Dysbiosis in chronic periodontitis: Key microbial players and interactions with the human host

HIV Infection and Exposure Increases Cariogenic Taxa, Reduces Taxonomic Turnover, and Homogenizes Spatial Differentiation for the Supragingival Microbiome

Background

The oral microbiome comprises distinct microbial communities that colonize diverse ecological niches across the oral cavity, the composition of which are influenced by nutrient and substrate availability, host genetics, diet, behavior, age, and other diverse host and environmental factors. Unlike other densely populated human-associated microbial ecosystems (e.g., gut, urogenital), the oral microbiome is regularly and directly exposed to the external environment and is therefore likely less stable over time. Cross sectional studies of the oral microbiome capture a glimpse of this temporal dynamism, yet a full appreciation of the relative stability, robusticity, and spatial structure of the oral environment is necessary to understand the role of microbial communities in promoting health or disease.

Results

Here we investigate the spatial and temporal stability of the oral microbiome over three sampling time points in the context of HIV infection and exposure. Individual teeth were sampled from a cohort of 565 Nigerian children with varying levels of tooth decay severity (i.e., caries disease). We collected 1,960 supragingival plaque samples and characterized the oral microbiome using a metataxonomic approach targeting an approximately 478 bp region of the bacterial rpoC gene. We found that both infection and exposure to HIV have significant effects on the stability of the supragingival plaque microbiome at both the spatial and temporal scale. Specifically, we detect (1) significantly lower taxonomic turnover of the oral community among exposed and infected children compared to unexposed children, (2) we find that HIV infection homogenizes the oral community across the anterior and posterior dentition, and (3) that impaired immunity (i.e., low CD4 count) and low taxonomic turnover over time in children living with HIV is associated with higher frequency of cariogenic taxa including Streptococcus mutans.

Conclusions

Our results document substantial community fluctuations over time in children unexposed to HIV independent of oral health status. This suggests that the oral community, under typical conditions, rapidly adapts to environmental perturbations to maintain homeostasis and that long-term taxonomic rigidity is a signal of community dysfunction, potentially leading to a higher incidence of oral disease including caries.

Differential Patterns of Gut and Oral Microbiomes in Hispanic Individuals with Cognitive Impairment

Alzheimer's disease and related dementias (ADRD) have been associated with alterations in both oral and gut microbiomes. While extensive research has focused on the role of gut dysbiosis in ADRD, the contribution of the oral microbiome remains relatively understudied. Furthermore, the potential synergistic interactions between oral and gut microbiomes in ADRD pathology are largely unexplored. This study aims to evaluate distinct patterns and potential synergistic effects of oral and gut microbiomes in a cohort of predominantly Hispanic individuals with cognitive impairment (CI) and without cognitive impairment (NC). We conducted 16S rRNA gene sequencing on stool and saliva samples from 32 participants (17 CI, 15 NC; 62.5% female, mean age = 70.4 ± 6.2 years) recruited in San Antonio, Texas, USA. Correlation analysis through MaAslin2 assessed the relationship between participants' clinical measurements (e.g., fasting glucose and blood cholesterol) and their gut and saliva microbial contents. Differential abundance analysis evaluated taxa with significant differences between CI and NC groups, and alpha and beta diversity metrics assessed within-sample and group compositional differences. Our analyses revealed no significant differences between NC and CI groups in fasting glucose or blood cholesterol levels. However, a clear association was observed between gut microbiome composition and levels of fasting glucose and blood cholesterol. While alpha and beta diversity metrics showed no significant differences between CI and NC groups, differential abundance analysis revealed an increased presence of oral genera such as Dialister , Fretibacterium , and Mycoplasma in CI participants. Conversely, CI individuals exhibited a decreased abundance of gut genera, including Shuttleworthia , Holdemania , and Subdoligranulum , which are known for their anti-inflammatory properties. No evidence was found for synergistic contributions between oral and gut microbiomes in the context of ADRD. Our findings suggest that similar to the gut microbiome, the oral microbiome undergoes significant modifications as individuals transition from NC to CI. Notably, the identified oral microbes have been previously associated with periodontal diseases and gingivitis. These results underscore the necessity for further investigations with larger sample sizes to validate our findings and elucidate the complex interplay between oral and gut microbiomes in ADRD pathogenesis.

Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy

Acute coronary syndrome (ACS) is a predominant cause of mortality, and the prompt and precise identification of this condition is crucial to minimize its impact. Recent research indicates that gut microbiota is associated with the onset, progression, and treatment of ACS. To investigate its role, we sequenced the gut microbiota of 38 ACS patients before and after percutaneous coronary intervention and statin therapy at three time points, examining differential species and metabolic pathways. We observed a decrease in the abundance of Parabacteroides, Escherichia, and Blautia in patients after treatment and an increase in the abundance of Gemalla, Klebsiella variicola, Klebsiella pneumoniae, and others. Two pathways related to sugar degradation were more abundant in patients before treatment, possibly correlated with disorders of sugar metabolism and risk factors, such as hyperglycemia, insulin resistance, and insufficient insulin secretion. Additionally, seven pathways related to the biosynthesis of vitamin K2 and its homolog were reduced after treatment, suggesting that ACS patients may gradually recover after therapy. The gut microbiota of patients treated with different statins exhibited notable differences after treatment. Rosuvastatin appeared to promote the growth of anti-inflammatory bacteria while reducing pro-inflammatory bacteria, whereas atorvastatin may have mixed effects on pro-inflammatory and anti-inflammatory bacteria while increasing the abundance of Bacteroides. Our research will provide valuable insights and enhance comprehension of ACS, leading to better patient diagnosis and therapy.

Dysbiosis and interactions of the mycobiome and bacteriome in mucosal lesions of erosive and non-erosive oral lichen planus patients

Background

Oral lichen planus (OLP) is a common oral mucosal disease, clinically categorized into erosive OLP (EOLP) and non-erosive OLP (NEOLP) based on symptoms, but its pathogenic mechanism remains unclear. This study aims to explore the relationship between OLP and the oral microbiome.

Methods

We collected oral mucosal samples from 49 patients and 10 healthy individuals and conducted 16S rRNA and ITS gene sequencing to explore the oral fungal and bacterial communities.

Results

We observed significantly lower α diversity of fungi in the EOLP group, with Candida being significantly enriched as the main dominant genus. In the NEOLP group, Aspergillaceae were significantly enriched. The EOLP group showed significant enrichment of Aggregatibacter and Lactobacillus, but the relative abundance of Streptococcus was notably lower than in the other two groups. In the NEOLP group, two species including Prevotella intermedia were significantly enriched. The microbial co-occurrence and co-exclusion networks display distinct characteristics across the three groups, with Lactobacillus assuming a significant bridging role in the ELOP group.

Conclusions

Our study indicates that EOLP and NEOLP experience varying degrees of dysbiosis at both the fungal and bacterial levels. Therefore, the pathogenic mechanisms and interactive relationships of these microbiota associated with OLP merit further in-depth investigation.

Impact of the gut microbiome on response and toxicity to chemotherapy in advanced esophageal cancer

Objective

To identify the gut bacteria associated with chemotherapeutic outcomes, t characterized the gut microbiota in patients with esophageal squamous cell carcinoma (ESCC) in this prospective study.

Design

Thirty-one patients with ESCC were enrolled. Chemotherapy was performed with paclitaxel and cisplatin (TP). Fecal samples were collected before and after treatment and analyzed using 16S rRNA sequencing.

Results

The species with differences in baseline abundance between partial response (PR) and non-PR groups was identified as Bacteroides plebeius (P = 0.043). The baseline abundance of B. plebeius was higher in the responder (R, PR + stable disease (SD)) group (P = 0.045) than in the non-responder (NR). The abundance of B. ovatus was identified as a predictor for distinguishing patients with PR from those without PR (sensitivity, 83.3 %; specificity, 69.6 %). The abundance of B. plebeius was positively associated with the response to PR + SD (R) in predicting responders in the receiver operating characteristic (ROC) curve analysis (area under the ROC curve = 0.865, P = 0.041). The abundance of B. plebeius and B.uniform was a predictor of grade (G) 3-4 chemotherapy toxicities. The sensitivity and specificity of the established multi-analyte microbial predictive model demonstrated a better predictive ability than a single parameter (B. uniform or B. plebeius).

