Ecology of the Oral Microbiome: Beyond Bacteria

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.

Profuse diversity and acidogenicity of the candida-biome of deep carious lesions of Severe Early Childhood Caries (S-ECC)

Introduction: The retentive niches of deep caries lesions have a distinct biome. Methods: We evaluated the site-specific (occlusal and proximal) Candida-biome of Severe-Early Childhood Caries (S-ECC) in 66- children (132 lesions). Asymptomatic primary molars fitting the definition of the International Caries Detection and Assessment-(ICDAS)-caries-code 5/6 were analyzed. Deep-dentinal sampling and simultaneous assessment of pH were performed. Clinical isolates were speciated using multiplex-PCR and evaluated for their acidogenic and aciduric potential.Results: Surprisingly, a high prevalence of Candida species (72.7%), either singly or in combination, was noted from both the proximal and occlusal cavities. C. tropicalis was the most prevalent species (47%; 34/72), followed by C. krusei (43.1%; 31/72) and C. albicans (40.3%; 29/72), with C. glabrata being the least (9.7%; 7/72). Over 45% low-pH niches (pH <7) of both sites yielded either dual or triple species of Candida. Genotyping revealed three distinct C. albicans genotypes (A, B, and C) with (14/29; 48.3%) of strains belonging to Genotype A. All four evaluated Candida species exhibited acidogenic and aciduric potential, C. tropicalis being the most potent.Conclusion: This, the first report of the high-density, multispecies, yeast colonization of deep-dentinal lesions in S-ECC, suggests that the Candida-biome plays a significant etiologic role in the condition, possibly due to their profound acidogenicity in milieus rich in dietary carbohydrates.

Oral Microbiota: A Major Player in the Diagnosis of Systemic Diseases

The oral cavity is host to a complex and diverse microbiota community which plays an important role in health and disease. Major oral infections, i.e., caries and periodontal diseases, are both responsible for and induced by oral microbiota dysbiosis. This dysbiosis is known to have an impact on other chronic systemic diseases, whether triggering or aggravating them, making the oral microbiota a novel target in diagnosing, following, and treating systemic diseases. In this review, we summarize the major roles that oral microbiota can play in systemic disease development and aggravation and also how novel tools can help investigate this complex ecosystem. Finally, we describe new therapeutic approaches based on oral bacterial recolonization or host modulation therapies. Collaboration in diagnosis and treatment between oral specialists and general health specialists is of key importance in bridging oral and systemic health and disease and improving patients' wellbeing.

Association between Oral Microbiome and Esophageal Diseases: A State-of-the-Art Review

BACKGROUND

Esophageal conditions result in significant morbidity and mortality worldwide. There is growing enthusiasm for discerning the role of microbiome in esophageal diseases. Conceivably, the focus has been on examining the role of local microbiome in esophageal diseases although this is somewhat limited by the invasive approach required to sample the esophageal tissue. Given the ease of sampling the oral cavity combined with the advances in genomic techniques, there is immense interest in discovering the role of the oral microbiome in esophageal conditions.

SUMMARY

In this review, we aim to discuss the current evidence highlighting the association between the oral microbiome and esophageal diseases. In particular, we have focused on summarizing the alterations in oral microbiome associated with malignant, premalignant, and benign esophageal cancers, inflammatory and infectious conditions, and esophageal dysmotility diseases. Identifying alterations in the oral microbiome is a key to advancing our understanding of the etiopathogenesis and progression of esophageal diseases, promoting novel diagnostics, and laying the foundation for personalized treatment approaches.

KEY MESSAGES

Further studies are needed to unravel the mechanisms by which the oral microbiome influences the development and progression of esophageal diseases, as well as to investigate whether alterations in the oral microbiome can impact the natural history of various esophageal diseases.

Efficacy of double antibiotics in hydroxypropyl methylcellulose for bactericidal activity against Enterococcus faecalis and Streptococcus gordonii in biofilm

OBJECTIVE

This study aimed to investigate the efficacy of double antibiotics, including ciprofloxacin and metronidazole, in a new vehicle, hydroxypropyl methylcellulose (HPMC), against Enterococcus faecalis and Streptococcus gordonii grown in biofilm.

DESIGN

Human mandibular premolars were prepared and divided into four groups: (i) negative control, (ii) positive control, (iii) infected with E. faecalis and S. gordonii for 21 days and intracanally medicated with double antibiotics in HPMC, and (iv) infected with E. faecalis and S. gordonii for 21 days and intracanally medicated with calcium hydroxide (UltraCal™). The efficacy of medication for 14 or 28 days was determined by bacterial cultures and RT-qPCR for absolute quantities of E. faecalis and S. gordonii cDNA and for relative mRNA expressions of pbp5 and gtfG genes.

