This study investigated the role of interleukin-17 (IL-17) and the oral microbiome in peri-implant inflammation and bone loss under hyperglycemic and normoglycemic conditions. Wild-type (WT) and diabetic (db/db) mice with maxillary implants underwent ligature placement with or without IL-17A neutralization. Bone loss, osteoclast activity, inflammatory cytokines, Th17/Treg balance, and expression of IL-17Family members were analyzed. The oral microbiota was profiled by 16S rRNA sequencing, and its inflammatory potential was evaluated by co-culture with immune cells. Diabetic db/db mice exhibited greater peri-implant bone loss, osteoclast numbers, and RANKL/OPG ratios than WT, accompanied by elevated Il17a expression, reduced anti-inflammatory cytokines, enhanced Th17-associated inflammatory features, and altered FOXP3⁺ cell profiles. IL-17A neutralization significantly attenuated, but did not fully normalize, heightened inflammatory responses in db/db mice, whereas ligature-induced Il17f upregulation was observed only in db/db mice. Microbial alterations were partially shifted toward control profiles by IL-17A inhibition in WT mice, while diabetes-associated changes persisted regardless of ligation or anti-IL-17A. In vitro, peri-implant microbiota induced pro-inflammatory cytokine responses in splenocytes, with residual inflammatory responses remaining more evident in DB-derived microbiota after IL-17A inhibition. These findings suggest that peri-implantitis in diabetes is exacerbated by heightened IL-17-mediated inflammation and persistent microbial alterations, underscoring the need for more comprehensive therapeutic approaches to address the disease under diabetic conditions.

We announce the release of 579 pangenomes derived from 8,115 genomes curated by the Human Oral Microbiome Database, capturing shared and variable gene content across oral microbial taxa. This openly accessible resource supports both online and offline exploration, enabling systematic studies of microbial function, evolution, and community structure.

BACKGROUND:The microbiome is a dynamic system that changes throughout life. Studies have revealed the relationship between periodontal disease and the oral microbiota; however, the impact of periodontal disease on the expression of senescence markers and on the inflammaging of the oral and systemic microbiome remains unclear. We hypothesized that aging increases the periodontitis-induced changes in the oral and systemic microbiome and is accompanied by an altered inflammatory response. METHODS:Experimental periodontitis was induced in 18-month-old (old) and 8-month-old (young) C57BL/6 mice by placing ligatures around the second maxillary molars. Bone morphometric analyses were conducted to assess bone loss. Senescence- and inflammatory-related gene expression in the gingiva was measured by quantitative polymerase chain reaction (qPCR). Serum inflammatory markers were evaluated via immunoassay. Oral, brain, and gut microbial content were analyzed using next-generation sequencing. RESULTS:Maxillary bone loss was significantly higher in the old mice with periodontal disease than in young mice. Senescence and inflammatory markers were higher in old mice than in young ones, and periodontitis increased their expression. The alpha diversity of the oral and brain microbial communities differed significantly between old and young mice. Treponema denticola, Fusobacterium nucleatum, Porphyromonas gingivalis, P. pasteri, and Prevotella nigrescens were only detected in the brains of old animals with periodontitis. CONCLUSION:Periodontopathogens and oral commensals are either only found in the brains of old animals with periodontal disease or are more prevalent in the brains of old animals, suggesting that aging and periodontitis may contribute to the dissemination of oral bacteria to the brain. PLAIN LANGUAGE SUMMARY:Aging may increase the periodontitis-induced changes in the oral and systemic microbiome, which an altered inflammatory response may accompany. Experimental periodontitis was created in old and young mouse models. Bone loss, senescence, and inflammatory gene expression and serum inflammatory markers were assessed in each model, and oral, brain, and gut microbial content was analyzed. Senescence and inflammatory markers were higher in old mice than in young ones, and periodontitis increased their expression. Our results suggested that aging and periodontitis may contribute to the dissemination of oral bacteria to the brain.