Conclusion

The abundance of gut microbiota B. plebeius and B. ovatus are associated with the efficacy of TP chemotherapy in patients with ESCC. The abundance of B. plebeius and B.uniform may related to the toxicity of TP chemotherapy.

Hemophore-like proteins of the HmuY family in the oral and gut microbiome: unraveling the mystery of their evolution

SUMMARY

Heme (iron protoporphyrin IX, FePPIX) is the main source of iron and PPIX for host-associated pathogenic bacteria, including members of the Bacteroidota (formerly Bacteroidetes) phylum. Porphyromonas gingivalis, a keystone oral pathogen, uses a unique heme uptake (Hmu) system, comprising a hemophore-like protein, designated as the first member of the novel HmuY family. Compared to classical, secreted hemophores utilized by Gram-negative bacteria or near-iron transporter domain-based hemophores utilized by Gram-positive bacteria, the HmuY family comprises structurally similar proteins that have undergone diversification during evolution. The best characterized are P. gingivalis HmuY and its homologs from Tannerella forsythia (Tfo), Prevotella intermedia (PinO and PinA), Bacteroides vulgatus (Bvu), and Bacteroides fragilis (BfrA, BfrB, and BfrC). In contrast to the two histidine residues coordinating heme iron in P. gingivalis HmuY, Tfo, PinO, PinA, Bvu, and BfrA preferentially use two methionine residues. Interestingly, BfrB, despite conserved methionine residue, binds the PPIX ring without iron coordination. BfrC binds neither heme nor PPIX in keeping with the lack of conserved histidine or methionine residues used by other members of the HmuY family. HmuY competes for heme binding and heme sequestration from host hemoproteins with other members of the HmuY family to increase P. gingivalis competitiveness. The participation of HmuY in the host immune response confirms its relevance in relation to the survival of P. gingivalis and its ability to induce dysbiosis not only in the oral microbiome but also in the gut microbiome or other host niches, leading to local injuries and involvement in comorbidities.

Screening for Selenomonas noxia in a Pediatric and Adolescent Patient Population Reveals Differential Oral Prevalence across Age Groups

Selenomonas noxia, a gram-negative anaerobe usually present in periodontitis, may be linked to overweight and obese adults. Recent advancements include a valid qPCR screening, enabling an effective prevalence study among pediatric patients aged 7 to 17 years. The aim of this study was to complete a retrospective screening of saliva samples from an existing biorepository using a validated qPCR screening protocol. The pediatric study sample (n = 87) comprised nearly equal numbers of males and females, mostly minority patients (67%), with an average age of 13.2 years. Screening for Selenomonas noxia revealed 34.4% (n = 30/87) positive samples, evenly distributed between males and females (p = 0.5478). However, an age-dependent association was observed with higher percentages of positive samples observed with higher ages (13.3% among 7 to 10 years; 34.6% among 11 to 13 years; 54.8% among 14-17 years), which was statistically significant (p = 0.0001). Although these findings revealed no noteworthy distinctions between males or females and minorities and non-minorities, the notable contrast between younger (7 to 10 years) and older (11 to 17 years) participants, possibly influenced by factors such as hormones and behavioral traits, will require further investigation of this patient population.

Comparative analysis of Porphyromonas gingivalis A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems

Porphyromonas gingivalis strains exhibit different phenotypes in vitro, different virulence potential in animal models, and different associations with human diseases, with strains classified as virulent/more virulent (e.g., A7436 and W83) or as less virulent/avirulent (e.g., ATCC 33277). In this study, we comparatively analyzed the A7436 and ATCC 33277 strains to better understand their variability. Global gene expression analysis in response to heme and iron limitation revealed more pronounced differences in the A7436 than in the ATCC 33277 strain; however, in both strains, the largest changes were observed in genes encoding hypothetical proteins, genes whose products participate in energy metabolism, and in genes encoding proteins engaged in transport and binding proteins. Our results confirmed that variability between P. gingivalis strains is due to differences in the arrangement of their genomes. Analysis of gene expression of heme acquisition systems demonstrated that not only the availability of iron and heme in the external environment but also the ability to store iron intracellularly can influence the P. gingivalis phenotype. Therefore, we assume that differences in virulence potential may also be due to differences in the production of systems involved in iron and heme acquisition, mainly the Hmu system. In addition, our study showed that hemoglobin, in a concentration-dependent manner, differentially influences the virulence potential of P. gingivalis strains. We conclude that iron and heme homeostasis may add to the variability observed between P. gingivalis strains.

IMPORTANCE

Periodontitis belongs to a group of multifactorial diseases, characterized by inflammation and destruction of tooth-supporting tissues. P. gingivalis is one of the most important microbial factors involved in the initiation and progression of periodontitis. To survive in the host, the bacterium must acquire heme as a source of iron and protoporphyrin IX. P. gingivalis strains respond differently to changing iron and heme concentrations, which may be due to differences in the expression of systems involved in iron and heme acquisition. The ability to accumulate iron intracellularly, being different in more and less virulent P. gingivalis strains, may influence their phenotypes, production of virulence factors (including proteins engaged in heme acquisition), and virulence potential of this bacterium.

The oral microbiome: diversity, biogeography and human health

The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.

The impact of arthritogenic viruses in oral tissues

Arthritis and periodontitis are inflammatory diseases that share several immunopathogenic features. The expansion in the study of virus-induced arthritis has shed light on how this condition could impact other parts of the human body, including the mouth. Viral arthritis is an inflammatory joint disease caused by several viruses, most notably the alphaviruses Chikungunya virus (CHIKV), Sindbis virus (SINV), Ross River virus (RRV), Mayaro virus (MAYV), and O'nyong'nyong virus (ONNV). These viruses can induce an upsurge of matrix metalloproteinases and immune-inflammatory mediators such as Interleukin-6 (IL6), IL-1β, tumor necrosis factor, chemokine ligand 2, and receptor activator of nuclear factor kappa-B ligand in the joint and serum of infected individuals. This can lead to the influx of inflammatory cells to the joints and associated muscles as well as osteoclast activation and differentiation, culminating in clinical signs of swelling, pain, and bone resorption. Moreover, several data indicate that these viral infections can affect other sites of the body, including the mouth. The human oral cavity is a rich and diverse microbial ecosystem, and viral infection can disrupt the balance of microbial species, causing local dysbiosis. Such events can result in oral mucosal damage and gingival bleeding, which are indicative of periodontitis. Additionally, infection by RRV, CHIKV, SINV, MAYV, or ONNV can trigger the formation of osteoclasts and upregulate pro-osteoclastogenic inflammatory mediators, interfering with osteoclast activation. As a result, these viruses may be linked to systemic conditions, including oral manifestations. Therefore, this review focuses on the involvement of alphavirus infections in joint and oral health, acting as potential agents associated with oral mucosal inflammation and alveolar bone loss. The findings of this review demonstrate how alphavirus infections could be linked to the comorbidity between arthritis and periodontitis and may provide a better understanding of potential therapeutic management for both conditions.

Metagenomic analysis of healthy and diseased peri-implant microbiome under different periodontal conditions: a cross-sectional study

BACKGROUND

Peri-implantitis is a polybacterial infection that can lead to the failure of dental implant rehabilitation. This study aimed to profile the microbiome of the peri-implant plaque and estimate the effect of periodontitis on it among 40 Chinese participants with dental implant prostheses and presenting with varying peri-implant and periodontal health states.

METHODS

Submucosal plaque samples were collected from four distinct clinical categories based on both their implant and periodontal health status at sampling point. Clinical examinations of dental implant and remaining teeth were carried out. Metagenomic analysis was then performed.

