Metatranscriptome of the Oral Microbiome in Health and Disease

Characteristics of gut microbiome in patients with pediatric solid tumor

Background

Pediatric solid tumors are a common malignant disease in children, and more and more studies have proved that there is an inseparable relationship between adult tumors and intestinal microbiome, but the changes in the intestinal microbiota of pediatric solid tumor (PST) patients have been scarcely examined. This study aims to examine the differences in the intestinal microbiota features between patients diagnosed with PST and healthy controls (HCs).

Methods

To elucidate the unique characteristics of the gut microbiota in pediatric patients with solid tumors, we recruited 23 PST patients and 20 HCs. A total of 43 stool samples were gathered, and then 16S rRNA sequencing was performed.

Results

We noticed a noticeable pattern of elevated diversity in the gut microbiota within the PST groups. The differences in microbial communities among two groups were remarkable, regarding the analysis at the class level, the abundance of Bacilli was markedly increased in PST patients compared to HCs (P < 0.05), regarding the analysis at the genus level, The presence of Enterococcus was significantly higher in PST cases compared to HCs (P < 0.01), while Lachnospiraceae unclassified, Lachnospira, Haemophilus and Colidextribacter in PST cases, the abundance was significantly reduced. (P < 0.05), 6 genera, including Bacilli, Lactobacillales, Enterococcaceae and Morganella, showed a significant enrichment compared to healthy controls, while 10 genera, including Bilophila, Colidextribacter, Pasteurellales, Haemophilus, Lachnospiraceae unclassified, Lachnospira and Fusobacteriales, were significant reduction in the PST groups.

Conclusion

Our research conducted the characterization analysis of the gut microbiota in PST patients for the first time. More importantly, there are some notable differences in the gut microbiota between PST patients and healthy controls, which we believe is an interesting finding.

Metabolomics for dental caries diagnosis: Past, present, and future

Dental caries, a prevalent global infectious condition affecting over 95% of adults, remains elusive in its precise etiology. Addressing the complex dynamics of caries demands a thorough exploration of taxonomic, potential, active, and encoded functions within the oral ecosystem. Metabolomic profiling emerges as a crucial tool, offering immediate insights into microecosystem physiology and linking directly to the phenotype. Identified metabolites, indicative of caries status, play a pivotal role in unraveling the metabolic processes underlying the disease. Despite challenges in metabolite variability, the use of metabolomics, particularly via mass spectrometry and nuclear magnetic resonance spectroscopy, holds promise in caries research. This review comprehensively examines metabolomics in caries prevention, diagnosis, and treatment, highlighting distinct metabolite expression patterns and their associations with disease-related bacterial communities. Pioneering in approach, it integrates singular and combinatory metabolomics methodologies, diverse biofluids, and study designs, critically evaluating prior limitations while offering expert insights for future investigations. By synthesizing existing knowledge, this review significantly advances our comprehension of caries, providing a foundation for improved prevention and treatment strategies.

Bacteria of healthy periodontal tissues as candidates of probiotics: a systematic review

OBJECTIVES

The use of probiotics could promote the balance of the subgingival microbiota to contribute to periodontal health. This study aimed to identify the potential of bacteria commonly associated with healthy periodontal tissues as probiotic candidates.

MATERIAL AND METHODS

A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines using the PubMed, Scopus, Science Direct, ProQuest, and Ovid databases as well as the combination of Medical Subject Headings (MeSH) and non-MeSH terms. Based on the selection criteria, original studies published in English and identifying the microorganisms present in the periodontium of healthy individuals and patients with periodontitis using the high-throughput 16S ribosomal gene sequencing technique were included.

RESULTS

Out of 659 articles, 12 met the criteria for this review. These articles were published from 2012 to 2020 and mainly originated from the United States, China, and Spain. Most of these studies reported adequate criteria for selecting participants, using standardized clinical criteria, and compliance with quality based on the tools used. In periodontal healthy tissue were identified species like Actinomyces viscosus, Actinomyces naeslundii, Haemophilus parainfluenzae, Rothia dentocariosa, Streptococcus sanguinis, Streptococcus mitis, Streptococcus oralis, Streptococcus gordonii, Streptococcus intermedius, and Prevotella nigrescens which have recognized strains with a capacity to inhibit periodontopathogens.

CONCLUSIONS

S. sanguinis, S. oralis, S. mitis, and S. gordonii are among the bacterial species proposed as potential probiotics because some strains can inhibit periodontopathogens and have been reported as safe for humans.

The multifaceted role of c-di-AMP signaling in the regulation of Porphyromonas gingivalis lipopolysaccharide structure and function

Background

This study unveils the intricate functional association between cyclic di-3',5'-adenylic acid (c-di-AMP) signaling, cellular bioenergetics, and the regulation of lipopolysaccharide (LPS) profile in Porphyromonas gingivalis, a Gram-negative obligate anaerobe considered as a keystone pathogen involved in the pathogenesis of chronic periodontitis. Previous research has identified variations in P. gingivalis LPS profile as a major virulence factor, yet the underlying mechanism of its modulation has remained elusive.

Methods

We employed a comprehensive methodological approach, combining two mutants exhibiting varying levels of c-di-AMP compared to the wild type, alongside an optimized analytical methodology that combines conventional mass spectrometry techniques with a novel approach known as FLATn.

Results

We demonstrate that c-di-AMP acts as a metabolic nexus, connecting bioenergetic status to nuanced shifts in fatty acid and glycosyl profiles within P. gingivalis LPS. Notably, the predicted regulator gene cdaR, serving as a potent regulator of c-di-AMP synthesis, was found essential for producing N-acetylgalactosamine and an unidentified glycolipid class associated with the LPS profile.

Conclusion

The multifaceted roles of c-di-AMP in bacterial physiology are underscored, emphasizing its significance in orchestrating adaptive responses to stimuli. Furthermore, our findings illuminate the significance of LPS variations and c-di-AMP signaling in determining the biological activities and immunostimulatory potential of P. gingivalis LPS, promoting a pathoadaptive strategy. The study expands the understanding of c-di-AMP pathways in Gram-negative species, laying a foundation for future investigations into the mechanisms governing variations in LPS structure at the molecular level and their implications for host-pathogen interactions.

Characterization and functional prediction of the dental plaque microbiome in patients with alveolar clefts

Introduction

Alveolar cleft (AC) is a common congenital defect in people with cleft lip and palate (CLP). Alveolar bone grafting (ABG) is typically performed during adolescence, resulting in the fissure remaining in the mouth for a longer length of time. Patients with AC have a greater rate of oral diseases such as dental caries than the normal population, and the precise characteristics of the bacterial alterations caused by AC are unknown.

Methods

We recruited a total of 87 subjects and collected dental plaque samples from AC adolescents (AAP), post-operative ABG adolescents (PAP), healthy control adolescents (CAP), AC young adults (AYP), post-operative ABG young adults (PYP), and healthy control young adults (CYP). The sequencing of 16S rRNA genes was performed.

Results

The microbial composition of plaque from alveolar cleft patients differed significantly from age-matched healthy controls. Linear discriminant analysis effect size (LEfSe) analysis revealed that AAP was enriched for Neisseria, Haemophilus, Fusobacterium, Rhodococcus, Aggregatibacter, Gemella, and Porphyromonas, whereas AYP was enriched for Capnocytophaga, Rhodococcus, and Actinomyces-f0332. There were phenotypic differences in facultatively anaerobic, Gram-negative, Gram-positive, and oxidative stress tolerance between the AYP group with longer alveolar cleft and the healthy control group according to Bugbase phenotypic predictions. Alveolar bone grafting did not alter the functional phenotype of alveolar cleft patients but reduced the number of differential genera between alveolar cleft patients and healthy controls at both ages.

