Human Oral Microbe Identification Microarray Research Articles

Effectiveness of the Human Oral Microbe Identification Microarray in Identifying Periodontal Pathogens: A Systematic Review

The aim of this review was to investigate the effectiveness of the Human Oral Microbe Identification Microarray (HOMIM) in identifying and quantifying bacterial species of the oral microbiome in periodontal disease. The search for articles was conducted in CENTRAL, CINAHL, MEDLINE and EMBASE by two reviewers, and included articles published in English between January 1990 and December 2021. The selected articles were human observational studies in adults between 18 and 65 years, presenting specific predefined keywords. Articles were initially selected by title and abstract; articles that met the inclusion criteria were analyzed for methodological quality using a detailed checklist for quality assessment. Data were extracted and reported using the PRISMA tool. The study design, sample, follow-up period, collection and microbial analysis methods, statistical treatment, results and discussion were quality assessed and risk of bias was evaluated using the Cochrane Risk-of-Bias tool. A narrative synthesis approach was used to synthesize and interpret the extracted data. From the initial search, 2931 articles were retrieved; 51 of these were then selected after screening by title and abstract. Subsequently, 8 articles met the inclusion after full-text reading and were classed according to methodological quality as high (2), moderate (3) or low (3). Studies included in this review were of high and medium quality. Data from the Human Oral Microbe Identification Microarray (HOMIM) provide much more robust results, showing major shifts between periodontal health and periodontal disease. Compared to earlier techniques such as Denaturing Gradient Gel Electrophoresis (DGGE), HOMIM represents a more effective approach for quantification due to its high sensitivity; thus, it is able to identify a high prevalence of periodontal pathogens and novel species in low abundance. The literature provides moderate evidence that the Human Oral Microbe Identification Microarray (HOMIM) is more effective in identifying and quantifying bacterial species of the oral microbiome in periodontal disease, compared to earlier molecular and non-molecular methods such as Denaturing Gradient Gel Electrophoresis (DGGE) and a culture-based approach with phenotypic tests.

Understanding the microbial components of periodontal diseases and periodontal treatment-induced microbiological shifts.

In the mid-1960s the microbial aetiology of periodontal diseases was introduced based on classical experimental gingivitis studies . Since then, numerous studies have addressed the fundamental role that oral microbiota plays in the initiation and progression of periodontal diseases. Recent advances in laboratory identification techniques have contributed to a better understanding of the complexity of the oral microbiome in both health and disease. Modern culture-independent methods such as human oral microbial identification microarray and next-generation sequencing have been used to identify a wide variety of microbial taxa residing in the gingival sulcus and the periodontal pocket. The first theory of the 'non-specific plaque' hypothesis gave rise to the 'ecological plaque' hypothesis and more recently to the 'polymicrobial synergy and dysbiosis hypothesis'. Periodontitis is now considered to be a multimicrobial inflammatory disease in which the various bacterial species within the dental biofilm are in a dysbiotic state and this imbalance favours the establishment of chronic inflammatory conditions and ultimately the destruction of tooth-supporting tissues. Apart from the known putative periodontal pathogens, the whole biofilm community is now considered to play a role in the establishment of inflammation and the initiation and progression of periodontitis in a susceptible host. Treatment is unlikely to eliminate putative pathogens but, when it is thoroughly performed it has the potential to establish a healthy ecosystem by altering the microbial community in numbers and composition and also contribute to the maturation of the host immune response.

Effect of mechanically stimulated saliva on initial human dental biofilm formation

This study evaluated the impact of mechanically stimulated saliva on initial bacterial colonization. Interaction between oral bacteria and both unstimulated and stimulated saliva was examined in vitro by laying labeled bacteria over SDS-PAGE-separated salivary proteins. The effects of chewing on in vivo biofilm, microbial composition, and spatial arrangement were examined in two human volunteers using an intraoral stent containing retrievable enamel chips. In vitro experiments showed that bacterial binding to proteins from stimulated saliva was lower than that to proteins from unstimulated saliva. Lack of binding activity was noted with Streptococcus mutans and Lactobacillus casei. Human Oral Microbe Identification Microarray (HOMIM) analyses revealed a consistent chewing-related increase in the binding of Streptococcus anginosus and Streptococcus gordonii. Immunofluorescence microscopy demonstrated the presence of multi-species colonies and cells bearing different serotypes of the coaggregation-mediating streptococcal cell-surface receptor polysaccharides (RPS). Differences in bacterial colonization were noted between the two volunteers, while the type 4 RPS-reactive serotype was absent in one volunteer. Cells reacting with antibody against Rothia or Haemophilus were prominent in the early biofilm. While analysis of the data obtained demonstrated inter-individual variations in both in vitro and in vivo bacterial binding patterns, stimulating saliva with multiple orosensory stimuli may modulate oral bacterial colonization of tooth surfaces.

