA genes from saliva in atrophic glossitis patients and healthy individuals to explore the composition and diversity of oral microbiome. In our reports, it showed a lower diversity of bacteria and fungi in atrophic glossitis patients than in healthy individuals. The data further suggests that Lactobacillus and Saccharomycetales were potential indicators for the initiation and development of atrophic glossitis. Moreover, we also discuss the relationship between the oral microbial ecology and atrophic glossitis.

The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey

Background

Supragingival plaque and saliva are commonly used for microbiome analysis. Many epidemiological studies have identified deciduous teeth caries as a risk factor for caries development in first permanent molar (FPM); nevertheless, to the best of our knowledge, there are no reports on the effects of deciduous teeth caries on the microbiome of healthy FPM. Additionally, it remains unclear whether saliva can be used instead of supragingival plaque for caries microbial studies. Therefore, we aimed to elucidate this issue, and to characterize and compare the oral microbiome of healthy FPMs in children with different caries statuses and that from children with and without caries in a similar microhabitat, by PacBio sequencing. Currently, few studies have investigated the oral microbiome of children using this technique.

Methods

Thirty children (aged 7–9 years) with mixed dentition were enrolled; 15 had dental caries, and 15 did not. Supragingival plaques of deciduous molars and maxillary FPMs, and non-stimulating saliva samples were collected. DNA was extracted and the v1–v9 regions of 16S rRNA were amplified. Subsequently, PacBio sequencing and bioinformatic analyses were performed for microbiome identification.

Results

The microbial alpha diversity of the saliva samples was lower than that of the supragingival plaque (p < 0.05); however, no differences were detected between deciduous teeth and FPMs (p > 0.05). In addition, the alpha and beta diversity of children with and without caries was also similar (p > 0.05). Nonmetric multidimensional scaling and Adonis analyses indicated that the microbial structure of salivary and supragingival plaque samples differ (p < 0.05). Further analysis of deciduous teeth plaque showed that Streptococcus mutans, Propionibacterium acidifaciens, and Veillonella dispar were more abundant in children with caries than in those without (p < 0.05); while in FPMs plaque, Selenomonas noxia was more abundant in healthy children (p < 0.05). No differences in microorganisms abundance were found in the saliva subgroups (p > 0.05).

Conclusion

We have determined that supragingival plaque was the best candidate for studying carious microbiome. Furthermore, S. mutans, V. dispar, and P. acidifaciens were highly associated with deciduous teeth caries. S. noxia may be associated with the abiding health of FPM; however, this requires additional studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-021-01683-0.

Compositional Data Analysis of Periodontal Disease Microbial Communities

Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Culture-independent methods, such as next-generation sequencing (NGS) of bacteria 16S amplicon and shotgun metagenomic libraries, have greatly expanded our understanding of PD biodiversity, identified novel PD microbial associations, and shown that PD biodiversity increases with pocket depth. NGS studies have also found PD communities to be highly host-specific in terms of both biodiversity and the response of microbial communities to periodontal treatment. As with most microbiome work, the majority of PD microbiome studies use standard data normalization procedures that do not account for the compositional nature of NGS microbiome data. Here, we apply recently developed compositional data analysis (CoDA) approaches and software tools to reanalyze multiomics (16S, metagenomics, and metabolomics) data generated from previously published periodontal disease studies. CoDA methods, such as centered log-ratio (clr) transformation, compensate for the compositional nature of these data, which can not only remove spurious correlations but also allows for the identification of novel associations between microbial features and disease conditions. We validated many of the studies’ original findings, but also identified new features associated with periodontal disease, including the genera Schwartzia and Aerococcus and the cytokine C-reactive protein (CRP). Furthermore, our network analysis revealed a lower connectivity among taxa in deeper periodontal pockets, potentially indicative of a more “random” microbiome. Our findings illustrate the utility of CoDA techniques in multiomics compositional data analysis of the oral microbiome.

Anna Karenina and the subgingival microbiome associated with periodontitis

BACKGROUND

Although localized aggressive periodontitis (LAP), generalized aggressive periodontitis (GAP), and chronic periodontitis (CP) are microbially driven diseases, our inability to separate disease-specific associations from those common to all three forms of periodontitis has hampered biomarker discovery. Therefore, we aimed to map the genomic content of, and the biological pathways encoded by, the microbiomes associated with these clinical phenotypes. We also estimated the extent to which these biomes are governed by the Anna Karenina principle (AKP), which states that eubiotic communities are similar between individuals while disease-associated communities are highly individualized.

METHODS

We collected subgingival plaque from 25 periodontally healthy individuals and diseased sites of 59 subjects with stage 3 periodontitis and used shotgun metagenomics to characterize the aggregate of bacterial genes.