Conclusions

Our study systematically characterized the supragingival plaque microbiota of alveolar cleft patients, post-alveolar bone grafting patients, and matched healthy controls in two ages to gain a better understanding of plaque ecology and microbiology associated with alveolar clefts.

Metatranscriptome and Resistome of the Endodontic Microbiome

INTRODUCTION

In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression in endodontic infections.

METHODS

Root canal samples were collected from ten teeth, including five primary and five persistent/secondary endodontic infections. RNA from endodontic samples was extracted, and RNA sequencing was performed on a NovaSeq6000 system (Illumina). Taxonomic analysis was performed using the Kraken2 bacterial database. Then, sequences with a taxonomic classification were annotated against the Universal Protein Knowledgebase for functional annotation and the Comprehensive Antibiotic Resistance Database for AR-like gene identification.

RESULTS

Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria represented the dominant phyla, whereas Fusobacteria, Spirochetes, and Synergistetes were among the nondominant phyla. The top ten species were mainly represented by obligate (or quasiobligate) anaerobes, including Gram-negative (eg, Capnocytophaga sp. oral taxon 323, Fusobacterium nucleatum, Prevotella intermedia, Prevotella oris, Tannerella forsythia, and Tannerella sp. oral taxon HOT-286) and Gram-positive species (eg, Olsenella uli and Parvimonas micra). Transcripts encoding moonlighting proteins (eg, glycolytic proteins, translational elongation factors, chaperonin, and heat shock proteins) were highly expressed, potentially affecting bacterial adhesion, biofilm formation, host defense evasion, and inflammation induction. Endodontic bacteria expressed genes conferring resistance to antibiotic classes commonly used in dentistry, with a high prevalence and expression of tetracycline and lincosamide resistance genes. Antibiotic efflux and antibiotic target alteration/protection were the main resistance mechanisms.

CONCLUSIONS

Metatranscriptomics revealed the activity of potential endodontic pathogens, which expressed putative virulence factors and a wide diversity of genes potentially involved in AR.

Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes

The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.

A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review

One of the most promising areas of research in palaeomicrobiology is the study of the human microbiome. In particular, ancient dental calculus helps to reconstruct a substantial share of oral microbiome composition by mapping together human evolution with its state of health/oral disease. This review aims to trace microbial characteristics in ancient dental calculus to describe the evolution of the human host-oral microbiome relationship in oral health or disease in children and adults. Following the PRISMA-Extension for Scoping Reviews guidelines, the main scientific databases (PubMed, Scopus, Lilacs, Cochrane Library) have been drawn upon. Eligibility criteria were established, and all the data collected on a purpose-oriented collection form were analysed descriptively. From the initial 340 records, only 19 studies were deemed comprehensive enough for the purpose of this review. The knowledge of the composition of ancient oral microbiomes has broadened over the past few years thanks to increasingly well-performing decontamination protocols and additional analytical avenues. Above all, metagenomic sequencing, also implemented by state-of-the-art bioinformatics tools, allows for the determination of the qualitative-quantitative composition of microbial species associated with health status and caries/periodontal disease. Some microbial species, especially periodontal pathogens, do not appear to have changed in history, while others that support caries disease or oral health could be connected to human evolution through lifestyle and environmental contributing factors.

Transcriptomic features of programmed and inflammatory cell death in gingival tissues

The local gingival tissue environment with homeostasis and tissue-destructive events of periodontitis demonstrates major changes in histological features and biology of the oral/sulcular epithelium, fibroblasts, vascular cells, inflammatory cell infiltration, and alveolar bone.

OBJECTIVE

This study used an experimental periodontitis model to detail the gingival transcriptome related to cell death processes of pyroptosis, necroptosis, ferroptosis, and cuproptosis.

MATERIALS AND METHODS

Healthy Macaca mulatta primates stratified by age, ≤3 years (young), 7-12 years (adolescent), 12-15 years (adult), and 17-23 years (aged), provided gingival tissue biopsies for microarray analysis focused on 257 genes representative of the four cell death processes and bacterial plaque samples for 16S rRNA gene analysis.

RESULTS

Age differences in the profiles of gene expression in healthy tissues were noted for cuproptosis, ferroptosis, necroptosis, and pyroptosis. Major differences were then observed with disease initiation, progression, and resolution also related to the age of the animals. Distinct bacterial families/consortia of species were significantly related to the gene expression differences for the cell death pathways.

CONCLUSIONS

These results emphasized age-associated differences in the gingival tissue molecular response to changes in the quality and quantity of bacteria accumulating with the disease process reflected in regulated cell death pathways that are both physiological and pathophysiological.

Baltimore oral epidemiology, disease effects, and HIV evaluation study (BEEHIVE) study protocol: a prospective cohort study

BACKGROUND

As antiretroviral therapy has become widely available and highly effective, HIV has evolved to a manageable, chronic disease. Despite this health advancement, people living with HIV (PLWH) are at an increased risk for age-related non-communicable diseases (NCDs) compared to HIV-uninfected individuals. Similarly, PLWH are at an increased risk for selected oral diseases. PLWH with a history of injecting drugs experience an even greater burden of disease than their counterparts. The overall objective of the Baltimore Oral Epidemiology, Disease Effects, and HIV Evaluation (BEEHIVE) study is to determine the combined effects of HIV infection and NCDs on oral health status. The specific aims of the study are to: (1) determine to what extent HIV status influences access to and utilization of oral health care services; (2) determine to what extent HIV status affects self-reported and clinical oral health status; (3) determine to what extent HIV status influences the progression of periodontitis; and (4) determine to what extent HIV status impacts the periodontitis-associated oral microbiome signature.

METHODS

The BEEHIVE study uses a prospective cohort study design to collect data from participants at baseline and at a 24-month follow-up visit. Data are collected through questionnaire assessments, clinical examinations, and evaluation of oral microbiological samples to determine the drivers of oral disease among a high-risk population of PLWH with a history of injection drug use and prevalent comorbid NCDs. The established AIDS Linked to the Intravenous Experience (ALIVE) cohort serves as the source of participants for the BEEHIVE Study.

DISCUSSION

Upon completion of the BEEHIVE study, the knowledge gained will be important in informing future clinical and preventive interventions that can be implemented into medical and dental practice to ultimately help eliminate long-standing oral health inequities that PLWH experience.

Epithelial-derived interleukin-23 promotes oral mucosal immunopathology

At mucosal surfaces, epithelial cells provide a structural barrier and an immune defense system. However, dysregulated epithelial responses can contribute to disease states. Here, we demonstrated that epithelial cell-intrinsic production of interleukin-23 (IL-23) triggers an inflammatory loop in the prevalent oral disease periodontitis. Epithelial IL-23 expression localized to areas proximal to the disease-associated microbiome and was evident in experimental models and patients with common and genetic forms of disease. Mechanistically, flagellated microbial species of the periodontitis microbiome triggered epithelial IL-23 induction in a TLR5 receptor-dependent manner. Therefore, unlike other Th17-driven diseases, non-hematopoietic-cell-derived IL-23 served as an initiator of pathogenic inflammation in periodontitis. Beyond periodontitis, analysis of publicly available datasets revealed the expression of epithelial IL-23 in settings of infection, malignancy, and autoimmunity, suggesting a broader role for epithelial-intrinsic IL-23 in human disease. Collectively, this work highlights an important role for the barrier epithelium in the induction of IL-23-mediated inflammation.