Subgingival microbiome in Chinese patients with generalized aggressive periodontitis compared to healthy controls

ObjectiveThe aim of the study was to profile the subgingival microbiome of Chinese adults with generalized aggressive periodontitis (GAgP) using human oral microbe identification microarray (HOMIM), and to compare the results with matched periodontal healthy controls. Design15 subjects with GAgP and 15 age- and gender- matched periodontal healthy controls were included. Subgingival plaque samples were collected from the deepest pockets of patients with GAgP and matched sites in controls and then analyzed by 16S rRNA-based microarrays. Student's paired t-test was used to compare clinical parameters and mean number of bacterial taxa detected between the two groups. Fisher's exact probability test and Wilcoxon Rank Sum were used to compare bacterial species between all samples. A multiple linear regression model was used for correlations among age, gender and bacterial with clinical parameters. ResultsFrom a total sum of 379 strains tested, 171 bacterial strains were detected from subgingival plaques of the GAgP patients, more than the 157 strains detected in control group. Mean number of subgingival bacterial taxa detected in GAgP group was 68 (SD = 21.06) while in control group was 45 (SD = 21.60). 47 bacterial taxa were detected more frequently in GAgP group while 12 taxa were more prevalent in control group. The significantly more prevalent and abundant taxa of bacteria in GAgP group included Filifactor alocis, Desulfobulbus sp., Fretibacterium sp., Porphyromonas gingivalis, Tannerella forsythia, Porphyromon as endodontalis, Peptostreptococcaceae spp., Parvimonas micra, Eubacterium nodatum and Eubacterium saphenum. Meanwhile the more abundant taxa in control group were Streptococcus spp. and Pseudomonas aeruginosa. ConclusionsThere are more taxa of bacteria in subgingival plaques of Chinese patients with GAgP than in healthy controls. F. alocis, Desulfobulbus sp., Fretibacterium sp., P. gingivalis and T. forsythia are strongly associated with GAgP. High-throughout microbiological results may help dentists have a better understanding of subgingival microbiome of GAgP.

Microbiome at sites of gingival recession in children with Hutchinson-Gilford progeria syndrome.

Hutchinson-Gilford progeria syndrome (HGPS) is a rare premature aging disorder with significant oral and dental abnormalities. Clinical symptoms include various features of accelerated aging such as alopecia, loss of subcutaneous fat, bone abnormalities, and premature cardiovascular disease. In addition, children with HGPS have been observed to suffer from generalized gingival recession. Whether periodontal manifestations associated with this syndrome are the results of changes in the oral flora is unknown. The present study aimed to identify the microbial composition of subgingival sites with gingival recession in children with HGPS. Nine children with HGPS were enrolled in this study. Plaque samples were collected from teeth with gingival recession. DNA samples were analyzed using the Human Oral Microbe Identification Microarray (HOMIM). Microbial profiles from HGPS children were compared with microbial profiles of controls from healthy individuals (n=9) and patients with periodontal disease (n=9). Comparison of microbial compositions of HGPS samples with periodontal health samples demonstrated significant differences for two bacterial taxa; Porphyromonas catoniae and Prevotella oulora were present in children with HGPS, but not normal controls. There were statistically significant differences of 20 bacterial taxa between HGPS and periodontal disease groups. Typical periodontal pathogens were not present at sites with gingival recession in HGPS children. The microbial compositions of sites of gingival recession and attachment loss in HGPS were generally more similar to those of periodontal health than periodontal disease. Species other than typical periodontal pathogens may be involved in this recession.