RESULTS

The microbiome of the peri-implantitis sites differed from that of healthy implant sites, both taxonomically and functionally. Moreover, the predominant species in peri-implantitis sites were slightly affected by the presence of periodontitis. T. forsythia, P. gingivalis, T. denticola, and P. endodontalis were consistently associated with peri-implantitis and inflammatory clinical parameters regardless of the presence of periodontitis. Prevotella spp. and P. endodontalis showed significant differences in the peri-implantitis cohorts under different periodontal conditions. The most distinguishing function between diseased and healthy implants is related to flagellar assembly, which plays an important role in epithelial cell invasion.

CONCLUSIONS

The composition of the peri-implant microbiome varied in the diseased and healthy states of implants and is affected by individual periodontal conditions. Based on their correlations with clinical parameters, certain species are associated with disease and healthy implants. Flagellar assembly may play a vital role in the process of peri-implantitis.

The oral microbial odyssey influencing chronic metabolic disease

INTRODUCTION

Since the oral cavity is the gateway to the gut, oral microbes likely hold the potential to influence metabolic disease by affecting the gut microbiota.

METHOD

A thorough review of literature has been performed to link the alterations in oral microbiota with chronic metabolic disease by influencing the gut microbiota.

RESULT

A strong correlation exists between abnormalities in oral microbiota and several systemic disorders, such as cardiovascular disease, diabetes, and obesity, which likely initially manifest as oral diseases. Ensuring adequate oral hygiene practices and cultivating diverse oral microflora are crucial for the preservation of general well-being. Oral bacteria have the ability to establish and endure in the gastrointestinal tract, leading to the development of prolonged inflammation and activation of the immune system. Oral microbe-associated prophylactic strategies could be beneficial in mitigating metabolic diseases.

CONCLUSION

Oral microbiota can have a profound impact on the gut microbiota and influence the pathogenesis of metabolic diseases.

A novel plasmonic optical-fiber-based point-of-care test for periodontal MIP-1α detection

The analysis of salivary biomarkers as expression of periodontal health conditions has been proposed as a useful aid to conventional diagnostic approaches. In this study, we present a point-of-care test (POCT) exploiting a surface plasmon resonance (SPR)-based optical biosensor to detect salivary macrophage inflammatory protein (MIP)-1α, a promising marker of periodontitis. A plastic optical fiber (POF) was suitably modified and functionalized by an antibody self-assembled monolayer against MIP-1α for plasmonic detection. The proposed SPR-POF biosensor showed high selectivity and very low limit of detection for MIP-1α of 129 fM (1.0 pg/mL) in phosphate-buffered saline and 346 fM (2.7 pg/mL) in saliva. As a proof of concept, this POCT was also able to discriminate between a periodontitis patient and a healthy subject. The obtained results support the future application of this technology for an on-site detection and real-time monitoring of periodontal health conditions for diagnostic and therapeutic purposes.

Gut microbiota interacts with inflammatory responses in acute pancreatitis

Acute pancreatitis (AP) is one of the most common acute abdominal conditions, and its incidence has been increasing for years. Approximately 15-20% of patients develop severe AP (SAP), which is complicated by critical inflammatory injury and intestinal dysfunction. AP-associated inflammation can lead to the gut barrier and function damage, causing dysbacteriosis and facilitating intestinal microbiota migration. Pancreatic exocrine deficiency and decreased levels of antimicrobial peptides in AP can also lead to abnormal growth of intestinal bacteria. Meanwhile, intestinal microbiota migration influences the pancreatic microenvironment and affects the severity of AP, which, in turn, exacerbates the systemic inflammatory response. Thus, the interaction between the gut microbiota (GM) and the inflammatory response may be a key pathogenic feature of SAP. Treating either of these factors or breaking their interaction may offer some benefits for SAP treatment. In this review, we discuss the mechanisms of interaction of the GM and inflammation in AP and factors that can deteriorate or even cure both, including some traditional Chinese medicine treatments, to provide new methods for studying AP pathogenesis and developing therapies.

Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis

In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes in the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.

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

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

Transmission of fungi and protozoa under grazing conditions from lactating yaks to sucking yak calves in early life

Microbiota from mothers is an essential source of microbes in early-life rumen microbiota, but the contribution of microbiota from different maternal sites to the rumen microbiota establishment in neonates needs more data. To fill this gap, we collected samples from the mouth, teat skin, and rumen of lactating yaks and from the rumen of sucking calves concomitantly on seven occasions between days 7 and 180 after birth under grazing conditions. We observed that the eukaryotic communities clustered based on sample sites, except for the protozoal community in the teat skin, with negative correlations between fungal and protozoal diversities in the rumen of calves. Furthermore, fungi in the dam's mouth, which is the greatest source of the calf's rumen fungi, accounted for only 0.1%, and the contribution of the dam's rumen to the calf's rumen fungi decreased with age and even disappeared after day 60. In contrast, the average contribution of the dam's rumen protozoa to the calf's rumen protozoa was 3.7%, and the contributions from the dam's teat skin (from 0.7 to 2.7%) and mouth (from 0.4 to 3.3%) increased with age. Thus, the divergence in dam-to-calf transmissibility between fungi and protozoa indicates that the foundation of these eukaryotic communities is shaped by different rules. This study provides the first measurements of the maternal contribution to the fungal and protozoal establishment in the rumen of sucking and grazing yak calves in early life, which could be beneficial for future microbiota manipulation in neonatal ruminants. KEY POINTS: • Dam to calf transfer of rumen eukaryotes occurs from multiple body sites. • A minor proportion of rumen fungi in calves originated from maternal sites. • The inter-generation transmission between rumen fungi and protozoa differs.

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.

Hemophore-like proteins produced by periodontopathogens are recognized by the host immune system and react differentially with IgG antibodies

Aims

Hemophore-like proteins sequester heme from host hemoproteins. We aimed to determine whether the host immune system can recognize not only Porphyromonas gingivalis HmuY but also its homologs expressed by other periodontopathogens, and how periodontitis influences the production of respective antibodies.

Methods

The reactivity of total bacterial antigens and purified proteins with serum IgG antibodies of 18 individuals with periodontitis and 17 individuals without periodontitis was examined by enzyme-linked immunosorbent assay (ELISA). To compare IgG reactivity between groups with and without periodontitis and within the various dilutions of sera, statistical analysis was performed using the Mann-Whitney U-test and two-way ANOVA test with the post-hoc Bonferroni test.

Results

Individuals with periodontitis produced IgG antibodies reacting more strongly not only with total P. gingivalis antigens (P = 0.0002; 1:400) and P. gingivalis HmuY (P = 0.0016; 1:100) but also with Prevotella intermedia PinA (P = 0.0059; 1:100), and with low efficiency with P. intermedia PinO (P = 0.0021; 1:100). No increase in the reactivity of IgG antibodies with Tannerella forsythia Tfo and P. gingivalis HusA was found in individuals with periodontitis.

Conclusions

Although hemophore-like proteins are structurally related, they are differentially recognized by the host immune system. Our findings point to specific antigens, mainly P. gingivalis HmuY and P. intermedia PinA, whose immunoreactivity could be further investigated to develop markers of periodontitis.

Pilot Study on the Prevalence of Entamoeba gingivalis in Austria-Detection of a New Genetic Variant

Entamoeba gingivalis is a parasitic protist that resides in the oral cavity. Although E. gingivalis has been frequently detected in individuals with periodontitis, its precise role in this context remains to be established, since E. gingivalis is also regularly found in healthy individuals. Sequence data on E. gingivalis are still scarce, with only a limited number of sequences available in public databases. In this study, a diagnostic PCR protocol was established in order to obtain a first impression on the prevalence of E. gingivalis in Austria and enable a differentiation of isolates by targeting the variable internal transcribed spacer regions. In total, 59 voluntary participants were screened for E. gingivalis and almost 50% of the participants were positive, with a significantly higher prevalence of participants with self-reported gingivitis. Moreover, in addition to the established subtypes ST1 and ST2, a potentially new subtype was found, designated ST3. 18S DNA sequencing and phylogenetic analyses clearly supported a separate position of ST3. Interestingly, subtype-specific PCRs revealed that, in contrast to ST2, ST3 only occurred in association with ST1. ST2 and ST1/ST3 were more often associated with gingivitis; however, more data will be necessary to corroborate this observation.