A novel method for sampling subgingival microbiome: a comparative metatranscriptomic study

The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by rotationally swabbing the supragingival area, named subgingival-P (for proxy) samples. We sampled and metatranscriptomically analyzed subgingival and subgingival-P samples of three different teeth in 20 individuals. The subgingival-P samples were comparable to the subgingival samples in the relative abundances of microorganisms and microbial gene expression levels. Our data demonstrate that the novel method of collecting and analyzing the subgingival-P samples can act as a proxy for the subgingiva, paving the way for large and diverse studies investigating the role of the subgingival microbiome in health and disease.

Oral microbiota-host interaction: the chief culprit of alveolar bone resorption

There exists a bidirectional relationship between oral health and general well-being, with an imbalance in oral symbiotic flora posing a threat to overall human health. Disruptions in the commensal flora can lead to oral diseases, while systemic illnesses can also impact the oral cavity, resulting in the development of oral diseases and disorders. Porphyromonas gingivalis and Fusobacterium nucleatum, known as pathogenic bacteria associated with periodontitis, play a crucial role in linking periodontitis to accompanying systemic diseases. In periodontal tissues, these bacteria, along with their virulence factors, can excessively activate the host immune system through local diffusion, lymphatic circulation, and blood transmission. This immune response disruption contributes to an imbalance in osteoimmune mechanisms, alveolar bone resorption, and potential systemic inflammation. To restore local homeostasis, a deeper understanding of microbiota-host interactions and the immune network phenotype in local tissues is imperative. Defining the immune network phenotype in periodontal tissues offers a promising avenue for investigating the complex characteristics of oral plaque biofilms and exploring the potential relationship between periodontitis and associated systemic diseases. This review aims to provide an overview of the mechanisms underlying Porphyromonas gingivalis- and Fusobacterium nucleatum-induced alveolar bone resorption, as well as the immunophenotypes observed in host periodontal tissues during pathological conditions.

Application of omics technologies in cariology research: A critical review with bibliometric analysis

OBJECTIVES

To review the application of omics technologies in the field of cariology research and provide critical insights into the emerging opportunities and challenges.

DATA & SOURCES

Publications on the application of omics technologies in cariology research up to December 2022 were sourced from online databases, including PubMed, Web of Science and Scopus. Two independent reviewers assessed the relevance of the publications to the objective of this review.

STUDY SELECTION

Studies that employed omics technologies to investigate dental caries were selected from the initial pool of identified publications. A total of 922 publications with one or more omics technologies adopted were included for comprehensive bibliographic analysis. (Meta)genomics (676/922, 73 %) is the predominant omics technology applied for cariology research in the included studies. Other applied omics technologies are metabolomics (108/922, 12 %), proteomics (105/922, 11 %), and transcriptomics (76/922, 8 %).

CONCLUSION

This study identified an emerging trend in the application of multiple omics technologies in cariology research. Omics technologies possess significant potential in developing strategies for the detection, staging evaluation, risk assessment, prevention, and management of dental caries. Despite the numerous challenges that lie ahead, the integration of multi-omics data obtained from individual biological samples, in conjunction with artificial intelligence technology, may offer potential avenues for further exploration in caries research.

CLINICAL SIGNIFICANCE

This review presented a comprehensive overview of the application of omics technologies in cariology research and discussed the advantages and challenges of using these methods to detect, assess, predict, prevent, and treat dental caries. It contributes to steering research for improved understanding of dental caries and advancing clinical translation of cariology research outcomes.

Oral microbiome characteristics in patients with pediatric solid tumor

Background

Pediatric solid tumor, the abnormal proliferation of solid tissues in children resulting in the formation of tumors, represent a prevailing malignant ailment among the younger population. Extensive literature highlights the inseparable association linking oral microbiome and adult tumors, but due to differences in age of onset, characteristics of onset, etc., there are many differences between Pediatric solid tumors and adult tumors, and therefore, studying the relationship between Pediatric solid tumor and the oral microbiota is also essential.

Methods

To unravel the distinct characteristics of the oral microbiota within Pediatric solid tumor patients, 43 saliva samples, encompassing 23 Pediatric solid tumor patients and 20 healthy controls, were diligently procured. A meticulous screening process ensued, and conducted microbial MiSeq sequencing after screening.

Results

We documented the oral microbiome attributes among pediatric diagnosed with solid tumors (PST), and meanwhile, we observed a significant trend of decreased oral microbiota diversity in the pediatric solid tumor group. There were notable disparities in microbial communities observed between the two groups, 18 genera including Veillonellaceae, Firmicutes unclassified, Coriobacteriia, Atopobiaceae, Negativicutes, were significantly enriched in PST patients, while 29 genera, including Gammaproteobacteria, Proteobacteria, Burkholderiales, Neisseriaceae, were dominant in the HCs group. It was found that PST group had 16 gene functions, including Amino acid metabolism, Cysteine and methionine metabolism, Photosynthesis antenna proteins, Arginine and proline metabolism, and Aminoacyl tRNA biosynthesi, were significantly dominant, while 29 gene functions that prevailed in HCs.

Conclusion

This study characterized the oral microbiota of Pediatric solid tumor patients for the first time, and importantly, targeted biomarkers of oral microbiota may serve as powerful and non-invasive diagnostic tools for pediatric solid tumor patients.

The short-term impact of comprehensive caries treatment on the supragingival microbiome of severe early childhood caries

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.

Compositional and functional changes in the salivary microbiota related to oral leukoplakia and oral squamous cell carcinoma: a case control study

BACKGROUND

Oral squamous cell carcinoma (OSCC) is one of the most common malignant tumours with increasing incidence, and oral leukoplakia (OLK) has a strong tendency to undergo malignant transformation. The oral microbiota may influence oral cancer progression, but the salivary bacterial composition and functional changes in OSCC and OLK have not been comprehensively elucidated. Therefore, we compared salivary bacteria in OLK and OSCC patients with healthy controls (HC).

METHODS

Metagenomic sequencing was used to compare the bacterial composition and functional changes of 18 OSCC patients, 21 OLK patients and 21 HC. Spearman correlation was used to identify possible associations between functions and bacteria.

RESULTS

Gemella was the most differentially enriched genus in OSCC. At the species level, Streptococcus sp. NPS 308, Streptococcus agalactiae, Gemella haemolysans and Gemella morbillorum were slightly increased in OLK and OSCC. Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that OSCC was mainly associated with metabolism functions, including lipid metabolism, carbohydrate metabolism and glycan biosynthesis and metabolism. The synthesis and degradation of ketone bodies, cysteine and methionine metabolism and glycerolipid metabolism differed significantly among the three groups, and were highest in OSCC and lowest in HC. And G. haemolysans was significantly associated with these selected metabolic pathways.

CONCLUSIONS

Metagenomic analysis revealed significant differences in the salivary microbiota among OSCC, OLK and HC. Thus, salivary microbiota composition and functional changes may be associated with OSCC progression. Metabolism of nonessential amino acids such as cysteine and methionine in bacteria may play an important role in oral oncogenesis, and more studies of the mechanism between metabolisms of bacteria and oral oncogenesis are needed in the future.

Two-Omics Probe on the Potential of Pseudomonas sp. GDMCC 1.1703 Under Phenol Stress

Pseudomonas sp. harbors genetic diversity and readily adapts to environmental challenges, conferring upon it the ability to remediate. It is important to genetically determine the effects of bacterial application. The two-omics integration approach may shed more light on Pseudomonas isolates, filling the knowledge gap between genetic potential and dynamic function. In the present study, a strain from the Xi River was isolated using benzene-selective enrichment medium and phylogenetically identified as Pseudomonas sp. GDMCC 1.1703 by 16S rRNA gene sequencing. Its phenol degradability was optimally assessed at a rate of 45.7% (by statistics P < 0.05) in 12 h with a 200 mg/L concentration. Genomics and transcriptomics analyses were successively used to identify the genes and pathways responsible for phenol degradation. At least 42 genes were genomically identified to be involved in xenobiotic biodegradation. The degradative genes clustered into operons were hypothesized to have evolved through horizontal gene transfer. On the basis of genomic authentication, transcriptome analysis dynamically revealed that phenol degradation and responsive mechanisms were both upregulated as defense between the Ctrl (control) and PS (phenol-stressed) groups. Quantitative reverse transcription-PCR not only validated the key genes identified via RNA sequencing but also consistently confirmed the realistic intracellular expression. The approach of omics integration, which is effective in exploring the potential of isolates, will hopefully become an established method for determining the remediation potential of a candidate for development.