Background We previously demonstrated that Streptococcus mitis exhibits anticancer properties in vitro. Here, we sought to validate these findings in vivo. Because mice from different vendors harbor distinct microbiomes that can influence disease susceptibility and experimental outcomes, we also examined whether vendor-specific oral and gut microbiomes affect oral carcinogenesis and response to S. mitis intervention.Materials and methods Oral carcinogenesis was induced using 4-NQO in C57BL/6 mice from Jackson Laboratory and Taconic Biosciences (n = 32 per vendor). Mice were randomized to biweekly oral swabbing with S. mitis or vehicle for 28 weeks. Oral and fecal microbiomes were profiled at baseline and week 8. At week 32, tongues were evaluated for tumor development.Results Oral and gut microbiomes differed significantly between vendors. 4-NQO exposure induced marked microbial shifts and partial convergence of microbiome profiles. Jackson mice developed a significantly higher squamous cell carcinoma (SCC) burden. Several microbial taxa were associated with SCC, notably Clostridium, which was enriched in oral and fecal samples from Jackson mice. S. mitis reduced SCC burden in both cohorts and was accompanied by decreased Clostridium abundance.Conclusions These data support S. mitis as a potential anticancer agent and underscore the importance of microbiome context in preclinical cancer models.

ABSTRACT Metaproteomics aims to capture a taxonomically comprehensive snapshot of proteins in a sample. Design of reference databases is a key aspect of metaproteomic workflows, as these define what is ultimately seen. Databases tailored to focal biomes offer optimal performance, yet their construction often requires drawing on heterogeneous data sources, posing a challenge to reproducibility and documentation. Here we present maniFasta, a tool enabling users to generate standardized, reproducible, and robustly documented protein reference sets from diverse input sources and datatypes. Users provide information on their desired input types and sources, and the output is an integrated database comprising a protein sequence file (FASTA), with harmonized identifiers and standardized headers, and an associated provenance metadata table (manifest). We highlight the value of maniFasta in the context of salivary metaproteomics, addressing the need for a taxonomically comprehensive reference database. The AllOralsDB resource includes human proteins, as well as proteins from bacteria and archaea, fungi and other microeukaryotes, viruses and viroid-like elements, dietary sources, and common contaminants. Together, this work provides a community resource for oral and salivary metaproteomics ( https://www.homd.org/ftp/AllOralsDB/ ), and a versatile and accessible tool for constructing protein databases for metaproteomics generally ( https://github.com/KauffmanLab/maniFasta ).

Abstract Introduction Emerging research has increasingly linked the microbiome-gut-brain axis to the pathophysiology of mental health disorders such as depression. Sleep has been linked to both depression and the oral microbiome (OM). Given these interconnections, it is plausible sleep health moderates the association between depressive symptoms and OM diversity. This study, therefore, examines whether sleep health (e.g., duration, quality, disorders) moderates the association between depressive symptom severity and OM diversity. This approach enables a nuanced understanding of how such behavioral health factors as sleep might condition the association between depression and biological systems like the OM. Methods Data were derived from the National Health and Nutrition Examination Survey (2011-2012), focusing on emerging adults (ages 18-26 years) who completed the Patient Health Questionnaire (PHQ-9). We categorized self-reported sleep duration as very short, short, healthy, or long, following AASM guidelines. Participants indicated whether they had received diagnoses of sleep disorders or reported trouble sleeping. OM richness [observed operational taxonomic units (OTUs) at the genus level; Faith’s Phylogenetic Diversity (FPD)] or richness and evenness [Shannon-Wiener diversity (SWD); inverse Simpson index (ISI)] were characterized using several alpha diversity indices. We used Generalized Linear Models to examine interactions between PHQ-9 depression scores (range:0-27) and sleep health variables in relation to microbial diversity. Results Among the 1,168 participants (mean age: 22 years), 51% were females. Moderation analysis revealed interactions between PHQ-9 scores and sleep duration categories for SWD (F3,15) =11.77; p< 0.001; OTU (F3,15) = 4.94; p=0.027; and ISI (F3,15)=3.88; p=0.031). Among participants reporting very short or short sleep durations, higher PHQ-9 scores were associated with lower OM richness and evenness. Specifically, insufficient sleep appears to exacerbate the negative link between depressive symptoms and microbial diversity, while adequate sleep may buffer against this association. Reported sleep disorders and troubles sleeping did not moderate the associations. Conclusion Among emerging adults, the direction and strength of the association between depressive symptoms and oral microbiome diversity depend on sleep duration. These findings are consistent with studies suggesting the OM may be influenced by sleep health. Future research needs to investigate the potential role of circadian rhythms in these associations. Support (if any) P20GM139743 (PI: Carskadon)