RESULTS

Beta-dispersion metrics demonstrated that AKP was most evident in CP, followed by GAP and LAP. We discovered broad dysbiotic signatures spanning the three phenotypes, with over-representation of pathways that facilitate life in an oxygen-poor, protein- and heme-rich, pro-oxidant environment and enhance capacity for attachment and biofilm formation. Phenotype-specific indicators were more readily evident in LAP microbiome than GAP or CP. Genes that enable acetate-scavenging lifestyle, utilization of alternative nutritional sources, oxidative and nitrosative stress responses, and siderophore production were unique to LAP. An attenuation of virulence-related functionalities and stress response from LAP to GAP to CP was apparent. We also discovered that clinical phenotypes of disease resolved variance in the microbiome with greater clarity than the newly established grading system. Importantly, we observed that one third of the metagenome of LAP is unique to this phenotype while GAP shares significant functional and taxonomic features with both LAP and CP, suggesting either attenuation of an aggressive disease or an early-onset chronic disease.

CONCLUSION

Within the limitations of a small sample size and a cross-sectional study design, the distinctive features of the microbiomes associated with LAP and CP strongly persuade us that these are discrete disease entities, while calling into question whether GAP is a separate disease, or an artifact induced by cross-sectional study designs. Further studies on phenotype-specific microbial genes are warranted to explicate their role in disease etiology. Video Abstract.

The composition of microbial communities in inflammatory periodontal diseases in young adults Tatars

Host susceptibility and environmental factors are important for the development of gingivitis and periodontitis, but bacterial biofilms attached to the teeth and gingival tissues play a crucial role. We have analyzed and compared the subgingival microbial communities between subjects with dental plaque biofilm-induced generalized chronic gingivitis (CG), localized initial (Stage I) periodontitis (IP) and healthy controls (HC) of young people aged 18-19 years permanently residing in the city of Kazan (Tatarstan, Russia). The results showed that the α-diversity in groups with CG and IP was higher than in the healthy group. In a course of periodontal disease, a decrease in the relative abundance of dominates genera Rothia and Streptococcus was observed along with increase of class TM7-3 (Candidatus Saccharibacteria phylum) representatives. Also, the increase of red complex representatives Porphyromonadeceae, Treponema and Tannerella was detected together with statistically significant increase of Filifactor, Parvimonas, Peptostreptococcaceae, Veillonellaceae, Tissierelaceae and Mogibacteriaceae. Analysis of our data suggests that transition from HC to IP may be accompanied by a decrease in microbial diversity and a reduction in the abundance of family Rs-045 (Candidatus Saccharibacteria phylum), Desulfovibrionaceae Corynebacterium, Campylobacter and Selenomonas in young adults Kazan Tatars.

The salivary microbiota of Thai adults with metabolic disorders and association with diet

OBJECTIVE

This study aimed to investigate abundance of specific bacterial taxa in the saliva of 105 Thai adults with different BMI (lean, overweight, and obese) and T2DM subjects using qPCR targeting the 16S rRNA gene of various bacteria taxa.

DESIGN

We employed qPCR targeting 16S rRNA genes to explore the bacterial profiles and abundances in the saliva of Thai adult subjects with different BMI and T2DM. Multivariate statistical analyses (multiple factor analysis (MFA) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) were performed to assess the associations of salivary bacteria with diet, blood profile, gender, age, and use of antibiotics.

RESULTS

We found that abundance profiles of the examined salivary bacteria were similar across the four groups. When diet, blood profile, and gender, age, and use of antibiotics were considered, significant differences were noted between subgroups. A positive correlation was also found between consumption of carbonate soft drinks and Bacteroidetes, Gamma-proteobacteria, Veillonella, Fusobacterium and Fusobacterium nucleatum.

CONCLUSIONS

This is the first study demonstrating the relative abundance of salivary bacteria in adult Thai subjects with different levels of BMI and T2DM. Regardless of the similar pattern of bacterial profiles across groups, sPLS-DA analysis highlighted the influence of host variables (gender, age, and use of antibiotics) on the abundance of salivary microbiota. Our findings pave the way for further hypothesis testing to gain insight into the association between host factors and salivary microbiome.

Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome

A large proportion of bacteria, from a multitude of environments, are not yet able to be grown in the laboratory, and therefore microbiological and molecular biological investigations of these bacteria are challenging. A way to circumvent this challenge is to analyze the metagenome, the entire collection of DNA molecules that can be isolated from a particular environment or sample. This collection of DNA molecules can be sequenced and assembled to determine what is present and infer functional potential, or used as a PCR template to detect known target DNA and potentially unknown regions of DNA nearby those targets; however assigning functions to new or conserved hypothetical, functionally cryptic, genes is difficult. Functional metagenomics allows researchers to determine which genes are responsible for selectable phenotypes, such as resistance to antimicrobials and metabolic capabilities, without the prerequisite needs to grow the bacteria containing those genes or to already know which genes are of interest. It is estimated that a third of the resident species of the human oral cavity is not yet cultivable and, together with the ease of sample acquisition, makes this metagenome particularly suited to functional metagenomic studies. Here we describe the methodology related to the collection of saliva samples, extraction of metagenomic DNA, construction of metagenomic libraries, as well as the description of functional assays that have previously led to the identification of new genes conferring antimicrobial resistance.

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.

Clinical and Microbiological Profiles of Aggressive and Chronic Periodontitis in Congolese Patients: A Cross-sectional Study

Background:

Chronic and aggressive periodontitis were the main forms of periodontitis according to the 1999 classification of periodontal diseases and conditions. Their profile in Congolese patients is still undescribed.

Aim:

The aim of this study was to compare the profile of chronic periodontitis (ChP) with that of aggressive periodontitis (AgP) in Congolese patients.

Materials and Methods:

Thirty-two patients with ChP and 20 with AgP who consulted the dental services at any of the four medical centers in Kinshasa, from April 2017 to April 2018, were enrolled in the cross-sectional study. All patients underwent a full mouth examination, including assessment of the probing pocket depth and clinical attachment level at six sites per tooth. Microbial samples were collected in the deepest pocket in the maxilla and the deepest pocket in the mandible. A deoxyribonucleic acid (DNA) analysis was performed using DNA strip technology. Fisher exact test, the chi-square test, the t test, and the Mann–Whitney test were used for the statistical analysis.

Results:

Patients with AgP were significantly younger than those with ChP (P < 0.001). There was no significant difference in the prevalence of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, or Prevotella intermedia between the AgP and ChP groups (P > 0.05). Aggregatibacter actinomycetemcomitans was detected in 10% of cases in the AgP group and in none of those in the ChP group (P = 0.143).

Conclusion:

This study shows that the clinical profiles of ChP and AgP are similar in Congolese patients. There were no microbiological differences between these two forms of periodontitis.

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease

Efforts to map gingival tissue proteomes and microbiomes have been hampered by lack of sufficient tissue extraction methods. The pressure cycling technology (PCT) is an emerging platform for reproducible tissue homogenisation and improved sequence retrieval coverage. Therefore, we employed PCT to characterise the proteome and microbiome profiles in healthy and diseased gingival tissue. Healthy and diseased contralateral gingival tissue samples (total n = 10) were collected from five systemically healthy individuals (51.6 ± 4.3 years) with generalised chronic periodontitis. The tissues were then lysed and digested using a Barocycler, proteins were prepared and submitted for mass spectrometric analysis and microbiome DNA for 16S rRNA profiling analysis. Overall, 1,366 human proteins were quantified (false discovery rate 0.22%), of which 69 proteins were differentially expressed (≥2 peptides and p < 0.05, 62 up, 7 down) in periodontally diseased sites, compared to healthy sites. These were primarily extracellular or vesicle-associated proteins, with functions in molecular transport. On the microbiome level, 362 species-level operational taxonomic units were identified. Of those, 14 predominant species accounted for >80% of the total relative abundance, whereas 11 proved to be significantly different between healthy and diseased sites. Among them, Treponema sp. HMT253 and Fusobacterium naviforme and were associated with disease sites and strongly interacted (r > 0.7) with 30 and 6 up-regulated proteins, respectively. Healthy-site associated strains Streptococcus vestibularis, Veillonella dispar, Selenomonas sp. HMT478 and Leptotrichia sp. HMT417 showed strong negative interactions (r < −0.7) with 31, 21, 9, and 18 up-regulated proteins, respectively. In contrast the down-regulated proteins did not show strong interactions with the regulated bacteria. The present study identified the proteomic and intra-tissue microbiome profile of human gingiva by employing a PCT-assisted workflow. This is the first report demonstrating the feasibility to analyse full proteome profiles of gingival tissues in both healthy and disease sites, while deciphering the tissue site-specific microbiome signatures.

Isolation and Identification of Non- Commensal Pathogenic Bacteria in the Saliva of Patients Candidate for Liver Transplant: A Cross Sectional Study in Shiraz, South of Iran

Statement of the Problem

Liver cirrhosis is the end stage of liver failure. It is mentioned as one of the main etiologies of morbidity and mortality in the world. The human salivary bacteria may induce oral disorders and interact with other body microbiota.