Mechanism of Action of Streptococcus downii, a New Bacterial Species with Probiotic Potential

Streptococcus downii is a recently reported bacterial species of oral origin, with inhibitory capacity against Streptococcus mutans, Actinomyces naeslundii, Veillonella parvula and Aggregatibacter actinomycetemcomitans, which confers upon it the potential of being an oral probiotic. The aim of the present study was to identify the potential mechanisms by which S. downii exerts its inhibitory effect on S. mutans. To this end, the study assessed the consumption of glucose and proteins available in the culture medium, the modification of the pH, the production of short-chain fatty acids, the changes in the protein panel of the inhibition halo, the production of hydrogen peroxide and the effect of proteinase K. There were no differences in the glucose values or in the protein content of the medium, but there was a reduction in pH (with no effect on the growth of S. mutans). Significant increases were detected in the levels of lactic and formic acid (with no effect on the growth of S. mutans), as well as changes in the peptide panel (with no effect on the growth of S. mutans). The inhibitory effect was maintained in the presence of peroxidase but disappeared after adding proteinase K. Based on these results, it is suggested that the main mechanism of inhibition of S. downii against S. mutans is the production of bacteriocins.

Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation

Bacteria have to persist under low iron conditions in order to adapt to the nutritional immunity of a host. Since the knowledge of iron stimulon of Bacteroidetes is sparse, we examined oral (Porphyromonas gingivalis and Prevotella intermedia) and gut (Bacteroides thataiotaomicron) representatives for their ability to adapt to iron deplete and iron replete conditions. Our transcriptomics and comparative genomics analysis show that many iron-regulated mechanisms are conserved within the phylum. They include genes upregulated in low iron, as follows: fldA (flavodoxin), hmu (hemin uptake operon), and loci encoding ABC transporters. Downregulated genes were frd (ferredoxin), rbr (rubrerythrin), sdh (succinate dehydrogenase/fumarate reductase), vor (oxoglutarate oxidoreductase/dehydrogenase), and pfor (pyruvate:ferredoxin/flavodoxin oxidoreductase). Some genus-specific mechanisms, such as the sus of B. thetaiotaomicron coding for carbohydrate metabolism and the xusABC coding for xenosiderophore utilization were also identified. While all bacteria tested in our study had the nrfAH operon coding for nitrite reduction and were able to reduce nitrite levels present in culture media, the expression of the operon was iron dependent only in B. thetaiotaomicron. It is noteworthy that we identified a significant overlap between regulated genes found in our study and the B. thetaiotaomicron colitis study (W. Zhu, M. G. Winter, L. Spiga, E. R. Hughes et al., Cell Host Microbe 27:376-388, 2020, http://dx.doi.org/10.1016/j.chom.2020.01.010). Many of those commonly regulated genes were also iron regulated in the oral bacterial genera. Overall, this work points to iron being the master regulator enabling bacterial persistence in the host and paves the way for a more generalized investigation of the molecular mechanisms of iron homeostasis in Bacteroidetes. IMPORTANCE Bacteroidetes are an important group of anaerobic bacteria abundant both in the oral and gut microbiomes. Although iron is a required nutrient for most living organisms, the molecular mechanisms of adaptation to the changing levels of iron are not well known in this group of bacteria. We defined the iron stimulon of Bacteroidetes by examination of the transcriptomic response of Porphyromonas gingivalis and Prevotella intermedia (both belong to the oral microbiome) and Bacteroidetes thetaiotaomicron (belongs to the gut microbiome). Our results indicate that many of the iron-regulated operons are shared among the three genera. Furthermore, using bioinformatics analysis, we identified a significant overlap between our in vitro studies and transcriptomic data derived from a colitis study, thus underscoring the biological significance of our work. Defining the iron-dependent stimulon of Bacteroidetes can help to identify the molecular mechanisms of iron-dependent regulation as well as better understand the persistence of the anaerobes in the human host.

New Preventive Strategy against Oral Biofilm Formation in Caries-Active Children: An In Vitro Study

Quorum quenching (QQ) is the inhibition of bacterial communication, i.e., quorum sensing (QS). QS is a key mechanism in regulating biofilm formation and phenotype in complex bacterial communities, such as those found within cariogenic biofilms. Whereas QQ approaches were shown to effectively reduce biomass, knowledge of their impact on the taxonomic composition of oral polymicrobial biofilms remains scarce. Here, we investigate the effect of the QQ lactonase Aii20J on biomass production and taxonomical composition of biofilms. We collected supragingival plaque samples from 10 caries-free and 10 caries-active children and cultured them to generate in vitro biofilms. We describe significant biomass reductions upon Aii20J exposure, as assessed by crystal violet assays. Taxonomical profiling using 16S rRNA gene amplicon sequencing revealed no significant changes in bacterial composition at the genus level. Interestingly, at the species level Aii20J-treatment increased the abundance of Streptococcus cristatus and Streptococcus salivarius. Both S. cristatus and S. salivarius express pH-buffering enzymes (arginine deiminase and urease, respectively) that catalyze ammonia production, thereby potentially raising local pH and counteracting the biofilm's cariogenic potential. Within the limitations of the study, our findings provide evidence of the biofilm-modulating ability of QQ and offer novel insights into alternative strategies to restore homeostasis within dysbiotic ecosystems.

Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients

Introduction. Although the presence of micro-organisms in the blood of healthy humans is a relatively new concept, there is a growing amount of evidence that blood might have its own microbiome.Gap Statement. Previous research has targeted the taxonomic composition of the blood microbiome using DNA-based sequencing methods, while little information is known about the presence of microbial transcripts obtained from the blood and their relation to conditions connected with increased gut permeability.Aim. To detect potentially alive and active micro-organisms and investigate differences in taxonomic composition between healthy people and patients with irritable bowel syndrome (IBS), we used the metatranscriptomics approach.Methodology. We collected blood samples from 23 IBS patients and 26 volunteers from the general population, and performed RNAseq on the isolated RNA. Reads corresponding to microbial genomes were identified with Kraken 2's standard plus protozoa and fungi database, and re-estimated at genus level with Bracken 2.7. We looked for trends in the taxonomic composition, making a comparison between the IBS and control groups, accounting for other different factors.Results. The dominant genera in the blood microbiome were found to be Cutibacterium, Bradyrhizobium, Escherichia, Pseudomonas, Micrococcus, Delftia, Mediterraneibacter, Staphylococcus, Stutzerimonas and Ralstonia. Some of these are typical environmental bacteria and could partially represent contamination. However, analysis of sequences from the negative controls suggested that some genera which are characteristic of the gut microbiome (Mediterraneibacter, Blautia, Collinsella, Klebsiella, Coprococcus, Dysosmobacter, Anaerostipes, Faecalibacterium, Dorea, Simiaoa, Bifidobacterium, Alistipes, Prevotella, Ruminococcus) are less likely to be a result of contamination. Differential analysis of microbes between groups showed that some taxa associated with the gut microbiome (Blautia, Faecalibacterium, Dorea, Bifidobacterium, Clostridium, Christensenella) are more prevalent in IBS patients compared to the general population. No significant correlations with any other factors were identified.Conclusion. Our findings support the existence of the blood microbiome and suggest the gut and possibly the oral microbiome as its origin, while the skin microbiome is a possible but less certain source. The blood microbiome is likely influenced by states of increased gut permeability such as IBS.