Porphyromonas gingivalis induction of TLR2 association with Vinculin enables PI3K activation and immune evasion

Porphyromonas gingivalis is a Gram-negative anaerobic bacterium that thrives in the inflamed environment of the gingival crevice, and is strongly associated with periodontal disease. The host response to P. gingivalis requires TLR2, however P. gingivalis benefits from TLR2-driven signaling via activation of PI3K. We studied TLR2 protein-protein interactions induced in response to P. gingivalis, and identified an interaction between TLR2 and the cytoskeletal protein vinculin (VCL), confirmed using a split-ubiquitin system. Computational modeling predicted critical TLR2 residues governing the physical association with VCL, and mutagenesis of interface residues W684 and F719, abrogated the TLR2-VCL interaction. In macrophages, VCL knock-down led to increased cytokine production, and enhanced PI3K signaling in response to P. gingivalis infection, effects that correlated with increased intracellular bacterial survival. Mechanistically, VCL suppressed TLR2 activation of PI3K by associating with its substrate PIP2. P. gingivalis induction of TLR2-VCL led to PIP2 release from VCL, enabling PI3K activation via TLR2. These results highlight the complexity of TLR signaling, and the importance of discovering protein-protein interactions that contribute to the outcome of infection.

Role of ubiquitin-specific protease 5 in the inflammatory response of chronic periodontitis

BACKGROUND

The systemic inflammatory response caused by chronic periodontitis is a risk factor for multiple diseases. Ubiquitin-specific protease 5 (USP5) is a kind of deubiquitinase which mainly responsible for dissociating unanchored polyubiquitin. However, the functions of USP5 in chronic periodontitis have not been reported.

METHODS

Chronic periodontitis patients were recruited, and their periodontal samples were collected. The levels of USP5, tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and interleukin-1β (IL-1β) in gingival crevicular fluid were evaluated by ELISA. The expression of USP5, TNF-α, IL-6, and IL-1β in human periodontal ligament stem cells (PDLSCs) was estimated by qRT-PCR assay. The activation of STAT3 signaling was examined by Western blot.

RESULTS

USP5 was upregulated in the gingival crevicular fluid and gingival tissues of chronic periodontitis patients. USP5 expression was positively correlated with the expression of proinflammatory factors. USP5 knockdown and deubiquitinase inhibitor inhibited LPS-induced inflammatory responses in PDLSCs. Suppressing USP5 inhibited STAT3 signaling in PDLSCs.

CONCLUSION

Suppression deubiquitinase USP5 inhibits the inflammatory response of chronic periodontitis by suppressing STAT3 signaling.

Correlation of Redondovirus and Entamoeba gingivalis Detections in the Human Oral Cavity Suggests That This Amoeba Is Possibly the Redondovirus Host

The virome of the human oral cavity and the relationships between viruses and diseases such as periodontitis are scarcely deciphered. Redondoviruses were reported in the human oral cavity in 2019, including in periodontitis patients. Here, we aimed at detecting redondoviruses and at searching for a potential viral host in human saliva. Non-stimulated saliva was collected between December 2020 and June 2021. These samples were tested using real-time PCR regarding the presence of redondovirus and Entamoeba gingivalis DNA. Similarity searches were performed using BLAST against eukaryotic and prokaryotic sequences from GenBank. The redondovirus DNA was detected in 46% of the 28 human saliva samples. In addition, short fragments of redondovirus genomes were detected in silico within Entamoeba sequences. Finally, Entamoeba gingivalis DNA was detected in 46% of the 28 saliva samples, with a strong correlation between redondovirus DNA and E. gingivalis DNA detections, in 93% of the cases. Regarded together, these findings and previous ones strongly support the presence of redondoviruses in the human oral cavity and their association to E. gingivalis as their likely host.

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea

BACKGROUND

Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.

RESULTS

A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively.

CONCLUSIONS

Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.

Periodontal Disease Pathogens, Pathogenesis, and Therapeutics: The CRISPR-Cas Effect

Periodontal disease (PD) is an immune-inflammatory disease affecting the supporting structures of the teeth, which results in progressive destruction of the hard and soft tissues surrounding teeth, ultimately resulting in tooth loss. The primary etiological factor for this disease is the presence of pathogenic microorganisms. Pathogenic bacteria face antagonistic conditions and foreign DNA components during the infection stage and depend on defense mechanisms such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas to counter them. Virulence genes regulated by the CRISPR-Cas system are often expressed by bacteria as part of the stress response to the presence of stress conditions and foreign elements. There is ever-growing evidence regarding the role of CRISPR-Cas in virulence of periodontal pathogens. The same CRISPR-Cas system may also be targeted to reduce bacterial virulence and it may also be utilized to develop diagnostic and therapeutic strategies for prevention and control of PD progression. This review article describes the CRISPR-Cas systems in the periodontal dysbiotic microbial communities, their role in the virulence of periodontal pathogens, and their potential role in understanding the pathogenesis of periodontitis and treatment of PD.

Oral Microbiota in Children and Adolescents with Type 1 Diabetes Mellitus: Novel Insights into the Pathogenesis of Dental and Periodontal Disease

The oral microbiota can be influenced by multiple factors, but only a few studies have focused on the role of glycemic control in determining early alterations of oral microbiota and their association with pathogenesis of both periodontitis and caries. The aim of this study is to evaluate the interplay between bacteria composition, oral hygiene, and glycemic control in a cohort of children with T1D. A total of 89 T1D children were enrolled (62% males, mean age: 12.6 ± 2.2 years). Physical and clinical characteristics, glucometabolic parameters, insulin treatment, and oral hygiene habits data were collected. Microbiological analysis was performed from saliva samples. A high prevalence of cariogenic and periodontopathogens bacteria in our cohort was detected. In particular, in all subjects Actinomyces spp., Aggregatibacter actinomycetemcomitans, Prevotella intermedia, and Lactobacillus spp. were isolated. S. mutans was found in about half of the analyzed sample (49.4%), in particular in patients with imbalance values of glycemic control. Moreover, a higher presence of both S. mutans and Veillonella spp. was detected in subjects with poorer glycemic control, in terms of HbA1c, %TIR and %TAR, even adjusting for age, sex, and hygiene habits as covariates. Virtuous oral hygiene habits, such as frequency of toothbrush changes and professional oral hygiene, negatively correlated with the simultaneous presence of Tannerella forsythia, Treponema denticola, and Porphyromonas gingivalis, red complex bacteria. Our study shows it is crucial to pay attention to glycemic control and regular oral hygiene to prevent the establishment of an oral microbiota predisposing to dental and periodontal pathology in subjects with T1D since childhood.

Neutrophils in the periodontium: Interactions with pathogens and roles in tissue homeostasis and inflammation

Neutrophils are of key importance in periodontal health and disease. In their absence or when they are functionally defective, as occurs in certain congenital disorders, affected individuals develop severe forms of periodontitis in early age. These observations imply that the presence of immune-competent neutrophils is essential to homeostasis. However, the presence of supernumerary or hyper-responsive neutrophils, either because of systemic priming or innate immune training, leads to imbalanced host-microbe interactions in the periodontium that culminate in dysbiosis and inflammatory tissue breakdown. These disease-provoking imbalanced interactions are further exacerbated by periodontal pathogens capable of subverting neutrophil responses to their microbial community's benefit and the host's detriment. This review attempts a synthesis of these findings for an integrated view of the neutrophils' ambivalent role in periodontal disease and, moreover, discusses how some of these concepts underpin the development of novel therapeutic approaches to treat periodontal disease.

Variants in interferon gamma inducible protein 16 (IFI16) and absent in melanoma 2 (AIM2) genes that modulate inflammatory response are associated with periodontitis

OBJECTIVE

Evaluate the association of genetic variants of the interferon gamma inducible protein 16 (IFI16) and absent in melanoma 2 (AIM2) genes with periodontitis.