Purpose

The aim of the present study is to identify the pathogenic bacteria of non-oral origin from the saliva samples of patients with end stage liver failure.

Materials and Method

In this cross-sectional study, the saliva samples of 88 end stage liver disease cases and 84 age- and sex-matched healthy subjects were collected. The samples were cultured using gram staining and API20E Kit.

Results

According to the statistical analysis, the total amount of the non-commensal bacteria was significantly higher in chronic liver failure (CLF) group than controls (p= 0.001). There was no significant difference between both groups for the presence of other bacteria (p= 0.001) except for Escherichia coli (E. coli). E. coli was isolated from the saliva of 15 cases and only 2 controls.

Conclusion

Oral cavity may act as a reservoir for enteric bacteria such as E. coli in liver failure patients. Adequate oral and general hygiene might reduce the risk of systemic infection especially in immunocompromised cases.

Identification of bacteria associated with periapical abscesses of primary teeth by sequence analysis of 16S rDNA clone libraries

OBJECTIVE

This study aims to detect the predominant bacteria in acute periapical abscesses of primary teeth using culture-independent molecular methods based on 16S ribosomal DNA cloning.

METHODS

Purulent material was collected from nine children diagnosed with abscesses of endodontic origin. DNA was extracted and the 16S rRNA gene amplified with universal primer pairs 27F and 1492R. Amplified genes were cloned, sequenced by Applied Biosystems, and identified by comparison with known 16S rRNA gene sequences.

RESULTS

Bacterial DNA was present in all nine purulence samples. A total of 681 clones were classified into 8 phyla, 78 genera, and 125 species/phylotypes. The phyla were Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria, Tenericutes, Deinococcus-Thermus, and Spirochaetes. The most dominant genera were Streptococcus (13.3%), Fusobacterium (11.8%), Parvimonas (7.8%), Prevotella (6.7%), Sphingomonas (5.8%), and Hafnia (5.2%). Fusobacterium nucleatum (11.5%), Parvimonas micra (7.8%), Streptococcus intermedius (6.6%), Sphingomonas echinoides (5.3%), Hafnia alvei (5.2%), and Citrobacter freundii (4.9%) were the most common species/phylotypes. Among these species/phylotypes, F.nucleatum was the most prevalent (7/9). C. freundii, Carnobacterium maltaromaticum, and H. alvei were seldom detected species in acute periapical abscesses but had relatively high abundance and prevalence.

CONCLUSION

Acute periapical abscesses are polymicrobial with certain prevalent bacteria, especially anaerobic bacterium. The most predominant and prevalent bacteria of acute periapical abscesses in children was F. nucleatum.

Clinical and Microbiological Evaluation of Surgical and Nonsurgical Treatment of Aggressive Periodontitis

The present study aimed to evaluate clinical and microbiological effects of surgical and nonsurgical periodontal therapy in generalized aggressive periodontitis (GAgP) treatment. Sixteen GAgP patients were included in this randomized split-mouth design clinical trial. Maxillary quadrants were allocated into two groups: Nonsurgical Therapy (NST) and Surgical Therapy (ST). The following clinical parameters were assessed: plaque index (PI), bleeding on probing index (BoP), probing depth (PD), clinical attachment level (CAL) and gingival margin position (GMP). Concentrations of Porphyromonas gingivalis (Pg) and Aggregatibacter actinomycetemcomitans (Aa) in the subgingival biofilm were also determined. Clinical and microbiological parameters were assessed at baseline (n=16), 3 (n=15), 6 (n=15) and 12 months (n=8) after treatment. ST was able to promote higher PD reduction compared to NST in deep pockets at 12 months (p<0.05) and in posterior teeth at 6 months (p<0.05). In addition, higher gingival recession was observed in posterior teeth of the ST group at the 6th month (p<0.05). However, ST failed to promoted additional CAL gain in any timepoint (p>0.05). Moreover, microbiological evaluation showed no statistical difference in levels of Aa and Pg for both groups at all follow-up periods. Surgical therapy promoted similar clinical benefits to GAgP therapy. Moreover, both therapies failed to reduce Aa and Pg levels at different follow-up times.