INTRODUCTION:The objective of this clinical study was to identify and compare the bacterial taxa in teeth with infected dentin (ID) and its associated root canals with symptomatic irreversible pulpitis (SIP) using high-throughput next-generation sequencing. METHODS:Teeth diagnosed with symptomatic irreversible pulpitis were included, with samples collected from infected dentin adjacent to the pulp and from the root canal. A total of 20 samples were analyzed, comprising 10 from each site. The microbiomes were examined using 16S rRNA gene amplicon sequencing. RESULTS:At the phylum level, Firmicutes predominated in ID and SIP, followed by Proteobacteria, with all samples showing consistent detection of these phyla. Actinobacteria and Bacteroidetes were also frequently detected. At the genus level, both microbial communities were dominated by Lactobacillus, followed by Streptococcus and Olsenella. At the species level, however, the shared core microbiome was represented by individual taxa belonging to several predominant genera, including Lactobacillus ultunensis, Veillonella dispar, Streptococcus salivarius, Campylobacter rectus, Streptococcus parasanguinis clade 411, Oribacterium sp. HMT-078, and Fretibacterium fastidiosum. Notably, ID samples displayed a predominance of Gram-positive bacteria, accounting for 78.9% of the oral microbiota, whereas SIP samples showed a relative enrichment of Gram-negative anaerobes, which represented 31.5% of the community. CONCLUSION:In conclusion, ID and SIP samples shared a substantial core microbiome, supporting ecological continuity along the dentin-pulp infection pathway.

AimTo investigate the impact of hyperglycemia and systemic inflammation on experimental periodontitis/peri-implantitis in diabetic mice, focusing on osteoimmunological dysregulation and oral microbial alteration.Materials and methodsAfter implant placement, diabetic db/db mice were treated with Liraglutide, Indomethacin, or both, followed by ligature-induced experimental periodontitis/peri-implantitis. Samples were analyzed for bone loss, inflammatory cytokines, osteoclast activity, RAGE expression, IL-17-associated inflammatory responses, and Treg infiltration. The periodontal/peri-implant microbiota were examined by metagenomics and tested in vitro for inflammatory cytokine induction.ResultsLiraglutide, but not indomethacin, effectively reduced bone loss, immune cell infiltration, RAGE, IL-17A expression, and restored Foxp3+ Treg presence. Post-treatment cytokine responses were slightly different between peri-implantitis sites compared to those in periodontitis sites. Oral microbiota composition from diabetic mice differed significantly from that of normoglycemic mice. Liraglutide treatment produced the greatest deviation from the ligation-only profile and shifted the microbiome toward normoglycemic control. The peri-implant microbiome was more resistant to interventions than the periodontal communities. Hyperglycemia control alleviated microbiome-induced pro-inflammatory responses in vitro.ConclusionsDiabetic hyperglycemia is a more predominant driver than systemic inflammation in exacerbating periodontitis/peri-implantitis tissue destruction, immune dysregulation, and eliciting a pro-inflammatory oral microbial environment. The local inflammatory response and microbial alteration around the tooth and implant were similar but not identical.