METHODS

The study involved 117 individuals with periodontitis and 389 without periodontitis, all Brazilians, miscegenated. Individuals with periodontitis presented at least 4 teeth with ≥ 1 site with probing depth ≥ 4 mm; clinical attachment level ≥ 3 mm on the same site and bleeding upon stimulus. Genotyping was performed using the Infinium Multi-Ethnic AMR/AFR-8 Bead Chip focused on Hispanic and African American populations with approximately 2 million markers of the human genome. Multivariate logistic regression was performed to identify associations in additive, dominant and recessive models adjusted for covariates age, obesity, mouth breathing, flossing, asthma, and ancestry.

RESULTS

In IFI16, the rs75985579-A is positively associated with periodontitis in the additive (Odds Ratio adjusted (ORadjusted) 2.65, 95% confidence interval (CI):1.25-5.60, p value: 0.007) and dominant models (ORadjusted 2.56, 95%CI:1.13-5.81, p value: 0.017). In AIM2, the rs76457189-G, is associated negatively with periodontitis in two genetic models evaluated, additive (ORadjusted 0.21, 95%CI:0.05-0.94, p value: 0.022) and dominant (ORadjusted 0.21, 95%CI:0.05-0.94, p value: 0.022).

CONCLUSIONS

These results have shown that variants in the IFI16 and AIM2 genes are associated with periodontitis. Individuals with at least one A (adenine) allele of the rs75985579 (IFI16) are more than twice as likely to have periodontitis, while individuals with the G (guanine) allele of rs76457189 (AIM2) are less likely to be diagnosed with periodontitis, providing a negative association with periodontitis.

Understanding human health through metatranscriptomics

Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.

Selenomonas sputigena Interactions with Gingival Epithelial Cells That Promote Inflammation

Increased prevalence and abundance of Selenomonas sputigena have been associated with periodontitis, a chronic inflammatory disease of tooth-supporting tissues, for more than 50 years. Over the past decade, molecular surveys of periodontal disease using 16S and shotgun metagenomic sequencing approaches have confirmed the disease association of classically recognized periodontal pathogens such as Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia while highlighting previously underappreciated organisms such as Filifactor alocis and S. sputigena. Despite abundant clinical association between S. sputigena and periodontal disease, we have little to no understanding of its pathogenic potential, and virulence mechanisms have not been studied. In this study, we sought to characterize the response of gingival epithelial cells to infection with S. sputigena. Here, we show that S. sputigena attaches to gingival keratinocytes and induces expression and secretion of cytokines and chemokines associated with inflammation and leukocyte recruitment. We demonstrate that S. sputigena induces signaling through Toll-like receptor 2 (TLR2) and TLR4 but evades activation of TLR5. Cytokines released from S. sputigena-infected keratinocytes induced monocyte and neutrophil chemotaxis. These results show that S. sputigena-host interactions have the potential to contribute to bacterially driven inflammation and tissue destruction, the hallmark of periodontitis. Characterization of previously unstudied pathogens may provide novel approaches to develop therapeutics to treat or prevent periodontal disease.

Impact of 16S rRNA Gene Redundancy and Primer Pair Selection on the Quantification and Classification of Oral Microbiota in Next-Generation Sequencing

This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated. Next, 39 primer pairs were used to search for matches in the genomes and obtain amplicons. For each primer, we calculated the number of gene amplicons, variants, genomes, and species detected and the percentage of coverage at the species level with no MAs (SC-NMA). The results showed that 94.09% of oral bacteria and 52.59% of oral archaea had more than one intragenomic 16S rRNA gene. From 1.29% to 46.70% of bacterial species and from 4.65% to 38.89% of archaea detected by the primers had MAs. The best primers were the following (SC-NMA; region; position for Escherichia coli [GenBank version no. J01859.1]): KP_F048-OP_R030 for bacteria (93.55%; V3 to V7; 342 to 1079), KP_F018-KP_R063 for archaea (89.63%; V3 to V9; undefined to 1506), and OP_F114-OP_R121 for both domains (92.52%; V3 to V9; 340 to 1405). In addition to 16S rRNA gene redundancy, the presence of MAs must be controlled to ensure an accurate interpretation of microbial diversity data. The SC-NMA is a more useful parameter than the conventional coverage percentage for selecting the best primer pairs. The pairs used the most in the oral microbiome literature were not among the best performers. IMPORTANCE Hundreds of publications have studied the oral microbiome through 16S rRNA gene sequencing. However, none have assessed the number of 16S rRNA genes in the genomes of oral microbes, or how the use of primer pairs targeting different regions affects the detection of MAs from different taxa. Here, we found that almost all oral bacteria and more than half of oral archaea have more than one intragenomic 16S rRNA gene. The performance of the primer pairs in not detecting MAs increases as the length of the amplicon augments. As none of those most employed in the oral literature were among the best performers, we selected a series of primers to detect bacteria and/or archaea based on their percentage of species detected without MAs. The intragenomic 16S rRNA gene redundancy and the presence of MAs between distinct taxa need to be considered to ensure an accurate interpretation of microbial diversity data.

Local and Systemic Effects of Porphyromonas gingivalis Infection

Porphyromonas gingivalis, a gram-negative anaerobe, is a leading etiological agent in periodontitis. This infectious pathogen can induce a dysbiotic, proinflammatory state within the oral cavity by disrupting commensal interactions between the host and oral microbiota. It is advantageous for P. gingivalis to avoid complete host immunosuppression, as inflammation-induced tissue damage provides essential nutrients necessary for robust bacterial proliferation. In this context, P. gingivalis can gain access to the systemic circulation, where it can promote a prothrombotic state. P. gingivalis expresses a number of virulence factors, which aid this pathogen toward infection of a variety of host cells, evasion of detection by the host immune system, subversion of the host immune responses, and activation of several humoral and cellular hemostatic factors.

Weak direct current exerts synergistic effect with antibiotics and reduces the antibiotic resistance: An in vitro subgingival plaque biofilm model

BACKGROUND AND OBJECTIVE

Weak direct current (DC) exerts killing effect and synergistic killing effect with antibiotics in some specific bacteria biofilms. However, the potential of weak DC alone or combined with periodontal antibiotics in controlling periodontal pathogens and plaque biofilms remains unclear. The objective of this study was to investigate whether weak DC could exert the anti-biofilm effect or enhance the killing effect of metronidazole (MTZ) and/or amoxicillin-clavulanate potassium (AMC) on subgingival plaque biofilms, by constructing an in vitro subgingival plaque biofilm model.

METHODS

The pooled subgingival plaque and saliva of patients with periodontitis (n = 10) were collected and cultured anaerobically on hydroxyapatite disks in vitro for 48 h to construct the subgingival plaque biofilm model. Then such models were stimulated with 0 μA DC alone (20 min/12 h), 1000 μA DC alone (20 min/12 h), 16 μg/ml MTZ, 16 μg/ml AMC or their combination, respectively. Through viable bacteria counting, metabolic activity assay, quantitative real-time PCR absolute quantification and 16S rDNA sequencing analysis, the anti-biofilm effect of 1000 μA DC and enhanced killing effects of 1000 μA DC combined with antibiotics (MTZ, AMC or MTZ+AMC) were explored.

RESULTS

The old subgingival plaque model (48 h) had no significant difference in total bacterial loads from subgingival plaque in situ, which achieved a similarity of 80%. The 1000 μA DC plus MTZ or AMC for 12 h showed a stronger synergistic killing effect than the same combination for 20 min. The metabolic activity was reduced to the lowest by DC plus MTZ+AMC, as 37.4% of that in the control group, while average synergistic killing effect reached 1.06 log units and average total bacterial loads decreased to 0.87 log units. Furthermore, the relative abundance of the genera Porphyromonas, Prevotella, Treponema_2, and Tannerella were decreased significantly.

CONCLUSION

The presence of weak DC (1000 μA) improved the killing effect of antibiotics on subgingival plaque biofilms, which might provide a novel strategy to reduce their antibiotic resistance.