Local IL-10 level as a predictive factor in generalized aggressive periodontitis treatment response

Generalized aggressive periodontitis (GAgP) presents a reduced response to non-surgical therapy. However, it is not clear if the initial clinical, microbiological or immunological characteristics are impacting the worse response to treatment. This study aimed to identify the predictive value of clinical, microbiological and immunological patterns on the clinical response to therapy in GAgP patients. Twenty-four GAgP patients were selected, and gingival crevicular fluid (GCF) and subgingival biofilm were collected. Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythia levels were evaluated by qPCR, and IL-1β and IL-10 concentration by ELISA. Twelve patients were treated with SRP (scaling and root planning), and twelve with SRP plus 375 mg amoxicillin and 250 mg metronidazole (8/8 hours, 7 days) (SRP + AM). The clinical changes (Probing Pocket Depth [PPD] reduction and Clinical Attachment Level [CAL] gain) 6 months post-treatment were correlated to the initial clinical, inflammatory and microbiological variables using stepwise logistic regression (α = 5%). CAL gain at 6 months was 1.16 ± 0.77 for SRP and 1.74 ± 0.57 mm for SRP + AM (P > .05). PPD reduction was 1.96 ± 0.82 for SRP and 2.45 ± 0.77 mm for SRP + AM (P < .05). In the SRP group, IL-10 showed a predictive value for clinical response. The higher the IL-10 concentration at baseline, the higher the reduction in PPD at 6 months (P = .01, r = .68). However, when antimicrobials were administered, no significant influence was detected (P > .05). It can be concluded that the IL-10 levels in GFC act as a predictor of clinical response to GAgP. Moreover, the intake of antimicrobials appears to overlap the influence of the inflammatory response on clinical response to treatment. Clinical trial registration number: NCT03933501.

Advances in Directly Amplifying Nucleic Acids from Complex Samples

Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.

Comparison of the oral microbiome of patients with generalized aggressive periodontitis and periodontitis-free subjects

OBJECTIVE

The primary objectives of the study were to assess differences in complex subgingival bacterial composition between periodontitis-free persons and patients with generalized aggressive periodontitis (gAgP).

BACKGROUND

The composition of the oral microbiota plays an important role for both oral and systemic diseases. However, the complex nature of the oral microbiome and its homeostasis is still poorly understood.

MATERIAL AND METHODS

We compared the microbiome of 13 periodontitis-free persons to 13 patients with gAgP. The 16S rRNA genes were amplified, targeting the V3/V4 region using the MiSeq platform.

RESULTS

In total, 1713 different bacterial species were mapped according to the Greengenes database. Using the Shannon index, no significant differences in alpha diversity were found between the two study groups. In principal component and linear discriminant analyses, disease-specific differences in beta diversity of the microbiome composition were evaluated. Bacteroidetes, Spirochaetes, and Synergistetes were more abundant in gAgP whereas Proteobacteria, Firmicutes, and Actinobacteria were associated with a healthy periodontium. At the bacterial species level, we showed that Porphyromonas gingivalis is the strongest indicator of gAgP. Treponema denticola and Tanerella forsythia of the "red complex" as well as Filifactor alocis were among the ten best biomarkers for gAgP.

CONCLUSIONS

These results broaden our knowledge of disease-specific differences in the microbial community associated with generalized AgP. A more complex view of the composition of the oral microbiome describes the etiology of generalized AgP in more detail. These results could help to individually adapt periodontal therapy in these patients.

Evaluation of biofilm formation on novel copper-catalyzed azide-alkyne cycloaddition (CuAAC)-based resins for dental restoratives

OBJECTIVE

For the past several decades, the resins used in dental restorations have been plagued with numerous problems, including their implication in biofilm formation and secondary caries. The need for alternative resins is critical, and evaluation of biofilm formation on these resins is essential. The aim of this study was to evaluate in vitro biofilm formation on the surface of novel copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC)-based resins and composites.

METHODS

CuAAC-based resins/composites made from varying azide monomers and different copper concentrations were compared with BisGMA-TEGDMA resins/composites that served as the control. Biofilms were formed using a mono-species model containing a luciferase-expressing strain of Streptococcus mutans. Luciferase activity was measured and the number of viable bacteria was enumerated on biofilms associated with each resin and composite.

RESULTS

A significant reduction (p<0.05) in luciferase activity, and the number of viable bacteria recovered from biofilms on CuAAC-based resins and composites was observed in comparison to biofilms associated with the BisGMA-TEGDMA controls.

SIGNIFICANCE

CuAAC-based resins do still allow for the formation of biofilms; however, the statistically significant reduction of growth that was associated with the CuAAC resin may enhance the longevity of restorations that incorporate CuAAC-based materials.