Interbacterial Adhesion Networks within Early Oral Biofilms of Single Human Hosts.

Specific interbacterial adhesion, termed coaggregation, is well established for three early colonizers of the plaque biofilm: streptococci, actinomyces, and veillonellae. However, little is known about interactions of other early colonizers and about the extent of interactions within the bacterial community from a single host. To address these gaps, subject-specific culture collections from two individuals were established using an intraoral biofilm retrieval device. Molecular taxonomy (Human Oral Microbe Identification Microarray [HOMIM]) analysis of biofilm samples confirmed the integrity and completeness of the collections. HOMIM analysis verified the isolation of Streptococcus gordonii and S. anginosus from only one subject, as well as isolation of a previously uncultivated streptococcal phylotype from the other subject. Strains representative of clonal diversity within each collection were further characterized. Greater than 70% of these streptococcal strains from each subject coaggregated with at least one other coisolate. One-third of the strains carry a known coaggregation mediator: receptor polysaccharide (RPS). Almost all nonstreptococcal isolates coaggregated with other coisolates. Importantly, certain Rothia strains demonstrated more coaggregations with their coisolated bacteria than did any Streptococcus or Actinomyces strain, and certain Haemophilus isolates participated in twice as many. Confocal microscopy of undisturbed biofilms showed that Rothia and Haemophilus each occur in small multispecies microcolonies. However, in confluent high-biomass regions, Rothia occurred in islands whereas Haemophilus was distributed throughout. Together, the data demonstrate that coaggregation networks within an individual's oral microflora are extensive and that Rothia and Haemophilus can be important initiators of cell-cell interactions in the early biofilm.IMPORTANCE Extensive involvement of specific interbacterial adhesion in dental plaque biofilm formation has been postulated based on in vitro coaggregation between oral bacteria from culture collections that are not subject specific. In the present study, subject-specific culture collections were obtained from early plaque biofilm of two volunteers, and coaggregations within each culture collection were assayed. Coaggregations, several of which involved a coaggregation-mediating cell surface molecule known from well-studied streptococci, were widespread. Unexpectedly, the little-studied organisms Haemophilus and Rothia participated in the greatest numbers of interactions with community members; these two organisms showed different distributions within the undisturbed biofilm. The data show that coaggregation networks encompass most organisms within the biofilm community of each individual, and they indicate prominent participation of organisms such as Haemophilus and Rothia in early plaque biofilm formation.

Ligature-associated bacterial profiles are linked to type 2 diabetes mellitus in a rat model and influenced by antibody treatment against TNF-α or RAGE.

There is a bidirectional relationship between periodontal disease (PD) and type 2 diabetes mellitus (T2D). T2D may lead to ecological perturbations in the oral environment, which may facilitate an altered microbiota. However, previous studies have been inconclusive in determining the effect of T2D on oral bacterial profiles. Therefore, we aimed to evaluate the influence of T2D on the ligature‐associated bacterial profile in a diabetic rat model with PD and investigated the impact of blocking inflammatory pathways with antibodies targeting either Tumor Necrosis Factor α (TNF‐α) or the receptor of advanced glycation end‐products (RAGE). A total of 62 Zucker obese rats (45 T2D) and 17 lean (non‐T2D) were divided into 4 treatment groups; lean with PD, obese with PD, obese with PD and anti‐TNF‐α treatment, and obese with PD with anti‐RAGE treatment. Periodontal disease was ligature induced. Ligature‐associated bacterial profiles were analyzed using Human Oral Microbe Identification Microarray (HOMIM). Ligature‐associated bacterial profiles differed between lean and obese rats. Furthermore, treatment with antibodies against TNF‐α or RAGE had an impact on subgingival bacterial profiles. T2D phenotypes are associated with different ligature‐associated bacterial profiles and influenced by treatment with antibodies against TNF‐α or RAGE.

The subgingival microbiome, systemic inflammation and insulin resistance: The Oral Infections, Glucose Intolerance and Insulin Resistance Study.