First molecular detection of Entamoeba gingivalis subtypes in individuals from Turkey

Entamoeba gingivalis is a parasitic protozoan that colonizes the human oral cavity and there are two subtypes (ST1 and ST2) that have been identified to date. However, there are no reports on the molecular detection or characterization of E. gingivalis in Turkey. The objective of this study was to detect the presence of E. gingivalis in Turkish healthy individuals and those with periodontal disease and to subtype the isolates using molecular techniques. Samples from the oral cavity of 94 individuals were taken and the presence of E. gingivalis was determined by PCR using primers for SsrRNA and the amplicons were then confirmed by DNA sequencing. Each participant completed a questionnaire that included demographic data, habits and lifestyle, as well as health status. The presence of E. gingivalis was detected in a total of 19 samples (11 patients and eight healthy individuals). Molecular characterization determined that 12 samples belonged to ST1 and seven samples belonged to ST2. The presence of E. gingivalis was higher in patients with periodontal disease than in healthy individuals, and this association was statistically significant (P < .05). This study constitutes the first report of molecular detection and subtyping of E. gingivalis in Turkey.

Oral microbiome contributes to the failure of orthodontic temporary anchorage devices (TADs)

BACKGROUND

The stability of temporary anchorage devices (TADs) is critical in orthodontic clinics. The failure of TADs is multifactorial, and the role of the oral microbiome has not been clearly defined. Herein, we attempted to analyze the contribution of the oral microbiome to the failure of TADs.

METHODS

Next-generation sequencing was adopted for analyzing the microbiome on the TADs from orthodontic patients. 29 TADs (15 failed TADs and 14 successful TADs) were used for 16S rRNA gene sequencing. A total of 135 TADs (62 failed TADs and 73 successful TADs) were collected to conduct metagenomic sequencing. Additionally, 34 verified samples (18 failed TADs and 16 successful TADs) were collected for quantitative real-time polymerase chain reaction analysis (qRT-PCR).

RESULTS

Successful and failed TADs demonstrated discrepancies in microbiome structure, composition, and function. Clear separations were found in β-diversity in 16S rRNA gene sequencing as well as metagenomic sequencing (p < 0.05). Metagenomic sequencing showed that Prevotella intermedia, Eikenella corrodens, Parvimonas spp., Neisseria elongata, and Catonella morbi were enriched in the failed groups. qRT-PCR also demonstrated that the absolute bacteria load of Prevotella intermedia was higher in failed TADs (p < 0.05). Considering functional aspects, the failed group showed enriched genes involved in flagellar assembly, bacterial chemotaxis, and oxidative phosphorylation.

CONCLUSIONS

This study illustrated the compositional and functional differences of microorganisms found on successful and failed TADs, indicating that controlling bacterial adhesion on the surface of TADs is essential for their success rate.

Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis

Redondoviruses are circular Rep-encoding single-stranded DNA (CRESS) viruses of high prevalence in healthy humans. Redondovirus abundance is increased in oro-respiratory samples from individuals with periodontitis, acute illness, and severe COVID-19. We investigated potential host cells supporting redondovirus replication in oro-respiratory samples and uncovered the oral amoeba Entamoeba gingivalis as a likely host. Redondoviruses are closely related to viruses of Entamoeba and contain reduced GC nucleotide content, consistent with Entamoeba hosts. Redondovirus and E. gingivalis co-occur in metagenomic data from oral disease and healthy human cohorts. When grown in xenic cultures with feeder bacteria, E. gingivalis was robustly positive for redondovirus RNA and DNA. A DNA proximity-ligation assay (Hi-C) on xenic culture cells showed enriched cross-linking of redondovirus and Entamoeba DNA, supporting E. gingivalis as the redondovirus host. While bacteria are established hosts for bacteriophages within the human virome, this work shows that eukaryotic commensals also contribute an abundant human-associated virus.

Differences of gut microbiota and behavioral symptoms between two subgroups of autistic children based on γδT cells-derived IFN-γ Levels: A preliminary study

Background

Autism Spectrum Disorders (ASD) are defined as a group of pervasive neurodevelopmental disorders, and the heterogeneity in the symptomology and etiology of ASD has long been recognized. Altered immune function and gut microbiota have been found in ASD populations. Immune dysfunction has been hypothesized to involve in the pathophysiology of a subtype of ASD.

Methods

A cohort of 105 ASD children were recruited and grouped based on IFN-γ levels derived from ex vivo stimulated γδT cells. Fecal samples were collected and analyzed with a metagenomic approach. Comparison of autistic symptoms and gut microbiota composition was made between subgroups. Enriched KEGG orthologues markers and pathogen-host interactions based on metagenome were also analyzed to reveal the differences in functional features.

Results

The autistic behavioral symptoms were more severe for children in the IFN-γ-high group, especially in the body and object use, social and self-help, and expressive language performance domains. LEfSe analysis of gut microbiota revealed an overrepresentation of Selenomonadales, Negatiyicutes, Veillonellaceae and Verrucomicrobiaceae and underrepresentation of Bacteroides xylanisolvens and Bifidobacterium longum in children with higher IFN-γ level. Decreased metabolism function of carbohydrate, amino acid and lipid in gut microbiota were found in the IFN-γ-high group. Additional functional profiles analyses revealed significant differences in the abundances of genes encoding carbohydrate-active enzymes between the two groups. And enriched phenotypes related to infection and gastroenteritis and underrepresentation of one gut-brain module associated with histamine degradation were also found in the IFN-γ-High group. Results of multivariate analyses revealed relatively good separation between the two groups.

Conclusions

Levels of IFN-γ derived from γδT cell could serve as one of the potential candidate biomarkers to subtype ASD individuals to reduce the heterogeneity associated with ASD and produce subgroups which are more likely to share a more similar phenotype and etiology. A better understanding of the associations among immune function, gut microbiota composition and metabolism abnormalities in ASD would facilitate the development of individualized biomedical treatment for this complex neurodevelopmental disorder.

Tobacco smoke exacerbates Filifactor alocis pathogenicity

AIM

Filifactor alocis has recently emerged as a periodontal pathobiont that appears to thrive in the oral cavity of smokers. We hypothesized that identification of smoke-responsive F. alocis genes would provide insight into adaptive strategies and that cigarette smoke would enhance F. alocis pathogenesis in vivo.

MATERIALS AND METHODS

F. alocis was grown in vitro and cigarette smoke extract-responsive genes determined by RNAseq. Mice were exposed, or not, to mainstream 1R6F research cigarette smoke and infected with F. alocis, or not, in an acute ligature model of periodontitis. Key clinical, infectious, and immune data were collected.

RESULTS

In culture, F. alocis growth was unaffected by smoke conditioning and only a small number of genes were specifically regulated by smoke exposure. Reduced murine mass, differences in F. alocis-cognizant antibody production, and altered immune profiles as well as altered alveolar bone loss were all attributable to smoke exposure and/or F. alocis infection in vivo.

CONCLUSIONS

F. alocis is well-adapted to tobacco-rich conditions and its pathogenesis is enhanced by tobacco smoke exposure. A smoke-exposed ligature model of periodontitis shows promise as a tool with which to further unravel mechanisms underlying tobacco-enhanced, bacteria-induced disease.

Gut Microbiota and Cognitive Function Among Women Living with HIV

BACKGROUND

Altered gut microbiota has been associated with cognitive dysfunction and Alzheimer's disease, but little is known among people living with HIV.

OBJECTIVE

To examine associations between gut microbiota and cognitive impairment among women with or without HIV.

METHODS

This is a cross-sectional study of 446 women (302 HIV+) who had completed a neuropsychological test battery and stool sample collected within 1 year. Gut microbiota composition was quantified using 16SV4 rRNA gene sequencing and microbial functional pathways were predicted using PICRUSt. Cognitive domains included attention, executive function, learning, memory, fluency, processing speed, and motor function. Cognitive impairment was defined as two or more domains with T scores < 1 SD below mean. ANCOM-II was used to identify taxa and functional pathways associated with cognitive impairment, and the associations were further examined by multivariable logistic regression.