A multicentre study reveals dysbiosis in the microbial co-infection and antimicrobial resistance gene profile in the nasopharynx of COVID-19 patients

The impact of SARS-CoV-2 infection on the nasopharyngeal microbiome has not been well characterised. We sequenced genetic material extracted from nasopharyngeal swabs of SARS-CoV-2-positive individuals who were asymptomatic (n = 14), had mild (n = 64) or severe symptoms (n = 11), as well as from SARS-CoV-2-negative individuals who had never-been infected (n = 5) or had recovered from infection (n = 7). Using robust filters, we identified 1345 taxa with approximately 0.1% or greater read abundance. Overall, the severe cohort microbiome was least diverse. Bacterial pathogens were found in all cohorts, but fungal species identifications were rare. Few taxa were common between cohorts suggesting a limited human nasopharynx core microbiome. Genes encoding resistance mechanisms to 10 antimicrobial classes (> 25% sequence coverages, 315 genes, 63 non-redundant) were identified, with β-lactam resistance genes near ubiquitous. Patients infected with SARS-CoV-2 (asymptomatic and mild) had a greater incidence of antibiotic resistance genes and a greater microbial burden than the SARS-CoV-2-negative individuals. This should be considered when deciding how to treat COVID-19 related bacterial infections.

Impact of Growth Rate on the Protein-mRNA Ratio in Pseudomonas aeruginosa

Our understanding of how bacterial pathogens colonize and persist during human infection has been hampered by the limited characterization of bacterial physiology during infection and a research bias toward in vitro, fast-growing bacteria. Recent research has begun to address these gaps in knowledge by directly quantifying bacterial mRNA levels during human infection, with the goal of assessing microbial community function at the infection site. However, mRNA levels are not always predictive of protein levels, which are the primary functional units of a cell. Here, we used carefully controlled chemostat experiments to examine the relationship between mRNA and protein levels across four growth rates in the bacterial pathogen Pseudomonas aeruginosa. We found a genome-wide positive correlation between mRNA and protein abundances across all growth rates, with genes required for P. aeruginosa viability having stronger correlations than nonessential genes. We developed a statistical method to identify genes whose mRNA abundances poorly predict protein abundances and calculated an RNA-to-protein (RTP) conversion factor to improve mRNA predictions of protein levels. The application of the RTP conversion factor to publicly available transcriptome data sets was highly robust, enabling the more accurate prediction of P. aeruginosa protein levels across strains and growth conditions. Finally, the RTP conversion factor was applied to P. aeruginosa human cystic fibrosis (CF) infection transcriptomes to provide greater insights into the functionality of this bacterium in the CF lung. This study addresses a critical problem in infection microbiology by providing a framework for enhancing the functional interpretation of bacterial human infection transcriptome data. IMPORTANCE Our understanding of bacterial physiology during human infection is limited by the difficulty in assessing bacterial function at the infection site. Recent studies have begun to address this question by quantifying bacterial mRNA levels in human-derived samples using transcriptomics. One challenge for these studies is the poor predictivity of mRNA for protein levels for some genes. Here, we addressed this challenge by measuring the transcriptomes and proteomes of P. aeruginosa grown at four growth rates. Our results revealed that the growth rate does not impact the genome-wide correlation of mRNA and protein levels. We used statistical methods to identify the genes for which mRNA and protein were poorly correlated and developed an RNA-to-protein (RTP) conversion factor that improved the predictivity of protein levels across strains and growth conditions. Our results provide new insights into mRNA-protein correlations and tools to enhance our understanding of bacterial physiology from transcriptome data.

Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases

Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.

The significant clinical correlation of the intratumor oral microbiome in oral squamous cell carcinoma based on tissue-derived sequencing

Background: The microbiota is a critical component of the complex human microenvironment, impacting various physiological processes and disease development via the microbe-host interaction. In particular, the oral microbiota profoundly affects tumor development and progression. There is increasing evidence that oral microbiota is associated with the development of oral cancer, especially oral squamous cell carcinoma (OSCC). Methods: We comprehensively analyzed the oral microbiota in 133 OSCC samples worldwide. Subsequently, we evaluated the microbial compositions between OSCC patients and healthy people and their correlation with clinical parameters. The value of the oral microbiota as a diagnostic and prognostic biomarker was also determined. Results: This study found differences in critical oral microbiota between OSCC and normal controls. The most notable differences are present in p_Firmicutes, p_Actinobacteria, c_Fusobacteriia, o_Fusobacteriales, f_Fusobacteriaceae, and g_Fusobacterium. All six-level oral microorganisms were also associated with the clinical characteristics of OSCC, particularly with the clinical outcomes (survival time and status). We developed a predictive model based on this. We found that five different oral microorganisms have high confidence and can be used for clinical diagnosis and prognostic prediction, except for p_Actinobacteria. Conclusion: This study revealed that the intratumor oral microbiota of OSCC patients worldwide and the microbial signatures of OSCC patients possess similar properties in different regions, further refining the shortcomings of the current research field. We revealed that the oral microbiota could be used as a biomarker to reflect human health and disease progression status. This will provide new directions for tumor microbiome research. This means we can develop strategies through diet, probiotics, and antibiotics for cancer prevention and treatment.

A clinically validated human saliva metatranscriptomic test for global systems biology studies

The authors report here the development of a high-throughput, automated, inexpensive and clinically validated saliva metatranscriptome test that requires less than 100 μl of saliva. RNA is preserved at the time of sample collection, allowing for ambient-temperature transportation and storage for up to 28 days. Critically, the RNA preservative is also able to inactivate pathogenic microorganisms, rendering the samples noninfectious and allowing for safe and easy shipping. Given the unique set of convenience, low cost, safety and technical performance, this saliva metatranscriptomic test can be integrated into longitudinal, global-scale systems biology studies that will lead to an accelerated development of precision medicine, diagnostic and therapeutic tools.

Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases

Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.

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.

Oral mitis group streptococci: A silent majority in our oral cavity

Members of the oral mitis group streptococci including Streptococcus oralis, Streptococcus sanguinis, and Streptococcus gordonii are the most abundant inhabitants of human oral cavity and dental plaque, and have been implicated in infectious complications such as bacteremia and infective endocarditis. Oral mitis group streptococci are genetically close to Streptococcus pneumoniae; however, they do not produce cytolysin (pneumolysin), which is a key virulence factor of S. pneumoniae. Similar to S. pneumoniae, oral mitis group streptococci possess several cell surface proteins that bind to the cell surface components of host mammalian cells. S. sanguinis expresses long filamentous pili that bind to the matrix proteins of host cells. The cell wall-anchored nuclease of S. sanguinis contributes to the evasion of the neutrophil extracellular trap by digesting its web-like extracellular DNA. Oral mitis group streptococci produce glucosyltransferases, which synthesize glucan (glucose polymer) from sucrose of dietary origin. Neuraminidase (NA) is a virulent factor in oral mitis group streptococci. Influenza type A virus (IAV) relies on viral NA activity to release progeny viruses from infected cells and spread the infection, and NA-producing oral streptococci elevate the risk of IAV infection. Moreover, oral mitis group streptococci produce hydrogen peroxide (H₂ O₂ ) as a by-product of sugar metabolism. Although the concentrations of streptococcal H₂ O₂ are low (1-2 mM), they play important roles in bacterial competition in the oral cavity and evasion of phagocytosis by host macrophages and neutrophils. In this review, we intended to describe the diverse pathogenicity of oral mitis group streptococci.