Inflammation might link microbial exposures to insulin resistance. We investigated the cross-sectional association between periodontal microbiota, inflammation and insulin resistance. The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) enrolled 152 diabetes-free adults (77% female) aged 20-55years (mean=34±10). Three hundred and four subgingival plaque samples were analysed using the Human Oral Microbe Identification Microarray to measure the relative abundances of 379 taxa. C-reactive protein, interleukin-6, tumour necrosis factor-α and adiponectin were assessed from venous blood and their z-scores were summed to create an inflammatory score (IS). Insulin resistance was defined via the HOMA-IR. Associations between the microbiota and both inflammation and HOMA-IR were explored using multivariable linear regressions; mediation analyses assessed the proportion of the association explained by inflammation. The IS was inversely associated with Actinobacteria and Proteobacteria and positively associated with Firmicutes and TM7 (p-values<0.05). Proteobacteria levels were associated with insulin resistance (p<0.05). Inflammation explained 30-98% of the observed associations between levels of Actinobacteria, Proteobacteria or Firmicutes and insulin resistance (p-values<0.05). Eighteen individual taxa were associated with inflammation (p<0.05) and 22 with insulin resistance (p<0.05). No findings for individual taxa met Bonferroni-adjusted statistical significance. Bacterial measures were related to inflammation and insulin resistance among diabetes-free adults.

Effectiveness of enamel matrix derivative on the clinical and microbiological outcomes following surgical regenerative treatment of peri-implantitis. A randomized controlled trial.

This randomized clinical trial aimed at comparing radiological, clinical and microbial effects of surgical treatment of peri-implantitis alone or in combination with enamel matrix derivative (EMD). Twenty-six subjects were treated with open flap debridement and decontamination of the implant surfaces with gauze and saline preceding adjunctive EMD or no EMD. Bone level (BL) change was primary outcome and secondary outcomes were changes in pocket depth (PD), plaque, pus, bleeding and the microbiota of the peri-implant biofilm analyzed by the Human Oral Microbe Identification Microarray over a time period of 12months. In multivariate modelling, increased marginal BL at implant site was significantly associated with EMD, the number of osseous walls in the peri-implant bone defect and a Gram+/aerobic microbial flora, whereas reduced BL was associated with a Gram-/anaerobic microbial flora and presence of bleeding and pus, with a cross-validated predictive capacity (Q(2) ) of 36.4%. Similar, but statistically non-significant, trends were seen for BL, PD, plaque, pus and bleeding in univariate analysis. Adjunctive EMD to surgical treatment of peri-implantitis was associated with prevalence of Gram+/aerobic bacteria during the follow-up period and increased marginal BL 12months after treatment.

The Prevalence of Oral Flora in the Biofilm Microbiota of the Endotracheal Tube

The endotracheal tube (ETT) is recognized as an independent factor for infection in intubated patients. The presence of biofilm contributes to the development of pneumonia. Standard culturing techniques are inadequate to detect many of the bacteria present in a biofilm. Delineation of the microbiota in the ETT is needed to further understand infections in ventilated patients. A prospective, observational study was performed at a university, Level I trauma center. Twenty ETT were collected at extubation. Bioluminal accretions were removed and quantified. DNA was extracted and 16S ribosomal RNA gene analysis performed using the Human Oral Microbe Identification Microarray. Twenty ETT were evaluated. Mean age was 47.5 years (19-82). Five were smokers. Mean ventilator days was 3.6 ± 3.1. Mean intensive care unit days was 7.8 ± 6.3. In those ETT, 87 different bacterial species were identified. Mean number of bacterial species identified was 16 ± 9 (3-35). There was no relationship between duration of intubation and number of species (P = 0.5). Nonsmokers had a greater variety of bacteria than smokers (P = 0.03). Patients with pneumonia did not have a greater variety of bacteria (P = 0.14). Parvimonas micra presence was associated with reintubation (P = 0.01). The most common species in smokers were different from nonsmokers. There is a wide variety of bacteria present in an ETT, many of which cannot be cultured by standard means. Variation is not correlated to duration of intubation or accretion volume. Studies to evaluate these bacteria and their interaction with the biofilm may further delineate factors in development of infections.