RESULTS

In overall sample, adjusting for multiple covariates including HIV status, we found that higher abundance of Methanobrevibacter, Odoribacter, Pyramidobacter, Eubacterium, Ruminococcus, and Gemmiger, and lower abundance of Veillonella were associated with cognitive impairment. The associations between these taxa and cognitive impairment were more profound in HIV+ women compared to HIV- women. Most associations with bacterial taxa were observed for learning and memory. We found accompanying microbial functional differences associated with cognitive impairment, including twelve enriched pathways and three depleted pathways.

CONCLUSIONS

In women with or without HIV infection, this study identified multiple altered gut bacterial taxa and functional pathways associated with cognitive impairment, supporting the potential role of gut microbiota in cognitive dysfunction and Alzheimer's disease.

The key players of dysbiosis in Noma disease; A systematic review of etiological studies

Noma is a rapidly progressing periodontal disease with up to 90% mortality in developing countries. Poor, immunocompromised and severely malnourished children (2 to 6 years old) are mostly affected by Noma. Prevention and effective management of Noma is hindered by the lack of sufficient cohesive studies on the microbial etiology of the disease. Research efforts have not provided a comprehensive unified story of the disease. Bridging the gap between existing studies gives an insight on the disease pathogenesis. This current systematic review of etiological studies focuses on the key players of dysbiosis in Noma disease. This review was performed in accordance with the Preferred Reporting Items for Systemic review and Meta-Analyses (PRISMA) statement. Web of Science, MEDLINE via PubMed, Cochrane Library, Scopus, and Science Direct were searched electronically for clinical trials which applied culture dependent or molecular techniques to identify oral microbiota from Noma patients. Trials which involved periodontal diseases except Noma were excluded. After screening 275 articles, 153 full-texts articles were assessed for eligibility of which eight full text articles were selected for data extraction and analysis. The results show that 308 samples from 169 Noma participants (6 months to 15 years old) have been used in clinical trials. There was some variance in the microbiome identified due to the use of 3 different types of samples (crevicular fluid, subgingival plaque, and swabbed pus) and the ambiguity of the stage or advancement of Noma in the studies. Other limitations of the studies included in this review were: the absence of age-matched controls in some studies; the constraints of colony morphology as a tool in distinguishing between virulent fusobacterium genus at the species level; the difficulty in culturing spirochaetes in the laboratory; the choice of primers in DNA amplification; and the selection of probe sets in gene sequencing. This systematic review highlights spirochaetes and P. intermedia as putative trigger organisms in Noma dysbiosis, shows that F. nucleatum promotes biofilms formation in late stages of the disease and suggests that future studies should be longitudinal, with high throughput genome sequencing techniques used with gingival plaque samples from early stages of Noma.

Modulatory Mechanisms of Pathogenicity in Porphyromonas gingivalis and Other Periodontal Pathobionts

The pathogenesis of periodontitis depends on a sustained feedback loop where bacterial virulence factors and immune responses both contribute to inflammation and tissue degradation. Periodontitis is a multifactorial disease that is associated with a pathogenic shift in the oral microbiome. Within this shift, low-abundance Gram-negative anaerobic pathobionts transition from harmless colonisers of the subgingival environment to a virulent state that drives evasion and subversion of innate and adaptive immune responses. This, in turn, drives the progression of inflammatory disease and the destruction of tooth-supporting structures. From an evolutionary perspective, bacteria have developed this phenotypic plasticity in order to respond and adapt to environmental stimuli or external stressors. This review summarises the available knowledge of genetic, transcriptional, and post-translational mechanisms which mediate the commensal-pathogen transition of periodontal bacteria. The review will focus primarily on Porphyromonas gingivalis.

Stimulation of Human Periodontal Ligament Fibroblasts Using Purified Dentilisin Extracted from Treponema denticola

Periodontal disease is a chronic multifactorial disease triggered by a complex of bacterial species. These interact with host tissues to cause the release of a broad array of pro-inflammatory cytokines, chemokines, and tissue remodelers, such as matrix metalloproteinases (MMPs), which lead to the destruction of periodontal tissues. Patients with severe forms of periodontitis are left with a persistent pro-inflammatory transcriptional profile throughout the periodontium, even after clinical intervention, leading to the destruction of teeth-supporting tissues. The oral spirochete, Treponema denticola , is consistently found at significantly elevated levels at sites with advanced periodontal disease. Of all T. denticola virulence factors that have been described, its chymotrypsin-like protease complex, also called dentilisin, has demonstrated a multitude of cytopathic effects consistent with periodontal disease pathogenesis, including alterations in cellular adhesion activity, degradation of various endogenous extracellular matrix-substrates, degradation of host chemokines and cytokines, and ectopic activation of host MMPs. Thus, the following model of T. denticola -human periodontal ligament cell interactions may provide new knowledge about the mechanisms that drive the chronicity of periodontal disease at the protein, transcriptional, and epigenetic levels, which could afford new putative therapeutic targets. This protocol was validated in: PLOS Pathog (2021), DOI: 10.1371/journal.ppat.1009311.

Enterotypical Prevotella and three novel bacterial biomarkers in preoperative stool predict the clinical outcome of colorectal cancer

BACKGROUND

A significant proportion of colorectal cancer (CRC) patients suffer from early recurrence and progression after surgical treatment. Although the gut microbiota is considered as a key player in the initiation and progression of CRC, most prospective studies have been focused on a particular pathobionts such as Fusobacterium nucleatum. Here, we aimed to identify novel prognostic bacteria for CRC by examining the preoperative gut microbiota through 16S ribosomal RNA gene sequencing.

RESULTS

We collected stool samples from 333 patients with primary CRC within 2 weeks before surgery and followed up the patients for a median of 27.6 months for progression and 43.6 months for survival. The sequence and prognosis data were assessed using the log-rank test and multivariate Cox proportional hazard analysis. The gut microbiota was associated with the clinical outcomes of CRC patients (P_progress = 0.011, P_decease = 0.007). In particular, the high abundance of Prevotella, a representative genus of human enterotypes, indicated lower risks of CRC progression (P = 0.026) and decease (P = 0.0056), while the occurrence of Alistipes assigned to Bacteroides sp., Pyramidobacter piscolens, Dialister invisus, and Fusobacterium nucleatum indicated a high risk of progression. A microbiota-derived hazard score considering the five prognostic bacteria accurately predicted CRC progression in 1000 random subsamples; it outperformed widely accepted clinical biomarkers such as carcinoembryonic antigen and lymphatic invasion, after adjustment for the clinicopathological stage (adjusted HR 2.07 [95% CI, 1.61-2.64], P = 7.8e-9, C-index = 0.78). PICRUSt2 suggested that microbial pathways pertaining to thiamine salvage and L-histidine degradation underlie the different prognoses.

CONCLUSIONS

The enterotypical genus Prevotella was demonstrated to be useful in improving CRC prognosis, and combined with the four pathobionts, our hazard score based on the gut microbiota should provide an important asset in predicting medical outcomes for CRC patients. Video Abstract.

Calculus as a Risk Factor for Periodontal Disease: Narrative Review on Treatment Indications When the Response to Scaling and Root Planing Is Inadequate

Background: Based on the 2018 classification of periodontal disease, a series of articles have been published describing the decision points of periodontal therapy and how the findings collected at those decision points can be used as guidelines for periodontal therapy. The articles are reviewed with a focus on the finding of inadequate calculus removal at the decision points and how that finding impacts treatment outcomes. Methods: A narrative review of the literature discussing the influence of calculus on inflammation was performed and the effects of inadequate removal of calculus during periodontal therapy were analyzed in light of the 2018 classification of periodontal disease, the decision points of periodontal therapy, and the guidelines of periodontal therapy. Results: The published literature supports that calculus is a major risk factor for periodontal inflammation. Recent studies indicate that the pathologic risk of calculus goes beyond the retention of biofilm and may represent a different pathophysiologic pathway for periodontal disease separate from the direct action of biofilm. The inadequate removal of calculus is a factor in the failure of periodontal therapy. Conclusions: The inadequate removal of calculus plays an important role in the frequent failure of non-surgical periodontal therapy to eliminate inflammation.