Stimulated and unstimulated saliva samples have significantly different bacterial profiles

Epidemiological studies use saliva on a regular basis as a non-invasive and easy-to-take sample, which is assumed to be a microbial representative of the oral cavity ecosystem. However, comparative studies between different kinds of saliva samples normally used in microbial studies are scarce. The aim of the current study was to compare oral microbiota composition between two different saliva samples collected simultaneously: non-stimulated saliva with paper points and stimulated saliva collected after chewing paraffin gum. DNA was extracted from saliva samples of ten individuals, then analyzed by 16S rRNA pyrosequencing to describe bacterial diversity. The results demonstrate significant differences between the microbiota of these two kinds of saliva. Stimulated saliva was found to contain an estimated number of species over three times higher than unstimulated saliva. In addition, bacterial composition at the class and genus level was radically different between both types of samples. When compared to other oral niches, both types of saliva showed some similarity to tongue and buccal mucosa, but they do not correlate at all with the bacterial composition described in supra- or sub-gingival dental plaque, questioning their use in etiological and epidemiological studies of oral diseases of microbial origin.

Novel human microbe-disease associations inference based on network consistency projection

Increasing evidence shows that microbes are closely related to various human diseases. Obtaining a comprehensive and detailed understanding of the relationships between microbes and diseases would not only be beneficial to disease prevention, diagnosis and prognosis, but also would lead to the discovery of new drugs. However, because of a lack of data, little effort has been made to predict novel microbe-disease associations. To date, few methods have been proposed to solve the problem. In this study, we developed a new computational model based on network consistency projection to infer novel human microbe-disease associations (NCPHMDA) by integrating Gaussian interaction profile kernel similarity of microbes and diseases, and symptom-based disease similarity. NCPHMDA is a non-parametric and global network based model that combines microbe space projection and disease space projection to achieve the final prediction. Experimental results demonstrated that the integrated space projection of microbes and diseases, and symptom-based disease similarity played roles in the model performance. Cross validation frameworks and case studies further illustrated the superior predictive performance over other methods.

Characterizing oral microbial communities across dentition states and colonization niches

METHODS

The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and subgingival biofilm samples were collected from orally and systemically healthy children and mother-child dyads in predentate, primary, mixed, and permanent dentitions. 16S rRNA gene sequences were compared to the Human Oral Microbiome Database (HOMD). Functional potential was inferred using PICRUSt.

RESULTS

Unweighted and weighted UniFrac distances were significantly smaller between each mother-predentate dyad than infant-unrelated female dyads. Predentate children shared a median of 85% of species-level operational taxonomic units (s-OTUs) and 100% of core s-OTUs with their mothers. Maternal smoking, but not gender, mode of delivery, feeding habits, or type of food discriminated between predentate microbial profiles. The primary dentition demonstrated expanded community membership, structure, and function when compared to the predentate stage, as well as significantly lower similarity between mother-child dyads. The primary dentition also included 85% of predentate core s-OTUs. Subsequent dentitions exhibited over 90% similarity to the primary dentition in phylogenetic and functional structure. Species from the predentate mucosa as well as new microbial assemblages were identified in the primary supragingival and subgingival microbiomes. All individuals shared 65% of species between supragingival and subgingival habitats; however, the salivary microbiome exhibited less than 35% similarity to either habitat.

CONCLUSIONS

Within the limitations of a cross-sectional study design, we identified two definitive stages in oral bacterial colonization: an early predentate imprinting and a second wave with the eruption of primary teeth. Bacterial acquisition in the oral microbiome is influenced by the maternal microbiome. Personalization begins with the eruption of primary teeth; however, this is limited to phylogeny; functionally, individuals exhibit few differences, suggesting that microbial assembly may follow a defined schematic that is driven by the functional requirements of the ecosystem. This early microbiome forms the foundation upon which newer communities develop as more colonization niches emerge, and expansion of biodiversity is attributable to both introduction of new species and increase in abundance of predentate organisms.

Flagellin Glycoproteomics of the Periodontitis Associated Pathogen Selenomonas sputigena Reveals Previously Not Described O-glycans and Rhamnose Fragment Rearrangement Occurring on the Glycopeptides