Abstract P046: The Subgingival Microbiome, Systemic Inflammation and Insulin Resistance

Introduction: Chronic inflammation is hypothesized as a mechanism linking microbial exposures to insulin resistance. We investigated the association between periodontal microbiota, systemic inflammation and insulin resistance among diabetes-free adults. Hypotheses: We hypothesized that subgingival microbial signatures would be related to both inflammatory phenotype and measures of insulin resistance and that there would be evidence of mediation by inflammatory markers. Methods: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) enrolled 152 diabetes-free adults (77% female) aged 20-55 years (mean=34±10). 304 subgingival plaque samples (2 per participant) were analyzed using the Human Oral Microbe Identification Microarray (HOMIM) to measure the relative abundances of 379 taxa from eight different phyla. C-reactive protein, interleukin-6, tumor necrosis factor-α and adiponectin were assessed from venous blood and their z-scores were summed to create an inflammatory score (IS). Fasting glucose and insulin levels defined insulin resistance via the HOMA-IR. Associations between the subgingival microbiota and both inflammation and insulin resistance were explored using multivariable linear regression models adjusted for cardiometabolic risk factors; mediation analyses assessed the proportion of the association explained by inflammation. Results: The IS was inversely associated with the relative abundance of Actinobacteria and Proteobacteria and positively associated with Firmicutes and TM7 (all p-values&lt;0.05). The IS was positively associated with glucose, insulin and HOMA-IR (all p&lt;0.05). Proteobacteria levels were associated with insulin resistance (p&lt;0.05). Inflammation explained 30%-98% of the observed associations between levels of Actinobacteria, Proteobacteria or Firmicutes and insulin resistance (p-values&lt;0.05). 18 individual taxa were associated with inflammation (p&lt;0.05) and 22 with insulin resistance (p&lt;0.05). Conclusion: Subgingival microbial community structure and membership were related to systemic inflammation and insulin resistance in a sample of diabetes-free adults.

Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples

BackgroundOver 700 bacterial species reside in human oral cavity, many of which are associated with local or distant site infections. Extensive characterization of the oral microbiome depends on the technologies used to determine the presence and proportions of specific bacterial species in various oral sites.ObjectiveThe objective of this study was to compare the microbial composition of dental plaque at baseline using Human Oral Microbe Identification Microarray (HOMIM) and Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technologies, which are based on 16S rRNA.MethodsDental plaque samples were collected from 96 patients at baseline prior to a dental procedure involving manipulation of gingival tissues. The samples were surveyed for 293 and 597 oral bacterial species via HOMIM and HOMINGS, respectively, based on 16S rRNA gene sequences. We determined the concordance between the two technologies for common species. Genus level analysis was performed using HOMINGS-specific genus identification capabilities.ResultsHOMINGS detected twice the number of species in the same dental plaque samples compared to HOMIM. For the species detected by both HOMIM and HOMINGS, there was no difference in relative proportions of overall bacterial composition at the species, genus or phylum levels. Additionally, there was no difference in relative proportion for total species per patient between the two technologies.ConclusionHOMINGS significantly expanded oral bacterial species identification compared to HOMIM. The genus and species probes, combined in HOMINGS, provided a more comprehensive representation of oral bacterial community, critical for future characterization of oral microbes in distant site infections.

Microbial Profiling in Experimentally Induced Biofilm Overgrowth Among Patients With Various Periodontal States.

This study measures microbial composition changes during biofilm overgrowth and subsequent removal among patients with various states of periodontal disease. In this prospective cohort study, 175 participants with various periodontal states (five biofilm-gingival interface [BGI] groups) abstained from oral hygiene while using an acrylic stent. At day 21, participants reinstituted oral hygiene and were followed for 4 weeks. Clinical parameters were recorded, and subgingival plaque samples were analyzed at baseline, peak of induction (day 21), and resolution using 16S rRNA probes (human oral microbe identification microarray [HOMIM]). Using the change score (peak at induction minus baseline) for bleeding on probing and probing depth (PD), the patients were separated into high and low clinical responders. At baseline, synergistetes were more abundant in moderate and severe periodontitis (BGI-P2 and -P3) compared to mild periodontitis (BGI-P1), health (BGI-H), and gingivitis (BGI-G) (P = 0.005). Overall, at day 21 there was an increase in HOMIM scores of firmicutes (P ≤0.001), fusobacteria (P = 0.003), proteobacteria (P ≤0.001), synergistetes (P = 0.04), and bacteroidetes (P ≤0.001). At resolution, these phyla returned to baseline, except for synergistetes. Levels of synergistetes were significantly higher at day 21 (P ≤0.0001) and resolution (P = 0.0002) for high clinical responders compared to low responders. The association of synergistetes as a baseline predictor of incident PD increase, as well as the higher levels at day 21, indicates a pathogenic role for these organisms in disease progression in addition to the previously characterized fusobacteria, proteobacteria, firmicutes, and bacteroidetes.