Entamoeba gingivalis is associated with periodontal conditions in Chinese young patients: A cross-sectional study

Background

This study investigated the prevalence and relative abundance of Entamoeba gingivalis (E. gingivalis) in Chinese young patients with different periodontal conditions, and its association with subgingival microbial composition, periodontal parameters, and cytokines in gingival crevicular fluid.

Methods

Participants (age: 18–45 years) diagnosed with stage II–IV periodontitis, gingivitis, or periodontal health underwent periodontal examination and sampling. Subgingival plaque was analyzed by 16S+18S sequencing for E. gingivalis detection and microbial analysis. The distribution of E. gingivalis in subgingival plaque was illustrated by fluorescence in situ hybridization. Interleukin-1β, interleukin-8, and tumor necrosis factor-α in gingival crevicular fluid were measured by multiplexed flow cytometric assay.

Results

This cross-sectional study included 120 sites from 60 participants. The prevalence and relative abundance of E. gingivalis were significantly increased in periodontitis (p<0.05). The sites were classified into three subgroups according to the relative abundance of E. gingivalis: negative group (Eg0, n=56); low-abundance group (Eg1, n=32); and high-abundance group (Eg2, n=32). The subgingival microflora in the subgroups showed stepwise changes at both the phylum and genus levels. The microflora compositions were significantly altered from Eg0 to Eg2 (p<0.001). Co-occurrence network analysis showed that Porphyromonas, Treponema, Tannerella, Filifactor, TG5, and Desulfobulbus were highly correlated with E. gingivalis (r>0.6, p<0.001). Correlation analysis showed that E. gingivalis was closely associated with important periodontal parameters and cytokines (p<0.01).

Conclusion

E. gingivalis was enriched in periodontitis and closely associated with subgingival microbial dysbiosis, periodontal parameters and cytokines in gingival crevicular fluid. Thus, it may be an important pathogen in periodontal disease.

Assessing the effect of antihypertensives on plaque microbiota in patients with periodontitis and hypertension using 16S rRNA sequencing; a cross-sectional study

BACKGROUND

Periodontitis is initiated or accelerated by dysbiosis of oral microorganisms. When hypertension is accompanied in periodontitis patients, the changes of oral microbiota occur. Since there are no reports of antihypertensives, we assessed the effect of antihypertensives on the oral microbial profiles of patients with periodontitis.

METHODS

This study involved 95 participants divided into two groups: those with periodontitis and hypertension (P_HT) and those with periodontitis and taking medications for hypertension (P_mHT). Plaque samples were collected from the buccal, supragingival, and subgingival sites of the oral cavities of these patients. DNA was extracted, and the V3-V4 region of the 16S ribosomal RNA was sequenced and analyzed.

RESULTS

The P_HT and P_mHT groups were similar with respect to the alpha- and beta-diversity as well as the dominant phyla and genera but differed in the relative abundance of bacterial species (85 species). In the P_mHT group, the relative abundance of major periodontal pathogens was greatly increased. In particular, Tannerella forsythia, Treponema denticola, and Fretibacterium fastidiosum increased nearly three times the LDA score in the supragingival plaque. Also, there was an increase in relative abundance of Prevotella spp. associated with periodontitis and nitrate reduction, which was also evident in the supragingival plaque.

CONCLUSIONS

These findings indicate that antihypertensives induce dysbiotic changes in the oral microbiota of patients with periodontitis which are associated with increases in the relative abundance of periodontal pathogens. Therefore, more active periodontal treatment and supportive periodontal therapy are required in patients taking antihypertensives. This article is protected by copyright. All rights reserved.

The Expression of miR-34a in Gingival Crevicular Fluid of Chronic Periodontitis and Its Connection with the TLR/NF-κB Signaling Pathway

Objective

This study analyzed the expression of miR-34a in gingival crevicular fluid (GCF) of patients with chronic periodontitis and its connection with the Toll-like receptor (TLR)/nuclear factor kappa-B (NF-κB) signaling pathway.

Methods

We collected the GCF of the two groups of subjects, using RT-PCR to detect the expression of miR-34a and NF-κB p65 mRNA and TLR4 mRNA and ELISA to detect the inflammatory factor degree in GCF, and performed periodontal examinations on both groups.

Results

The gingival index, bleeding index, probe depth, and attachment loss indexes of periodontal examination in the observation group were remarkably superior to those in the control group (P < 0.05). The levels of IL-1β, IL-6, and TNF-α in the GCF of the observation group were higher than those of the control group (P < 0.05). The mRNA relative expression levels of miR-34a, NF-κB p65, and TLR4 in the GCF of the observation group were dramatically higher than those of the control group (P < 0.05). Correlation analysis showed that miR-34a was highly expressed in patients with chronic periodontitis.

Conclusion

There is an abnormally high expression of miR-34a in GCF of chronic periodontitis. Its expression is associated with the degree of periodontal inflammation, periodontal tissue damage, and the activation of the TLR/NF-κB signaling pathway and could be used as a potential index for auxiliary diagnosis and severity of the disease.

In vitro antimicrobial effect of titanium anodization on complex multispecies subgingival biofilm

Anodization is a routine industrial galvanic method that produces a titanium oxide layer on the surface of titanium. Considering the possibility that this technique could influence microbial adsorption and colonization, this in vitro study was conducted to evaluate the impact of a process of anodization applied to a titanium surface on the microbial profile of multispecies subgingival biofilm. Titanium discs produced by using two different processes-conventional and Anodization-were divided into two groups: conventional titanium discs with machined surface (cpTi) Control Group and titanium discs with anodic oxidation treatment (anTi) Test Group. Subgingival biofilm composed of 33 species was formed on the titanium discs that were positioned vertically in 96-well plates, for 7 days. The proportions and the counts of microbial species were determined using a DNA-DNA hybridization technique, and data were evaluated using Mann-Whitney test (p < 0.05). Mean total bacterial counts were lower in Test Group in comparison with Control Group (p < 0.05). Nine bacterial species differed significantly, and were found in higher levels in Control Group in comparison with Test Group, including T. forsythia, E. nodatum, and F. periodonticum. In conclusion, titanium discs with anodization could alter the microbial profile of the biofilm formed around them. Further clinical studies should be conducted to confirm the clinical impact of these findings.

Probiotic Monotherapy with Lactobacillus reuteri (Prodentis) as a Coadjutant to Reduce Subgingival Dysbiosis in a Patient with Periodontitis

(1) Background: Probiotics can be considered a non-invasive periodontal monotherapy for the modulation of microbiota when periodontal treatment is not accessible. The aim was to evaluate the ability of Lactobacillus reuteri Prodentis as monotherapy to modulate periodontal parameters and subgingival biofilm dysbiosis. (2) Methods: A 30-year-old patient with periodontitis was followed longitudinally after one month of daily consumption of L. reuteri Prodentis (T0). Periodontal measurements and microbial identification by Checkerboard DNA−DNA hybridization of 40 bacteria were compared between baseline (T0) and 30 days (T1) or 90 days (T2), using the Kruskal−Wallis (KW) and Mann−Whitney U (MW) tests. (3) Results: Low values of pocket depth, attachment level, dental plaque, gingival erythema (GE), and suppuration were observed at T0 vs. T1, with the clinical improvement of GE (p < 0.05, MW) and the recovery of tooth 46 fistulation. T1 vs. T0 comparisons showed lower levels (Lev) or proportions (Prop) of Parvimonas micra (Lev: p < 0.05, MW; Prop: p < 0.01, MW) and Streptococcus gordonii (Prop: p < 0.05, MW), and a predominance (Lev/Prop) of Actinomyces odontolyticus and Streptococcus mitis; lower levels and proportions of P. micra, Eubacterium saburreum, Porphyromonas gingivalis, and Tannerella forsythia were observed in tooth 46 (T1/T2 vs. T0). (4) Conclusions: Under monotherapy with L. reuteri Prodentis, periodontal measurements of the patient were maintained, with selective changes in the subgingival microbiota that were proportional to the time of probiotic administration, with any additional periodontal treatment.