Osteoimmunology in periodontitis; a paradigm for Th17/IL-17 inflammatory bone loss

Periodontitis is a prevalent human disease of inflammation-induced bone destruction. Through studies in patient lesions of rare and common forms of periodontitis and animal model experimentation, Th17/IL-17 related immune pathways have emerged as mediators of disease pathology. In this focused review, we examine mechanisms of induction, amplification and pathogenicity of Th17 cells in periodontitis.

Prevalence of periodontal disease in middle-aged and elderly patients and its influencing factors

OBJECTIVE

To explore the prevalence of periodontal disease in middle-aged and elderly patients and analyze its influencing factors.

METHODS

A total of 521 patients admitted to the Department of Stomatology of Fuyang District Chinese Medicine Hospital of Hangzhou from January 2019 to January 2022 were retrospectively collected as study subjects, including 176 patients aged 35-44 years old, 175 patients aged 45-64 years old, and 170 patients aged 65-74 years old. Community Periodontal Index (CPI) probe was used to detect gingival bleeding, periodontal pockets and attachment loss, and the prevalence of periodontal disease and its influencing factors were analyzed.

RESULTS

In the age group of 35-44, gingival bleeding was detected in 165 (93.75%) cases and dental calculus was detected in 176 (100.00%) cases; in the age group of 45-64, gingival bleeding was detected in 163 (93.14%) cases and dental calculus was detected in 161 (92.00%) cases; in the age group of 65-74, gingival bleeding was detected in 150 (88.24%) cases and dental calculus was detected in 162 (95.29%) cases. There were statistically significant differences in the detection rates of shallow periodontal pockets, deep periodontal pockets, and loss of periodontal attachment among the three groups (P<0.05). There wasalso asignificant difference in the detection rate of periodontitis among the three groups (P<0.05). Univariate analysis showed that gender, age, place of residence, smoking, alcohol consumption, brushing frequency, and dental cleaning in the past year were all associated with the occurrence of periodontitis (P<0.05). Logistic multi-factor regression analysis showed that age was a risk factor for the development of periodontitis in middle-aged and elderly patients (P<0.05).

CONCLUSION

The prevalence of periodontal disease in middle-aged and elderly individuals is high, with a high prevalence of gingival bleeding and shallow periodontal pockets. Age is an influencing factor on the incidence of periodontitis in middle-aged and elderly individuals.

Novel antibody assessment method for microbial compositional alteration in the oral cavity

Recently, it has been demonstrated that dysbiosis, an alteration in commensal microflora composition, is intimately involved in the onset of a variety of diseases. It is becoming increasingly evident that the composition of commensal microflora in the oral cavity is closely connected to oral diseases, such as periodontal disease, and systemic diseases, such as inflammatory bowel disease. Next-generation sequencing techniques are used as a method to examine changes in bacterial flora, but additional analytical methods to assess bacterial flora are needed to understand bacterial activity in more detail. In addition, the oral environment is unique because of the role of secretory antibodies contained in saliva in the formation of bacterial flora. The present study aimed to develop a new method for evaluating the compositional change of microbiota using flow cytometry (FCM) with specific antibodies against the bacterial surface antigen, as well as salivary antibodies. Using specific antibodies against Streptococcus mutans, a causative agent of dental caries, and human IgA, bacterial samples from human saliva were analyzed via FCM. The results showed that different profiles could be obtained depending on the oral hygiene status of the subjects. These results suggest that changes in the amount and type of antibodies that bind to oral bacteria may be an indicator for evaluating abnormalities in the oral flora. Therefore, the protocol established in this report could be applied as an evaluation method for alterations in the oral microbiota.

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We aimed to develop a new method for evaluating dysbiosis using flow cytometry.

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We used bacterial surface antigen-specific antibodies and salivary antibodies.

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Different profiles could be obtained depending on oral hygiene status.

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Changes in antibodies bound to oral bacteria may indicate oral flora abnormalities.

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Our method can be used to evaluate alterations in the oral microbiota.

Periodontitis may induce gut microbiota dysbiosis via salivary microbiota

The aim of this study was to identify whether periodontitis induces gut microbiota dysbiosis via invasion by salivary microbes. First, faecal and salivary samples were collected from periodontally healthy participants (PH group, n = 16) and patients with severe periodontitis (SP group, n = 21) and analysed by 16S ribosomal RNA sequencing. Significant differences were observed in both the faecal and salivary microbiota between the PH and SP groups. Notably, more saliva-sourced microbes were observed in the faecal samples of the SP group. Then, the remaining salivary microbes were transplanted into C57BL6/J mice (the C-PH group and the C-SP group), and it was found that the composition of the gut microbiota of the C-SP group was significantly different from that of the C-PH group, with Porphyromonadaceae and Fusobacterium being significantly enriched in the C-SP group. In the colon, the C-SP group showed significantly reduced crypt depth and zonula occludens-1 expression. The mRNA expression levels of pro-inflammatory cytokines, chemokines and tight junction proteins were significantly higher in the C-SP group. To further investigate whether salivary bacteria could persist in the intestine, the salivary microbiota was stained with carboxyfluorescein diacetate succinimidyl ester and transplanted into mice. We found that salivary microbes from both the PH group and the SP group could persist in the gut for at least 24 h. Thus, our data demonstrate that periodontitis may induce gut microbiota dysbiosis through the influx of salivary microbes.

Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era

Despite significant healthcare advances in the 21st century, the exact etiology of dental caries remains unsolved. The past two decades have witnessed a tremendous growth in our understanding of dental caries amid the advent of revolutionary omics technologies. Accordingly, a consensus has been reached that dental caries is a community-scale metabolic disorder, and its etiology is beyond a single causative organism. This conclusion was based on a variety of microbiome studies following the flow of information along the central dogma of biology from genomic data to the end products of metabolism. These studies were facilitated by the unprecedented growth of the next- generation sequencing tools and omics techniques, such as metagenomics and metatranscriptomics, to estimate the community composition of oral microbiome and its functional potential. Furthermore, the rapidly evolving proteomics and metabolomics platforms, including nuclear magnetic resonance spectroscopy and/or mass spectrometry coupled with chromatography, have enabled precise quantification of the translational outcomes. Although the majority supports ‘conserved functional changes’ as indicators of dysbiosis, it remains unclear how caries dynamics impact the microbiota functions and vice versa, over the course of disease onset and progression. What compounds the situation is the host-microbiota crosstalk. Genome-wide association studies have been undertaken to elucidate the interaction of host genetic variation with the microbiome. However, these studies are challenged by the complex interaction of host genetics and environmental factors. All these complementary approaches need to be orchestrated to capture the key players in this multifactorial disease. Herein, we critically review the milestones in caries research focusing on the state-of-art singular and integrative omics studies, supplemented with a bibliographic network analysis to address the oral microbiome, the host factors, and their interactions. Additionally, we highlight gaps in the dental literature and shed light on critical future research questions and study designs that could unravel the complexities of dental caries, the most globally widespread disease.