The oral microbiota, the second-largest microbial community in the human body, plays critical roles in systemic health and has been implicated in type 2 diabetes (T2D). To explore the potential causal pathways linking oral microbes, circulating metabolites, and T2D, we conducted a two-sample Mendelian randomization (MR) analysis using East Asian genome-wide association study (GWAS) datasets. Oral microbiome summary statistics were obtained from 2,948 individuals in CNGBdb, plasma metabolite data (136 metabolites) from a Singapore Chinese cohort, and T2D data from a large East Asian meta-analysis (25,079 cases; 29,611 controls). SNPs associated with oral microbial taxa ((p < 1×10−5) were used as instrumental variables, and causal estimates were derived primarily using inverse-variance weighting, with MR-Egger, weighted median, and MR-PRESSO as sensitivity analyses. Two-step MR identified causal effects of Gemella, Campylobacter_A, and TM7 taxa on T2D through modulation of specific acylcarnitines (e.g., C14:2, C16:1, C18:1), which increased T2D risk. Functional enrichment implicated insulin, PI3K-Akt, AMPK, TGF-$\beta$, and PPAR signaling pathways, suggesting metabolic and immune regulatory mechanisms. Genetic correlation analysis found methionine significantly correlated with T2D $(\text{rg}=0.848, \mathrm{p}=0.036)$, while colocalization provided suggestive lipid-related shared loci, particularly HexCer(d18:1/24:0) and SM(d18:1/16:0). Overall, our results indicate that specific oral microbes may promote T2D development by altering sphingolipid-related metabolism, highlighting potential mechanistic links between oral dysbiosis and metabolic dysfunction. These findings position the oral microbiome as a promising biomarker and therapeutic target in metabolic disease, underscoring the need for validation in larger and multi-ethnic cohorts.

The human mouth is densely colonized by microbial species. Evidence suggests reduced microbial diversity has been associated with chronic physical and mental health conditions; however, most of these small-scale studies have implicated the gut microbiome and involved children or adults. We examined associations of oral microbiome diversity with self-reported sleep duration among a representative sample of adolescents and young adults ages 16-26 years in the United States. This study used cross-sectional data from the National Health and Nutrition Examination Survey (NHANES, 2011-2012). Outcome variables: Oral microbiome alpha (α) diversity measures of richness and evenness: (1) Observed operational taxonomic units (OTU), (2) Faith’s phylogenetic diversity (FPD), (3) Shannon-Weiner index (SWI), and (4) Inverse Simpson index (ISI). Sleep exposure variables: self-reported sleep hours on weekdays or school/work days were categorized as very short, short, healthy, and long sleep according to AASM recommendations. Four separate Generalized Linear Models (GLM) were fitted to the sample to investigate associations between each α diversity measure and sleep duration, controlling for covariates. All descriptive and regression analyses adjusted for NHANES complex survey design. The sample included 1,332 participants, of whom 463 were ages 16-18 years, and 869 were ages 19-26 years. The mean age was 20.9 years, and 50.4% were females. Five in ten teenagers (50.6%) reported the recommended hours of sleep (8-10 hrs), while six in ten young adults (61.2%) had the recommended hours of sleep (7-9 hrs). OTU mean was 128.0 [95% CI:122.35–133.64]; FPD mean was 14.24 [13.87–14.62]; SWI mean was 4.61 [4.54–4.67]; and ISI mean was 0.90 [0.89–0.90]. Findings from GLM estimates showed that compared to those with healthy sleep duration, teenagers and young adults with long sleep duration (3% of participants) had significantly higher oral microbiome diversity, according to OTU, FPD, and SWI indicators: 43.0 [22.3–63.72]; 2.96 [1.16–4.76]; and 0.64 [0.07–1.21], respectively. No significant association was found between ISI and self-reported sleep duration. Oral microbiome diversity is positively associated with longer sleep duration among teenagers and young adults. Further research needs to determine the potential mechanisms behind the associations observed in this study. NIGMS grant #P20GM139743.