Flagellated, Gram-negative, anaerobic, crescent-shaped Selenomonas species are colonizers of the digestive system, where they act at the interface between health and disease. Selenomonas sputigena is also considered a potential human periodontal pathogen, but information on its virulence factors and underlying pathogenicity mechanisms is scarce. Here we provide the first report of a Selenomonas glycoprotein, showing that S. sputigena produces a diversely and heavily O-glycosylated flagellin C9LY14 as a major cellular protein, which carries various hitherto undescribed rhamnose- and N-acetylglucosamine linked O-glycans in the range from mono- to hexasaccharides. A comprehensive glycomic and glycoproteomic assessment revealed extensive glycan macro- and microheterogeneity identified from 22 unique glycopeptide species. From the multiple sites of glycosylation, five were unambiguously identified on the 437-amino acid C9LY14 protein (Thr149, Ser182, Thr199, Thr259, and Ser334), the only flagellin protein identified. The O-glycans additionally showed modifications by methylation and putative acetylation. Some O-glycans carried hitherto undescribed residues/modifications as determined by their respective m/z values, reflecting the high diversity of native S. sputigena flagellin. We also found that monosaccharide rearrangement occurred during collision-induced dissociation (CID) of protonated glycopeptide ions. This effect resulted in pseudo Y1-glycopeptide fragment ions that indicated the presence of additional glycosylation sites on a single glycopeptide. CID oxonium ions and electron transfer dissociation, however, confirmed that just a single site was glycosylated, showing that glycan-to-peptide rearrangement can occur on glycopeptides and that this effect is influenced by the molecular nature of the glycan moiety. This effect was most pronounced with disaccharides. This study is the first report on O-linked flagellin glycosylation in a Selenomonas species, revealing that C9LY14 is one of the most heavily glycosylated flagellins described to date. This study contributes to our understanding of the largely under-investigated surface properties of oral bacteria. The data have been deposited to the ProteomeXchange with identifier PXD005859.

Insights into the human oral microbiome

Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.

Role of oral and gut microbiome in nitric oxide-mediated colon motility

Periodontal disease (PD), a severe form of gum disease, is among the most prevalent chronic infection in humans and is associated with complex microbial synergistic dysbiosis in the subgingival cavity. The immune system of the body interacts with the microbes as the plaque extends and propagates below the gingival sulcus. Once bacteria reach the gingival sulcus, it can enter the blood stream and affect various areas of the human body. The polymicrobial nature of periodontal disease, if left untreated, promotes chronic inflammation, not only within the oral cavity, but also throughout the human body. Alterations seen in the concentrations of healthy gut microbiota may lead to systemic alterations, such as gut motility disorders, high blood pressure, and atherosclerosis. Although gut microbiome has been shown to play a vital role in intestinal motility functions, the role of oral bacteria in this setting remains to be investigated. It is unclear whether oral microbial DNA is present in the large intestine and, if so, whether it alters the gut microbiome. In addition, polybacterial infection induced PD reduced nitric oxide (NO) synthesis and antioxidant enzymes in rodent colon. In this review, we will discuss the interactions between oral and gut microbiome, specifics of how the oral microbiome may modulate the activities of the gut microbiome, and possible ramifications of these alterations.

The microbial community shifts of subgingival plaque in patients with generalized aggressive periodontitis following non-surgical periodontal therapy: a pilot study

The object of this study is to characterize the bacterial community of subgingival plaque of two subjects with generalized aggressive periodontitis (GAgP) pre- and post-treatment. We picked two patients with GAgP and used high-throughput 16S rDNA sequencing. V4 hypervariable region was picked for PCR amplification of subgingival samples. Then, the PCR products were sequenced through Illumina MiSeq platform. One month after therapy, both the clinical features and periodontal parameters improved obviously. Moreover, the composition and structure of subgingival bacterial community changed after initial periodontal therapy. Also, the composition of the subgingival microbiota was highly individualized among different patients. Bacteroidetes, Spirochaetes and Fusobacteria were related to pathogenicity of GAgP while Actinobacteria and Proteobacteria seemed associated with clinical symptoms resolution. In this study, we found the subgingival bacterial community was high in species richness but dominated by a few species or phylotypes, with significant shifts of microbiota that occurred after treatment. This study demonstrated the shift of the subgingival bacterial community before and after treatment by high-throughput 16S rDNA sequencing, and provided a concise method for analysis of microbial community for periodontal diseases.

The subgingival periodontal microbiota of the aging mouth

Different mechanisms have been hypothesized to explain the increase in prevalence and severity of periodontitis in older adults, including shifts in the periodontal microbiota. However, the actual impact of aging on the composition of subgingival biofilms remains unclear. In the present article, we provide an overview of the composition of the subgingival biofilm in older adults and the potential effects of age on the oral microbiome. In particular, this review covers the following topics: (i) the oral microbiota of an aging mouth; (ii) the effects of age and time on the human oral microbiome; (iii) the potential impact of inflammaging and immunosenescence in the host-oral microbiota interactions; and (iv) the relationship of the aging oral microbiota and Alzheimer's disease. Finally, we present analyses of data compiled from large clinical studies that evaluated the subgingival microbiota of periodontally healthy subjects and patients with periodontitis from a wide age spectrum (20-83 years of age).

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.