Oral microbiota species in acute apical endodontic abscesses

Background and objectivesAcute apical abscesses are serious endodontic diseases resulting from pulpal infection with opportunistic oral microorganisms. The objective of this study was to identify and compare the oral microbiota in patients (N=18) exhibiting acute apical abscesses, originating from the demographic region in Portland, Oregon. The study hypothesis is that abscesses obtained from this demographic region may contain unique microorganisms not identified in specimens from other regions.DesignEndodontic abscesses were sampled from patients at the Oregon Health & Science University (OHSU) School of Dentistry. DNA from abscess specimens was subjected to polymerase chain reaction amplification using 16S rRNA gene-specific primers and Cy3-dCTP labeling. Labeled DNA was then applied to microbial microarrays (280 species) generated by the Human Oral Microbial Identification Microarray Laboratory (Forsyth Institute, Cambridge, MA).ResultsThe most prevalent microorganisms, found across multiple abscess specimens, include Fusobacterium nucleatum, Parvimonas micra, Megasphaera species clone CS025, Prevotella multisaccharivorax, Atopobium rimae, and Porphyromonas endodontalis. The most abundant microorganisms, found in highest numbers within individual abscesses, include F. nucleatum, P. micra, Streptococcus Cluster III, Solobacterium moorei, Streptococcus constellatus, and Porphyromonas endodontalis. Strong bacterial associations were identified between Prevotella multisaccharivorax, Acidaminococcaceae species clone DM071, Megasphaera species clone CS025, Actinomyces species clone EP053, and Streptococcus cristatus (all with Spearman coefficients >0.9).ConclusionsCultivable and uncultivable bacterial species have been identified in endodontic abscesses obtained from the Portland, Oregon demographic region, and taxa identifications correlated well with other published studies, with the exception of Treponema and Streptococcus cristae, which were not commonly identified in endodontic abscesses between the demographic region in Portland, Oregon and other regions.

TLR4, NOD1 and NOD2 mediate immune recognition of putative newly identified periodontal pathogens

Periodontitis is a polymicrobial inflammatory disease that results from the interaction between the oral microbiota and the host immunity. Although the innate immune response is important for disease initiation and progression, the innate immune receptors that recognize both classical and putative periodontal pathogens that elicit an immune response have not been elucidated. By using the Human Oral Microbe Identification Microarray (HOMIM), we identified multiple predominant oral bacterial species in human plaque biofilm that strongly associate with severe periodontitis. Ten of the identified species were evaluated in greater depth, six being classical pathogens and four putative novel pathogens. Using human peripheral blood monocytes (HPBM) and murine bone-marrow-derived macrophages (BMDM) from wild-type (WT) and Toll-like receptor (TLR)-specific and MyD88 knockouts (KOs), we demonstrated that heat-killed Campylobacter concisus, Campylobacter rectus, Selenomonas infelix, Porphyromonas endodontalis, Porphyromonas gingivalis, and Tannerella forsythia mediate high immunostimulatory activity. Campylobacter concisus, C.rectus, and S.infelix exhibited robust TLR4 stimulatory activity. Studies using mesothelial cells from WT and NOD1-specific KOs andNOD2-expressing human embryonic kidney cells demonstrated that Eubacterium saphenum, Eubacterium nodatum and Filifactor alocis exhibit robust NOD1 stimulatory activity, and that Porphyromonas endodontalis and Parvimonas micra have the highest NOD2 stimulatory activity. These studies allowed us to provide important evidence on newly identified putative pathogens in periodontal disease pathogenesis showing that these bacteria exhibit different immunostimulatory activity via TLR4, NOD1, and NOD2 (Clinicaltrials.gov NCT01154855).