Immunoglobulin gene expression profiles and microbiome characteristics in periodontitis in nonhuman primates

Colonization of mucosal tissues throughout the body occurs by a wide array of bacteria in the microbiome that stimulate the cells and tissues, as well as respond to changes in the local milieu. A feature of periodontitis is the detection of adaptive immune responses to members of the oral microbiome that show specificity and changes with disease and treatment. Thus, variations in antibody responses are noted across the population and affected by aging, albeit, data are still unclear as to how these differences relate to disease risk and expression. This study used a nonhuman primate model of experimental periodontitis to track local microbiome changes as they related to the use and expression of a repertoire of immunoglobulin genes in gingival tissues. Gingival tissue biopsies from healthy tissues and following ligature-placement for disease initiation and progression provided gene expression analysis. Additionally, following removal of the ligatures, clinical healing occurs with gene expression in disease resolved tissues. Groups of 9 animals (young: <3 yrs., adolescent: 3-7 yrs., adult -12 to 15 yrs.; aged: 17-22 yrs) were used in the investigation. In healthy tissues, young and adolescent animals showed levels of expression of 78 Ig genes that were uniformly less than adults. In contrast, ⅔ of the Ig genes were elevated by > 2-fold in the aged samples. Specific increases in an array of the Ig gene transcripts were detected in adults at disease initiation and throughout progression, while increases in young and adolescent animals were observed only with disease progression, and in aged samples primarily late in disease progression. Resolved lesions continued to demonstrate elevated levels of Ig gene expression in only young, adolescent and adult animals. The array of Ig genes significantly correlated with inflammatory, tissue biology and hypoxia genes in the gingival tissues, with variations associated with age. In the young group of animals, specific members of the oral microbiome positively correlated with Ig gene expression, while in the older animals, many of these correlations were negative. Significant correlations were observed with a select assortment of bacterial OTUs and multiple Ig genes in both younger and older animal samples, albeit the genera/species showed little overlap. Incorporating this array of microbes and host responses clearly discriminated the various time points in transition from health to disease and resolution in both the young and adult animals. The results support a major importance of adaptive immune responses in the kinetics of periodontal lesion formation, and support aging effects on the repertoire of Ig genes that may relate to the increased prevalence and severity of periodontitis with age.

Cross-talk between the microbiome and chronic inflammation in esophageal cancer: potential driver of oncogenesis

Esophageal cancer (EC) is frequently considered a lethal malignancy and is often identified at a later stage. It is one of the major causes of cancer-related deaths globally. The conventional treatment methods like chemotherapy, radiotherapy, and surgery offer limited efficacy and poor clinical outcome with a less than 25% 5-year survival rate. The poor prognosis of EC persists despite the growth in the development of diagnostic and therapeutic modalities to treat EC. This underlines the need to elucidate the complex molecular mechanisms that drive esophageal oncogenesis. Apart from the role of the tumor microenvironment and its structural and cellular components in tumorigenesis, mounting evidence points towards the involvement of the esophageal microbiome, inflammation, and their cross-talk in promoting esophageal cancer. The current review summarizes recent research that delineates the underlying molecular mechanisms by which the microbiota and inflammation promote the pathophysiology of esophageal cancer, thus unraveling targets for potential therapeutic intervention.

Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective

The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. Here, we review historical and recent progress in our understanding of the oral microbiome, highlighting how oral microbiome research has significantly contributed to our understanding of microbial communities, with broad implications in polymicrobial diseases and across microbial community ecology. Further, we explore innovations and challenges associated with analyzing polymicrobial systems and suggest future directions of study. Finally, we provide a conceptual framework to systematically study microbial interactions within complex communities, not limited to the oral microbiota.

Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis

Periodontitis is an inflammatory disease that is characterized by progressive destruction of the periodontium and causes tooth loss in adults. Periodontitis is known to be associated with dysbiosis of the oral microflora, which is often linked to various diseases. However, the complexity of plaque microbial communities of periodontitis, antibiotic resistance, and enhanced virulence make this disease difficult to treat. In this study, using metagenomic shotgun sequencing, we investigated the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. We revealed a significant shift in the composition of oral microbiota as well as several functional pathways that were represented significantly more abundantly in periodontitis patients than in controls. In addition, we observed several positively selected ARGs and VirGs with the Ka/Ks ratio > 1 by analyzing our data and a previous periodontitis dataset, indicating that ARGs and VirGs in oral microbiota may be subjected to positive selection. Moreover, 5 of 12 positively selected ARGs and VirGs in periodontitis patients were found in the genomes of respiratory tract pathogens. Of note, 91.8% of the background VirGs with at least one non-synonymous single-nucleotide polymorphism for natural selection were also from respiratory tract pathogens. These observations suggest a potential association between periodontitis and respiratory infection at the gene level. Our study enriches the knowledge of pathogens and functional pathways as well as the positive selection of antibiotic resistance and pathogen virulence in periodontitis patients, and provides evidence at the gene level for an association between periodontitis and respiratory infection.

Oral Microbiome and Gingival Gene Expression of Inflammatory Biomolecules With Aging and Periodontitis

Although data describe the presence and increase of inflammatory mediators in the local environment in periodontitis vs. health in humans, details regarding how these responses evolve in the transition from health to disease, changes during disease progression, and features of a resolved lesion remain unknown. This study used a nonhuman primate model of ligature-induced periodontitis in young, adolescent, adult, and aged animals to document features of inflammatory response affected by age. Rhesus monkeys had ligatures tied and provided gingival tissue biopsy specimens at baseline, 0.5, 1, and 3 months of disease and at 5 months of the study, which was 2 months post-ligature removal for clinically resolved tissues. The transcriptome was assessed using microarrays for chemokine (n = 41), cytokine (n = 45), chemokine receptor (n = 21), cytokine receptor (n = 37), and lipid mediator (n = 31) genes. Limited differences were noted in healthy tissues for chemokine expression with age; however, chemokine receptor genes were decreased in young but elevated in aged samples. IL1A, IL36A, and IL36G cytokines were decreased in the younger groups, with IL36A elevated in aged animals. IL10RA/IL10RB cytokine receptors were altered with age. Striking variation in the lipid mediator genes in health was observed with nearly 60% of these genes altered with age. A specific repertoire of chemokine and chemokine receptor genes was affected by the disease process, predominated by changes during disease initiation. Cytokine/cytokine receptor genes were also elevated with disease initiation, albeit IL36B, IL36G, and IL36RN were all significantly decreased throughout disease and resolution. Significant changes were observed in similar lipid mediator genes with disease and resolution across the age groups. Examination of the microbiome links to the inflammatory genes demonstrated that specific microbes, including Fusobacterium, P. gingivalis, F. alocis, Pasteurellaceae, and Prevotella are most frequently significantly correlated. These correlations were generally positive in older animals and negative in younger specimens. Gene expression and microbiome patterns from baseline were distinctly different from disease and resolution. These results demonstrate patterns of inflammatory gene expression throughout the phases of the induction of a periodontal disease lesion. The patterns show a very different relationship to specific members of the oral microbiome in younger compared with older animals.

A quantitative framework reveals traditional laboratory growth is a highly accurate model of human oral infection

Bacterial behavior and virulence during human infection is difficult to study and largely unknown, as our vast knowledge of infection microbiology is primarily derived from studies using in vitro and animal models. Here, we characterize the physiology of Porphyromonas gingivalis, a periodontal pathogen, in its native environment using 93 published metatranscriptomic datasets from periodontally healthy and diseased individuals. P. gingivalis transcripts were more abundant in samples from periodontally diseased patients but only above 0.1% relative abundance in one-third of diseased samples. During human infection, P. gingivalis highly expressed genes encoding virulence factors such as fimbriae and gingipains (proteases) and genes involved in growth and metabolism, indicating that P. gingivalis is actively growing during disease. A quantitative framework for assessing the accuracy of model systems showed that 96% of P. gingivalis genes were expressed similarly in periodontitis and in vitro midlogarithmic growth, while significantly fewer genes were expressed similarly in periodontitis and in vitro stationary phase cultures (72%) or in a murine abscess infection model (85%). This high conservation in gene expression between periodontitis and logarithmic laboratory growth is driven by overall low variance in P. gingivalis gene expression, relative to other pathogens including Pseudomonas aeruginosa and Staphylococcus aureus Together, this study presents strong evidence for the use of simple test tube growth as the gold standard model for studying P. gingivalis biology, providing biological relevance for the thousands of laboratory experiments performed with logarithmic phase P. gingivalis Furthermore, this work highlights the need to quantitatively assess the accuracy of model systems.