RESULTS

There were significant decreases in the mean colony forming units and mean cDNA amounts of E. faecalis and S. gordonii in group (iii) on days 14 and 28 compared to those in group (ii) (p < 0.01). However, the mean cDNA amounts of E. faecalis and S. gordonii in group (iv) were found to be significantly increased on day 28 (p < 0.05). The mRNA expression of gtfG was significantly decreased in groups (iii) and (iv) on days 14 and 28, whereas that of pbp5 was significantly increased in group (iv) on days 14 and 28 (p < 0.01).

CONCLUSION

Double antibiotics in HPMC gel showed an in vitro efficacy against E. faecalis and S. gordonii grown in biofilm, suggesting its clinical application as an intracanal medicament for both primary and persistent infections.

Biofilm inhibition and bactericidal activity of NiTi alloy coated with graphene oxide/silver nanoparticles via electrophoretic deposition

Biofilm formation on medical devices can induce complications. Graphene oxide/silver nanoparticles (GO/AgNPs) coated nickel-titanium (NiTi) alloy has been successfully produced. Therefore, the aim of this study was to determine the anti-bacterial and anti-biofilm effects of a GO/AgNPs coated NiTi alloy prepared by Electrophoretic deposition (EPD). GO/AgNPs were coated on NiTi alloy using various coating times. The surface characteristics of the coated NiTi alloy substrates were investigated and its anti-biofilm and anti-bacterial effect on Streptococcus mutans biofilm were determined by measuring the biofilm mass and the number of viable cells using a crystal violet assay and colony counting assay, respectively. The results showed that although the surface roughness increased in a coating time-dependent manner, there was no positive correlation between the surface roughness and the total biofilm mass. However, increased GO/AgNPs deposition produced by the increased coating time significantly reduced the number of viable bacteria in the biofilm (p < 0.05). Therefore, the GO/AgNPs on NiTi alloy have an antibacterial effect on the S. mutans biofilm. However, the increased surface roughness does not influence total biofilm mass formation (p = 0.993). Modifying the NiTi alloy surface using GO/AgNPs can be a promising coating to reduce the consequences of biofilm formation.

Characterization of salivary microbiota in elderly patients with type 2 diabetes mellitus: a matched case-control study

OBJECTIVE

The importance of oral health in type 2 diabetes mellitus (T2DM) is widely recognized; however, oral microbiota characteristics associated with T2DM in the elderly population are not well-understood. This study was conducted to evaluate the characteristics of the salivary microbiota in elderly Japanese patients with T2DM.

METHODS

Saliva samples were collected from 42 elderly Japanese patients with T2DM and 42 age- and sex-matched subjects without T2DM (control). 16S ribosomal RNA metagenomic analysis and comparative analysis of both groups were performed. Random forest classification by machine learning was performed to discriminate between the salivary microbiota in the two groups.

RESULTS

There were significant differences in the overall salivary microbiota structure between the T2DM and control groups (beta diversity; unweighted UniFrac distances, p = 0.001; weighted UniFrac distances, p = 0.001). The phylum Firmicutes was abundant in patients with T2DM, whereas the phylum Bacteroidetes was abundant in controls. The T2DM prediction model by random forest based on salivary microbiota data was verified with a high predictive potential in five cross-validation tests (area under the curve (AUC) = 0.938 (95% CI, 0.824-1.000)).

CONCLUSION

Characterization revealed that the salivary microbiota profile of the elderly patients with T2DM is significantly distinct from that of the controls.

CLINICAL RELEVANCE

These data indicate the necessity of oral health management based on the characteristics of the salivary microbiota in elderly patients with T2DM. Our findings will contribute to future research on the development of new diagnostic and therapeutic methods for this purpose.

Microbial Screening Reveals Oral Site-Specific Locations of the Periodontal Pathogen Selenomonas noxia

INTRODUCTION

Selenomonas noxia (SN) is an important periodontal pathogen, associated with gingivitis and periodontitis. Many studies have found associations between SN and indicators of poor health outcomes, such as smoking, low socioeconomic status and obesity. However, less is known about the prevalence of this organism and more specifically about other oral site-specific locations that may harbor this organism.