Streptococcus sanguinis is a commensal member of the oral microbiome involved in opportunistic cardiovascular infections. In the present study, we investigated the contribution of ssa_0094, a gene strongly regulated by the two-component system VicRK, to functions associated with biofilm formation, immune evasion, and cardiovascular virulence. In silico analysis showed that ssa_0094 encodes a protein with a LysM domain, which is highly conserved among S. sanguinis. Although not an ubiquitous gene, several commensal streptococcal species of the oronasopharynx and zoonotic strains of Streptococcus suis harbor ssa_0094 homologues. A ssa_0094 isogenic mutant (SK0094) showed defects in initiating biofilms on saliva-coated surfaces, reduced hydrophobicity, and lower production of amyloid-like components when compared to the parent strain (SK36) or to the complemented mutant (SK0094+), although it showed mild changes in DNA release and production of H2O2. Deletion of ssa_0094 also impaired S. sanguinis binding to multiple human glycoproteins of plasma and/or extracellular matrix (ECM) (plasminogen, fibronectin, fibrinogen, fibrin, type I collagen, and elastin) and promoted clear increases in C3b deposition and in induction of NEtosis by neutrophils of peripheral blood. Moreover, SK0094 showed impaired invasiveness into HCAEC cells and reduced ex vivo persistence in human blood, but no clear change in virulence in a Galleria mellonella infection model. These findings indicate that ssa_0094 is highly conserved within S. sanguinis strains and required for biofilm initiation as well as for multiple functions of immune evasion and cardiovascular virulence in S. sanguinis in a host-specific fashion.

Objectives: The aim of this study was to assess the taxonomic diversity of the microbiota associated with periapical lesions of endodontic origin and to determine whether microbial profiles vary across different populations and clinical characteristics using a unified in silico analysis of next-generation sequencing (NGS) data. Methods: Raw 16S rRNA sequencing data from three published studies were retrieved from the NCBI Sequence Read Archive and reprocessed using a standardized bioinformatics pipeline. Amplicon sequence variants were inferred using DADA2, and taxonomic assignments were performed using BLASTN against a curated 16S rRNA reference database. Alpha and beta diversity analyses were conducted using QIIME 2 and R, and differential abundance was assessed with ANCOM-BC2. Statistical comparisons were made based on population, sex, symptomatology, and other clinical metadata. Results: A total of 38 periapical lesion samples yielded 566,223 high-confidence reads assigned to 347 bacterial species. Significant differences in microbial composition were observed between geographic regions (China vs. Spain), sexes, and symptoms. Core species such as Fretibacterium sp. HMT 360 and Porphyromonas endodontalis were prevalent across datasets. Porphyromonas gingivalis and Fusobacterium nucleatum were found in abundance across all three studies. Beta diversity metrics revealed distinct clustering by study and country. Symptomatic lesions were associated with higher abundance of Alloprevotella tannerae and Prevotella oris. Conclusions: The periapical lesion microbiota is taxonomically diverse and varies significantly by geographic and clinical features.