Clarithromycin as an Adjunct to One-Stage Full-Mouth Ultrasonic Periodontal Debridement in Generalized Aggressive Periodontitis: A Randomized Controlled Clinical Trial

BACKGROUND

The aim of the present study is to evaluate the periodontal clinical and microbiologic responses and possible adverse effects of clarithromycin (CLM) combined with periodontal mechanical therapy in the treatment of patients with generalized aggressive periodontitis.

METHODS

Forty patients were selected and randomly assigned into one of two groups: 1) CLM (n = 20): one-stage full-mouth ultrasonic debridement (FMUD) associated with CLM (500 mg, every 12 hours for 3 days); and 2) placebo (n = 20): FMUD associated with placebo pills. Clinical and microbiologic parameters were evaluated at baseline and 3 and 6 months postoperatively.

RESULTS

Both treatments presented statistically significant clinical and microbiologic improvements. However, the CLM group presented lower means of probing depth for pockets ≥7 mm at 6 months (4.0 ± 1.7 mm) compared with the placebo group (4.7 ± 1.3 mm) (P = 0.04). In addition, the CLM group also presented greater reduction of Porphyromonas gingivalis (Pg) DNA counts at 6 months (P = 0.0001).

CONCLUSION

Results from this study suggest both treatments are effective; however, adjunct use of CLM to FMUD leads to better reduction of deep pockets and Pg at 6 months compared with FMUD alone.

High‑throughput sequencing analyses of oral microbial diversity in healthy people and patients with dental caries and periodontal disease

Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high-throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people. Moreover, the reduction of Firmicutes and the increase of Proteobacteria in the children group, and the increase of Firmicutes and the reduction of Proteobacteria in the youth and adult groups, indicated that the age bracket and oral disease had largely influenced the tooth development and microbial development in the oral cavity. In addition, the traditional ‘pathogenic bacteria’ of Firmicutes, Proteobacteria and Bacteroidetes (accounted for >95% of the total sequencing number in each group) indicated that the ‘harmful’ bacteria may exert beneficial effects on oral health. Therefore, the data will provide certain clues for curing some oral diseases by the strategy of adjusting the disturbed microbial compositions in oral disease to healthy level.

Systemic antibiotics in the treatment of periodontitis

Despite the fact that several clinical studies have shown additional benefits when certain systemic antibiotics are used as adjuncts to periodontal treatment, clear guidelines for the use of these agents in the clinical practice are not yet available. Basic questions concerning the use of systemic antibiotics to treat periodontitis remain unanswered, such as: which drug(s) should be used; which patients would most benefit from treatment; which are the most effective protocols (i.e. doses and durations); and in which phase of the mechanical therapy should the drug(s) be administered? Although not all of those questions have been directly addressed by controlled randomized clinical trials, recent concepts related to the ecology of periodontal diseases, as well as the major advances in laboratory and clinical research methods that have occurred in the past decade, have significantly broadened our knowledge in this field. This article endeavored to provide a 'state of the art' overview on the use of systemic antibiotics in the treatment of periodontitis, based on the most recent literature on the topic as well as on a compilation of data from studies conducted at the Center of Clinical Trials at Guarulhos University (São Paulo, Brazil) from 2002 to 2012.

Detection and comparison of Selenomonas sputigena in subgingival biofilms in chronic and aggressive periodontitis patients

Background:

With the advent of DNA-based culture-independent techniques, a constantly growing number of Selenomonas phylotypes have been detected in patients with destructive periodontal diseases. However, the prevalence levels that have been determined in different studies vary considerably.

Aim:

The present study was undertaken to detect and compare the presence of Selenomonas sputigena in the subgingival plaque samples from generalized aggressive periodontitis (GAP), chronic generalized periodontitis, and periodontally healthy patients using conventional polymerase chain reaction (PCR) technique.

Materials and Methods:

A total of 90 patients were categorized as periodontally healthy individuals (Group I, n = 30), chronic generalized periodontitis (Group II, n = 30), and GAP (Group III, n = 30). The clinical parameters were recorded and subgingival plaque samples were collected. These were then subjected to conventional PCR analysis.

Statistical Analysis Used:

Kruskal–Wallis ANOVA test was used for multiple group comparisons followed by Mann–Whitney U-test for pairwise comparison.

Results:

On comparison between three groups, all the clinical parameters were found to be statistically highly significant. Comparing Groups I-II and I-III, the difference in detection was found to be statistically highly significant whereas in Groups II-III, it was statistically nonsignificant. On comparison of S. sputigena detected and undetected patients to clinical parameters in various study groups, the difference was found to be nonsignificant.

Conclusion:

S. sputigena was found to be significantly associated with chronic and aggressive periodontitis. Although the difference in its detection frequency in both groups was statistically nonsignificant when compared clinically, S. sputigena was more closely associated with the GAP.