Association between tobacco use and the upper gastrointestinal microbiome among Chinese men.

Tobacco causes many adverse health conditions and may alter the upper gastrointestinal (UGI) microbiome. However, the few studies that studied the association between tobacco use and the microbiome were small and underpowered. Therefore, we investigated the association between tobacco use and the UGI microbiome in Chinese men. We included 278 men who underwent esophageal cancer screening in Henan Province, China. Men were categorized as current, former, or never smokers from questionnaire data. UGI tract bacterial cells were characterized using the Human Oral Microbial Identification Microarray. Counts of unique bacterial species and genera estimated alpha diversity. For beta diversity, principal coordinate (PCoA) vectors were generated from an unweighted UniFrac distance matrix. Polytomous logistic regression models were used for most analyses. Of the 278 men in this study, 46.8% were current smokers and 12.6% were former smokers. Current smokers tended to have increased alpha diversity (mean 42.3 species) compared to never smokers (mean 38.9 species). For a 10 species increase, the odds ratio (OR) for current smoking was 1.29 (95% CI 1.04-1.62). Beta diversity was also associated with current smoking. The first two PCoA vectors were strongly associated with current smoking (PCoA1 OR 0.66; 95% CI 0.51-0.87; PCoA2 OR 0.73; 95% CI 0.56-0.95). Furthermore, Dialister invisus and Megasphaera micronuciformis were more commonly detected in current smokers than in never smokers. Current smoking was associated with both alpha and beta diversity in the UGI tract. Future work should consider how the UGI microbiome is associated with smoking-related diseases.

The oral mucosal and salivary microbial community of Behçet's syndrome and recurrent aphthous stomatitis

BackgroundBehçet's syndrome (BS) is a multisystem immune-related disease of unknown etiology. Recurrent aphthous stomatitis (RAS) is characterized by the presence of idiopathic oral ulceration without extraoral manifestation. The interplay between the oral microbial communities and the immune response could play an important role in the etiology and pathogenesis of both BS and RAS.ObjectiveTo investigate the salivary and oral mucosal microbial communities in BS and RAS.MethodsPurified microbial DNA isolated from saliva samples (54 BS, 25 healthy controls [HC], and 8 RAS) were examined by the human oral microbe identification microarray. Cultivable salivary and oral mucosal microbial communities from ulcer and non-ulcer sites were identified by matrix-assisted laser desorption/ionization time-of-flight analysis. Mycobacterium spp. were detected in saliva and in ulcer and non-ulcer oral mucosal brush biopsies following culture on Lowenstein-Jensen slopes and Mycobacterial Growth Indicator Tubes.ResultsThere was increased colonization with Rothia denticariosa of the non-ulcer sites of BS and RAS patients (p<0.05). Ulcer sites in BS were highly colonized with Streptococcus salivarius compared to those of RAS (p<0.05), and with Streptococcus sanguinis compared to HC (p<0.0001). Oral mucosa of HC were more highly colonized with Neisseria and Veillonella compared to all studied groups (p<0.0001).ConclusionsDespite the uncertainty whether the reported differences in the oral mucosal microbial community of BS and RAS are of causative or reactive nature, it is envisaged that restoring the balance of the oral microbial community of the ulcer sites may be used in the future as a new treatment modality for oral ulceration.

Biofilm community diversity after exposure to 0·4% stannous fluoride gels.

To test the effect of 0·4% stannous fluoride (SnF2 ) glycerine-based gels on specific portions of the bacterial community in both a clinical observational study and in vitro multispecies plaque-derived (MSPD) biofilm model. Potential changes to specific portions of the bacterial community were determined through the Human Oral Microbial Identification Microarray (HOMIM). Both the observational clinical study and the biofilm model showed that short-term use of 0·4% SnF2 gel has little effect on the bacterial community depicted by hierarchical cluster analysis. The amount of plaque accumulation on a subject's teeth, which was measured by plaque index scores, failed to show statistical significant changes over the two baselines or after treatment (P=0·9928). The in vitro results were similar when examining the effect of 0·4% SnF2 gels on biofilm adherence through a crystal violet assay (P=0·1157). The bacteria within the dental biofilms showed resilience in maintaining the overall community diversity after exposure to 0·4% SnF2 topical gels. The study supports that the immediate benefits of using 0·4% SnF2 gels in children may be strictly from fluoride ions inhibiting tooth demineralization rather than delivering substantial antimicrobial effects.