BACKGROUND:Subgingival dental plaque is an ecosystem playing a key role in supporting both oral health and systemic health. Menopause-related changes have the potential to disrupt its balance, which is crucial to postmenopausal well-being. Our study explored how circulating estradiol levels correlate with subgingival microbial composition using checkerboard DNA-DNA hybridization in premenopausal and postmenopausal women. We also demonstrated that combining this method with 16S ribosomal RNA (rRNA) sequencing insights remains valuable for examining subgingival ecology. METHODS:We assessed 40 bacterial species in 77 premenopausal and 81 postmenopausal women using checkerboard DNA-DNA hybridization and measured serum estradiol with enzyme-linked immunosorbent assay (ELISA). Women were categorized by subgingival dysbiosis severity using a modified Subgingival Microbial Dysbiosis Index (mSMDI). Six women from each normobiotic and dysbiotic subgroup across premenopausal and postmenopausal women underwent 16S rRNA sequencing analysis. RESULTS:DNA checkerboard analysis revealed that most observed variability in individual bacterial proportions is associated with periodontitis. Two species, Leptotrichia buccalis and Streptococcus constellatus, exhibited differences related to estradiol levels within the premenopausal group (p = 0.055 and p = 0.009, respectively). 16S rRNA sequencing confirmed the mSMDI's validity in categorizing normobiotic and dysbiotic states. Menopausal status was not associated with a dysbiotic shift in the subgingival microbiome despite significantly more attachment loss in postmenopausal compared to premenopausal women. CONCLUSIONS:Our results indicate that decreased estradiol levels or increased attachment loss during menopause are not associated with changes in species abundance or dysbiotic shifts in women. The mSMDI may be a useful tool for classifying subgingival ecology based on its normobiotic or dysbiotic inclination. PLAIN LANGUAGE SUMMARY:The microorganisms in the oral cavity, particularly those around the teeth and gums, form a complex community known as subgingival plaque. This ecosystem is crucial for maintaining both gum health and systemic health. While disease-related (dysbiotic) subgingival plaque causes gum disease (periodontitis), periodontitis further sustains a dysbiotic subgingival plaque microbial environment. Factors such as hormone levels can potentially influence the balance between health and disease-related subgingival plaque microorganisms. We investigated whether blood estradiol levels in women affect the abundance of specific bacteria in subgingival plaque and whether menopause alters the microbial balance in this community. We found that two bacterial species, Leptotrichia buccalis and Streptococcus constellatus, were positively associated with estradiol levels, but only in premenopausal women. Despite postmenopausal women having more severe periodontitis, their subgingival microbiome did not exhibit more dysbiotic characteristics than that of premenopausal women.

Restorative dental materials can frequently extend below the gingival margin, serving as a potential haven for microbial colonization, and altering the local oral microbiome to ignite infection. However, the contribution of dental materials on driving changes of the composition of the subgingival microbiome is under-investigated. This study evaluated the microbiome-modulating properties of three biomaterials, namely resin dental composites (COM), antimicrobial piezoelectric composites (BTO), and hydroxyapatite (HA), using an optimized in vitro subgingival microbiome model derived from patients with periodontal disease. Dental materials were subjected to static or cyclic loading (mastication forces) during biofilm growth. Microbiome composition was assessed by 16S rRNA gene sequencing. Dysbiosis was measured in terms of subgingival microbial dysbiosis index (SMDI). Biomaterials subjected to cyclic masticatory loads were associated with enhanced biofilm viability except on the antibacterial composite. Biomaterials held static were associated with increased biofilm biomass, especially on HA surfaces. Overall, the microbiome richness (Chao index) was similar for all the biomaterials and loading conditions. However, the microbiome diversity (Shannon index) for the HA beams was significantly different than both composites. In addition, beta diversity analysis revealed significant differences between composites and HA biomaterials, and between both loading conditions (static and cyclic). Under static conditions, microbiomes formed over HA surfaces resulted in increased dysbiosis compared to composites through the enrichment of periopathogens, including Porphyromonas gingivalis, Porphyromonas endodontalis, and Fretibacterium spp., and depletion of commensals such as Granulicatella and Streptococcus spp. Interestingly, cyclic loading reversed the dysbiosis of microbiomes formed over HA (depletion of periopathogenes) but increased the dysbiosis of microbiomes formed over composites (enrichment of Porphyromonas gingivalis and Fusobacterim nucleatum). Comparison of species formed on both composites (control and antibacterial) showed some differences. Commercial composites enriched Selenomonas spp. and depleted Campylobacter concisus. Piezoelectric composites effectively controlled the microbiome viability without significantly impacting the species abundance. Findings of this work open new understandings of the effects of different biomaterials on the modulation of oral biofilms and the relationship with oral subgingival infections.