Mucosal circadian rhythm pathway genes altered by aging and periodontitis

As circadian processes can impact the immune system and are affected by infections and inflammation, this study examined the expression of circadian rhythm genes in periodontitis.

METHODS

Macaca mulatta were used with naturally-occurring and ligature-induced periodontitis. Gingival tissue samples were obtained from healthy, diseased, and resolved sites in four groups: young (≤3 years), adolescent (3-7 years), adult (12-26) and aged (18-23 years). Microarrays targeted circadian rhythm (n = 42), inflammation/tissue destruction (n = 11), bone biology (n = 8) and hypoxia pathway (n = 7) genes.

RESULTS

The expression of many circadian rhythm genes, across functional components of the pathway, was decreased in healthy tissues from younger and aged animals, as well as showing significant decreases with periodontitis. Negative correlations of the circadian rhythm gene levels with inflammatory mediators and tissue destructive/remodeling genes were particularly accentuated in disease. A dominance of positive correlations with hypoxia genes was observed, except HIF1A, that was uniformly negatively correlated in health, disease and resolution.

CONCLUSIONS

The chronic inflammation of periodontitis exhibits an alteration of the circadian rhythm pathway, predominantly via decreased gene expression. Thus, variation in disease expression and the underlying molecular mechanisms of disease may be altered due to changes in regulation of the circadian rhythm pathway functions.

Can the Salivary Microbiome Predict Cardiovascular Diseases? Lessons Learned From the Qatari Population

Background: Many studies have linked dysbiosis of the gut microbiome to the development of cardiovascular diseases (CVD). However, studies assessing the association between the salivary microbiome and CVD risk on a large cohort remain sparse. This study aims to identify whether a predictive salivary microbiome signature is associated with a high risk of developing CVD in the Qatari population. Methods: Saliva samples from 2,974 Qatar Genome Project (QGP) participants were collected from Qatar Biobank (QBB). Based on the CVD score, subjects were classified into low-risk (LR < 10) (n = 2491), moderate-risk (MR = 10-20) (n = 320) and high-risk (HR > 30) (n = 163). To assess the salivary microbiome (SM) composition, 16S-rDNA libraries were sequenced and analyzed using QIIME-pipeline. Machine Learning (ML) strategies were used to identify SM-based predictors of CVD risk. Results: Firmicutes and Bacteroidetes were the predominant phyla among all the subjects included. Linear Discriminant Analysis Effect Size (LEfSe) analysis revealed that Clostridiaceae and Capnocytophaga were the most significantly abundant genera in the LR group, while Lactobacillus and Rothia were significantly abundant in the HR group. ML based prediction models revealed that Desulfobulbus, Prevotella, and Tissierellaceae were the common predictors of increased risk to CVD. Conclusion: This study identified significant differences in the SM composition in HR and LR CVD subjects. This is the first study to apply ML-based prediction modeling using the SM to predict CVD in an Arab population. More studies are required to better understand the mechanisms of how those microbes contribute to CVD.

Development and characterization of an oral microbiome transplant among Australians for the treatment of dental caries and periodontal disease: A study protocol

BACKGROUND

Oral microbiome transplantation (OMT) is a novel concept of introducing health-associated oral microbiota into the oral cavity of a diseased patient. The premise is to reverse the state of oral dysbiosis, and restore the ecological balance to maintain a stable homeostasis with the host immune system. This study will assess the effectiveness, feasibility, and safety of OMT using an interdisciplinary approach.

METHODS/DESIGN

To find donors suitable for microbial transplantation, supragingival plaque samples will be collected from 600 healthy participants. Each sample (200μL) will subsequently be examined in two ways: 1) 100μL of the sample will undergo high-throughput 16S rRNA gene amplicon sequencing and shotgun sequencing to identify the composition and characterisation of a healthy supragingival microbiome, 2) the remaining 100μL of the plaque sample will be mixed with 25% artificial saliva medium and inoculated into a specialised in-vitro flow cell model containing a hydroxyapatite disk. To obtain sufficient donor plaque, the samples would be grown for 14 days and further analysed microscopically and sequenced to examine and confirm the growth and survival of the microbiota. Samples with the healthiest microbiota would then be incorporated in a hydrogel delivery vehicle to enable transplantation of the donor oral microbiota. The third step would be to test the effectiveness of OMT in caries and periodontitis animal models for efficacy and safety for the treatment of oral diseases.

DISCUSSION

If OMTs are found to be successful, it can form a new treatment method for common oral diseases such as dental caries and periodontitis. OMTs may have the potential to modulate the oral microbiota and shift the ecological imbalances to a healthier state.

Oral microbial diversity analysis among atrophic glossitis patients and healthy individuals

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

Metagenomic and Metatranscriptomic Insight Into Oral Biofilms in Periodontitis and Related Systemic Diseases

The oral microbiome is one of the most complex microbial communities in the human body and is closely related to oral and systemic health. Dental plaque biofilms are the primary etiologic factor of periodontitis, which is a common chronic oral infectious disease. The interdependencies that exist among the resident microbiota constituents in dental biofilms and the interaction between pathogenic microorganisms and the host lead to the occurrence and progression of periodontitis. Therefore, accurately and comprehensively detecting periodontal organisms and dissecting their corresponding functional activity characteristics are crucial for revealing periodontitis pathogenesis. With the development of metagenomics and metatranscriptomics, the composition and structure of microbial communities as well as the overall functional characteristics of the flora can be fully profiled and revealed. In this review, we will critically examine the currently available metagenomic and metatranscriptomic evidence to bridge the gap between microbial dysbiosis and periodontitis and related systemic diseases.

Periodontitis associates with species-specific gene expression of the oral microbiota

The purpose of the present investigation was to characterize species-specific bacterial activity of the oral microbiota in periodontitis. We tested the hypotheses that chronic inflammation, i.e., periodontitis, associates with bacterial gene expression of the oral microbiota. Oral microbial samples were collected from three oral sites—subgingival plaque, tongue, and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species-specific bacterial activity as expressed by the ratio of specific messenger RNA reads to their corresponding genomic DNA reads. Here, we show the association of periodontitis with bacterial gene expression of the oral microbiota. While oral site was the main determinant of taxonomic composition as well as bacterial gene expression, periodontitis was significantly associated with a reduction of carbohydrate metabolism of the oral microbiota at three oral sites (subgingival plaque, tongue, and saliva). Data from the present study revealed the association of periodontitis with bacterial gene expression of the oral microbiota. Conditions of periodontitis was associated with bacterial activity of local subgingival plaque, but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis but also in other diseases with low-grade inflammation, such as type 2 diabetes mellitus.

Microbiome and Cancers of the Esophagus: A Review

Esophageal cancer (EC) is an aggressive malignant disease ranking amongst the leading causes of cancer deaths in the world. The two main histologic subtypes, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC), have distinct geographic and temporal patterns and risk factor profiles. Despite decades of research, the factors underlying these geo-temporal patterns are still not fully understood. The human microbiome has recently been implicated in various health conditions and disease, and it is possible that the microbiome may play an important role in the etiology of EC. Although studies of the microbiome and EC are still in their early stages, we review our current understanding of the potential links between ESCC, EAC, and bacterial communities in the oral cavity and esophagus. We also provide a summary of the epidemiology of EC and highlight some key challenges and future directions.

Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling

Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.