METHODS

Using an existing patient repository (n = 47) of DNA isolated from saliva and other oral sites (n = 235), including the dorsum of the tongue, lower lingual incisor, upper buccal molar and gingival crevicular fluid (GCF), molecular screening for SN was performed. Screening results were analyzed for associations between demographic variables (age, sex, race/ethnicity) and clinical information (body mass index or BMI, presence of orthodontic brackets, primary/mixed/permanent dentition).

RESULTS

qPCR screening revealed a total of n = 62/235 sites or 26.3% harboring SN with saliva and GCF (either alone or in combination with one or more sites) most often observed (Saliva, n = 23/27 or 85.18%, GCF, n = 14/27 or 51%). Analysis of site-specific data revealed most positive results were found among saliva and GCF alone or in combination, with fewer positive results observed among the tongue (33.3%), lower lingual incisor (29.6%), and upper buccal molar (25.9%). No significant associations were found between demographic or clinical variables and presence of SN at any site.

CONCLUSIONS

These results may be among the first to describe site-specific locations of S. noxia among various additional oral biofilm sites. These data may represent a significant advancement in our understanding of the sites and locations that harbor this organism, which may be important for our understanding of the prevalence and distribution of these organisms among patients of different ages undergoing different types of oral treatments, such as orthodontic treatment or therapy.

Aging-Related Metabolic Dysfunction in the Salivary Gland: A Review of the Literature

Aging-related salivary dysfunction commonly induces the poor oral health, including decreased saliva flow and dental caries. Although the clinical significance of the salivary glands is well-known, the complex metabolic pathways contributing to the aging-dysfunction process are only beginning to be uncovered. Here, we provide a comprehensive overview of the metabolic changes in aging-mediated salivary gland dysfunction as a key aspect of oral physiology. Several metabolic neuropeptides or hormones are involved in causing or contributing to salivary gland dysfunction, including hyposalivation and age-related diseases. Thus, aging-related metabolism holds promise for early diagnosis, increased choice of therapy and the identification of new metabolic pathways that could potentially be targeted in salivary gland dysfunction.

Dental biofilm of symptomatic COVID-19 patients harbours SARS-CoV-2

Aims

SARS‐CoV‐2 RNA has been recovered from different sites in the human body, including the mouth. The present study aimed to investigate the presence of SARS‐CoV‐2 RNA in the dental biofilm of symptomatic patients who tested positive in nasopharyngeal and oropharyngeal (NASO/ORO) samples.

Materials & Methods

An observational clinical study of individuals with flu‐like symptoms was conducted between July and September 2020. Dental biofilm (BIO) samples were collected and analysed using real‐time quantitative polymerase chain reaction (RT‐qPCR) to determine the virus's presence.

Results

Seventy participants (40 ± 9.8 years of age, 71.4% female) tested positive for SARS‐CoV‐2 RNA in NASO/ORO samples and were included in the study. Among them, 13 tested positive in BIO samples (18.6%; 95% CI: [9.5, 27.7]). The median and interquartile range of cycle quantification (Cq) for NASO/ORO and BIO samples were 15.9 [6.9] and 35.9 [4.0] (p = .001), respectively. BIO‐positive participants showed a higher virus load in NASO/ORO samples (p = .012) than those testing negative (Cq = 20.4 [6.1]).

Conclusions

Dental biofilms from symptomatic COVID‐19 patients harbour SARS‐CoV‐2 RNA and might be a potential reservoir with an essential role in COVID‐19 transmission.

Drift of the Subgingival Periodontal Microbiome during Chronic Periodontitis in Type 2 Diabetes Mellitus Patients

Since periodontitis and type 2 diabetes mellitus are complex diseases, a thorough understanding of their pathogenesis requires knowing the relationship of these pathologies with other disorders and environmental factors. In this study, the representability of the subgingival periodontal microbiome of 46 subjects was studied by 16S rRNA gene sequencing and shotgun sequencing of pooled samples. We examined 15 patients with chronic periodontitis (CP), 15 patients with chronic periodontitis associated with type 2 diabetes mellitus (CPT2DM), and 16 healthy subjects (Control). The severity of generalized chronic periodontitis in both periodontitis groups of patients (CP and CPT2DM) was moderate (stage II). The male to female ratios were approximately equal in each group (22 males and 24 females); the average age of the subjects was 53.9 ± 7.3 and 54.3 ± 7.2 years, respectively. The presence of overweight patients (Body Mass Index (BMI) 30–34.9 kg/m²) and patients with class 1–2 obesity (BMI 35–45.9 kg/m²) was significantly higher in the CPT2DM group than in patients having only chronic periodontitis or in the Control group. However, there was no statistically significant difference in all clinical indices between the CP and CPT2DM groups. An analysis of the metagenomic data revealed that the alpha diversity in the CPT2DM group was increased compared to that in the CP and Control groups. The microbiome biomarkers associated with experimental groups were evaluated. In both groups of patients with periodontitis, the relative abundance of Porphyromonadaceae was increased compared to that in the Control group. The CPT2DM group was characterized by a lower relative abundance of Streptococcaceae/Pasteurellaceae and a higher abundance of Leptotrichiaceae compared to those in the CP and Control groups. Furthermore, the CP and CPT2DM groups differed in terms of the relative abundance of Veillonellaceae (which was decreased in the CPT2DM group compared to CP) and Neisseriaceae (which was increased in the CPT2DM group compared to CP). In addition, differences in bacterial content were identified by a combination of shotgun sequencing of pooled samples and genome-resolved metagenomics. The results indicate that there are subgingival microbiome-specific features in patients with chronic periodontitis associated with type 2 diabetes mellitus.