BACKGROUND:Children affected by severe early childhood caries (S-ECC) usually need comprehensive caries treatment due to the extensive of caries. How the oral microbiome changes after caries therapy within the short-term warrant further study. AIM:This study aimed to investigate the short-term impact of comprehensive caries treatment on the supragingival plaque microbiome of S-ECC children. DESIGN:Thirty-three children aged 2-4 years with severe caries (dt > 7) were recruited. Comprehensive caries treatment was performed under general anesthesia in one session and included restoration, pulp treatment, extraction, and fluoride application. Supragingival plaque was sampled pre- and 1-month posttreatment. The genomic DNA of the supragingival plaque was extracted, and bacterial 16S ribosomal RNA gene sequencing was performed. RESULTS:Our data showed that the microbial community evenness significantly decreased posttreatment. Furthermore, comprehensive caries treatment led to more diverse microbial structures among the subjects. The interbacterial interactions reflected by the microbial community's co-occurrence network tended to be less complex posttreatment. Caries treatment increased the relative abundance of Corynebacterium matruchotii, Corynebacterium durum, Actinomyces naeslundii, and Saccharibacteria HMT-347, as well as Aggregatibacter HMT-458 and Haemophilus influenzae. Meanwhile, the relative abundance of Streptococcus mutans, three species from Leptotrichia, Neisseria bacilliformis, and Provotella pallens significantly decreased posttreatment. CONCLUSION:Our results suggested that comprehensive caries treatment may contribute to the reconstruction of a healthier supragingival microbiome.

Background Porphyromonas gingivalis (hereafter “ Pg ”) is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg . Insights into the factors shaping the striking strain-level variation in Pg , and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. One of the key forces often shaping strain-level diversity in microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg . Results Here we systematically addressed the question of whether Pg are infected by phages—and we found that they are. We found that prophages are common in Pg , they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg , and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain-level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures. Conclusion This work definitively establishes that phages are a major unrecognized force shaping the ecology and intra-species strain-level diversity of the well-studied oral pathogen Pg . The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg , and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly.

BACKGROUND:Periodontitis is primarily driven by subgingival biofilm dysbiosis. However, the quantification and impact of this periodontal dysbiosis on other oral microbial niches remain unclear. This study seeks to quantify the dysbiotic changes in tongue and salivary microbiomes resulting from periodontitis by applying a clinically relevant dysbiosis index to an integrated data analysis. METHODS:The National Center for Biotechnology Information (NCBI) database was searched to identify BioProjects with published studies on salivary and tongue microbiomes of healthy and periodontitis subjects. Raw sequence datasets were processed using a standardized bioinformatic pipeline and categorized by their ecological niche and periodontal status. The subgingival microbial dysbiosis index (SMDI), a dysbiosis index originally developed using the subgingival microbiome, was computed at species and genus levels and customized for each niche. Its diagnostic accuracy for periodontitis was evaluated using receiver operating characteristic curves. RESULTS:Four studies, contributing 328 microbiome samples, were included. At both species and genus levels, periodontitis samples had a higher SMDI, but the differences were only significant for subgingival biofilm and saliva (p < 0.001). However, SMDI showed good diagnostic accuracy for periodontitis status for all three niches (area under curve ranging from 0.76 to 0.90, p < 0.05). The dysbiosis index of subgingival biofilm was positively correlated with saliva consistently (p < 0.001) and with the tongue at the genus level (p = 0.036). CONCLUSIONS:While the impact on the tongue microbiome requires further investigation, periodontitis-associated dysbiosis affects the salivary microbiome and is quantifiable using the dysbiosis index. The diagnostic potential of salivary microbial dysbiosis as a convenient periodontal biomarker for assessing periodontal status has potential public health and clinical applications. PLAIN LANGUAGE SUMMARY:Periodontitis, a severe inflammation of the gums which causes bone loss, is a disease caused by an imbalance of good and bad bacteria under the gums. However, it is unclear how this bacterial imbalance in the gums affects the bacterial balance of other distinct parts of the mouth, such as the saliva and tongue. This study uses bacteria datasets of four previously published studies, contributing a total of 328 bacterial samples. The data were processed using a uniform data analysis workflow, and a bacterial score, the subgingival microbial dysbiosis index (SMDI), previously shown to capture periodontitis-associated bacteria imbalance, was calculated separately for samples from under the gums, the saliva, and the tongue. The SMDI was able to distinguish between health and periodontitis within each oral location, and in general, the scores were higher for periodontitis samples, though this difference was significant only for bacteria under the gums and in saliva. Saliva scores were also consistently correlated with bacteria under the gums. This study shows that periodontitis-associated bacterial imbalances are observed in oral locations beyond just under the gums, particularly the saliva. Thus, saliva bacteria may be used as a convenient biomarker for assessing gum disease, allowing for potential public health and clinical applications.