Bacterial Composition at the Implant-Abutment Connection under Loading in vivo.

Platform-switched implants have been demonstrated to prevent bone loss after loading. The present study evaluated bacterial composition of sites from implant-abutment connections of immediately loaded implants, which were placed in the anterior mandible. Ten patients participated in this study. A and B implant systems with two different prosthetic connections (Morse tapered vs internal polygonal butt-joint connections, respectively) were placed and loaded for 2 years. The abutments were removed (AB sample) after careful decontamination. Bacterial sampling of the abutments, inner part of the implants (before/visit 1 and after rinsing with chlorhexidine [CHX]/visit 2), and after new abutment connection and loading for 1 additional month, a new sampling (visit 3) was taken to compare the bacteria composition in association with the two connections. Bacterial profiles of samples were determined by using the human oral microbe identification microarray. A total of 240 samples were analyzed taken at different time intervals. Nonparametric statistical analysis (Wilcoxon Rank sum) with uncorrected alpha (p < .05) and after corrections (Benjamini-Hochberg) found no statistical significance between the two connections. No significant changes in the overall microbial profiles were detected at the different time intervals. However, there were trends toward presence of periodontitis-associated species at the B implants in all samples (AB, visit 1, even after CHX irrigation) and after decontamination, abutment replacement, and 1-month loading period. CHX irrigation does not seem to have any effect on decontamination of connections. As shown previously, there is significantly more bone loss around B implants compared with A implants. Although there was no statistical difference in the microbial profiles, there was indeed a trend for the presence of typical periodontal pathogens associated with the internal polygonal butt-joint connection. A possible scenario is that this connection tends to harbor the pathogens that may be involved in subsequent bone loss.

Highlights of This Issue

Yu and colleagues examined the human upper digestive tract microbial community and two cancer-predisposing states: 1) serum pepsinogen I/pepsinogen II ratio (PGI/II), a predictor of gastric cancer risk, and 2) esophageal squamous dysplasia, a precursor of esophageal squamous cell carcinoma, in a cross-sectional design. The Human Oral Microbe Identification Microarray was used to test the microbiome. Lower microbial richness in the upper digestive tract was independently associated with both cancer-predisposing states in the esophagus and stomach.Two studies in this issue focus on PAM50, a gene expression–based assay for breast cancer intrinsic subtype evaluation. In one study, Sweeney and colleagues used PAM50 to evaluate tumors and found an overall subtype distribution of 53.1% luminal A, 20.5% luminal B, 13.0% HER2-enriched, 9.8% basal-like, and 3.6% normal-like. In a second study, Caan and colleagues used PAM50 to categorize tumors and examine risks of recurrence and mortality. The PAM50 assay categorized intrinsic subtypes more accurately and better predicted recurrence and survival, compared to commonly used immunohistochemical methods.Hispanic females have the highest cervical cancer incidence rate of any racial or ethnic group in the United States. Reiter and colleagues examined human papillomavirus (HPV) vaccination uptake among a national sample of Hispanic adolescent females. Among this population, HPV vaccine initiation was 60.9%, completion was 36.0%, and follow-through was 59.1%. All vaccination outcomes were less common among participants without health insurance and vaccination did not differ by parents' preferred language. Many Hispanic females have not received the HPV vaccine, and HPV vaccination programs targeting Hispanics are needed.Although the relationship between oral contraceptive (OC) use and breast cancer risk has been studied extensively, changes in OC hormonal components and a better understanding of the heterogeneity of breast cancer warrant a new look at this relationship. Beaber and colleagues conducted a case–control study of invasive breast cancer among women in the Seattle–Puget Sound area. Lifetime duration of OC use for ≥15 years was associated with an increased breast cancer risk, and there were no statistically significant differences in risk by OC preparation. Long-term use of contemporary OCs and current use for ≥5 years was associated with an increased breast cancer risk.