The oral cavity may play a role as a reservoir and in the transmission and colonization of Helicobacter pylori. The route of transmission for H. pylori is not fully understood. The prevalence of this pathogen varies globally, affecting half of the world’s population, predominantly in developing countries. Here, we review the prevalence of H. pylori in the oral cavity, the characteristics that facilitate its colonization and dynamics in the oral microbiome, the heterogeneity and diversity of virulence of among strains, and noninvasive techniques for H. pylori detection in oral samples. The prevalence of H. pylori in the oral cavity varies greatly, being influenced by the characteristics of the population, regions where samples are collected in the oral cavity, and variations in detection methods. Although there is no direct association between the presence of H. pylori in oral samples and stomach infection, positive cases for gastric H. pylori frequently exhibit a higher prevalence of the bacterium in the oral cavity, suggesting that the stomach may not be the sole reservoir of H. pylori. In the oral cavity, H. pylori can cause microbiome imbalance and remodeling of the oral ecosystem. Detection of H. pylori in the oral cavity by a noninvasive method may provide a more accessible diagnostic tool as well as help prevent transmission and gastric re-colonization. Further research into this bacterium in the oral cavity will offer insights into the treatment of H. pylori infection, potentially developing new clinical approaches.

Background: Fusobacterium nucleatum, a pathobiont in periodontal disease, contributes to alveolar bone destruction. We assessed the efficacy of a new targeted antimicrobial, FP-100, in eradicating F. nucleatum from the oral microbial community in vitro and in vivo and evaluated its effectiveness in reducing bone loss in a mouse periodontitis model. Methods: A multispecies bacterial community was cultured and treated with two concentrations of FP-100 over two days. Microbial profiles were examined at 24-h intervals using 16S rRNA sequencing. A ligature-induced periodontitis mouse model was employed to test FP-100 in vivo. Results: FP-100 significantly reduced Fusobacterium spp. within the in vitro community (p < 0.05) without altering microbial diversity at a 2 mu M concentration. In mice, cultivable F. nucleatum was undetectable in FP-100-treated ligatures but persistent in controls. Beta diversity plots showed distinct microbial structures between treated and control mice. Alveolar bone loss was significantly reduced in the FP-100 group (p = 0.018), with concurrent decreases in gingival IL-1 beta and TNF-alpha expression (p = 0.052 and 0.018, respectively). Conclusion: FP-100 effectively eliminates F. nucleatum from oral microbiota and significantly reduces bone loss in a mouse periodontitis model, demonstrating its potential as a targeted therapeutic agent for periodontal disease.

Periodontal disease is common among older adults, with around 50% of all adults aged 30 years and older having some form of gum disease. Although the disease might seem minor, without early or proper diagnosis, the disease can affect all supporting structures of the teeth, including gums, periodontal ligament, and alveolar bone. This research can help find patterns common among people with periodontal disease and possibly prevent the effects of it in the elderly. Here, we explored the deep learning capabilities of convolutional neural networks (CNN) and VGG16 models for detecting disease-associated patterns derived from 16S rRNA gene sequences of plaque samples. The CNN model achieved a 90.2% accuracy for differentiating periodontal disease from health samples, with 76% precision and 86% recall. This model could lead to earlier detection and more effective treatment of periodontal disease, ultimately improving patients’ dental health outcomes and quality of life.