Helicobacter pylori infection is correlated with the incidence of erosive oral lichen planus and the alteration of the oral microbiome composition

BACKGROUND

Oral lichen planus (OLP), a common clinical oral disease, is associated with an increased risk of malignant transformation. The mechanism underlying the pathogenesis of OLP is unknown. Oral dysbacteriosis is reported to be one of the aetiological factors of OLP. Although Helicobacter pylori infection is associated with various oral diseases, the correlation between H. pylori infection and OLP is unclear. This study aimed to investigate the effect of H. pylori infection on OLP pathogenesis and oral microbiome composition in the Chinese population, which has a high incidence of H. pylori infection.

RESULT

In this study, saliva samples of 30 patients with OLP (OLP group) and 21 negative controls (NC group) were collected. H. pylori infection was detected using the carbon-13-labeled urea breath test (UBT). The saliva samples were divided into the following four groups based on the H. pylori status: H. pylori-positive OLP (OLP+), H. pylori-positive NC (NC+), H. pylori-negative OLP (OLP-), and H. pylori-negative NC (NC-). Oral microbiome compositions were significantly different between the OLP and NC groups and between the OLP- and OLP+ groups. Compared with those in the OLP- group, those in the OLP+ group had a higher incidence of erosive OLP and higher levels of salivary cytokines. In contrast, the oral microbiome composition and cytokine levels were not significantly different between the NC- and NC+ groups.

CONCLUSIONS

This is the first report to demonstrate that H. pylori infection is significantly correlated with the pathogenesis of erosive OLP.

Bacteriophage isolation from human saliva: a pilot study with high school students

Introduction

The microbiome of the human oral cavity is composed of numerous and diverse bacteria, archaea, eukarya and viruses [1]. Bacteriophages (abbreviated phages) are bacterial viruses that can attack and kill a target bacterium within minutes of infection. Very little is known about the impact of phages on the ecology of the oral microbiome and the aetiology of diseases of the oral cavity [2]. The lytic capacity of some phages suggests, that this may be promising antimicrobial agents that could be used to prevent or treat oral diseases [3]. The study aimed to isolate bacteriophages specific for Streptococcus mutans (causal agent of dental caries) and Enterococcus faecalis (causative agent of persistent apical periodontitis) from human saliva with the engagement of high school students in scientific research.

Materials and methods

Saliva samples were collected from 61 healthy donors, undergraduate students from Valsassina College, Lisbon, Portugal. All samples were examined for the presence of phages using the agar overlay method. The study was approved by the Egas Moniz Ethics Committee (approval number 636) and written informed consent was obtained from all subjects.

Results

Three to five days after inoculation with E. faecalis, uniform turbid lysis zones were generated by saliva samples collected from 6 of 61 individuals (9.8%). No plaques for S. mutans were evident after direct plating of the material.

Discussion and conclusions

It was possible to isolate E. faecalis, but not S. mutans bacteriophages. Our data is similar in prevalence to previous studies who also attempted to isolate lytic bacteriophage from oral E. faecalis [4]. The presence of E. faecalis phages in the saliva of healthy individuals suggests that they may play a role in the control of this bacterium in the oral cavity.

Maintaining homeostatic control of periodontal bone tissue

Alveolar bone is a unique osseous tissue due to the proximity of dental plaque biofilms. Periodontal health and homeostasis are mediated by a balanced host immune response to these polymicrobial biofilms. Dysbiotic shifts within dental plaque biofilms can drive a proinflammatory immune response state in the periodontal epithelial and gingival connective tissues, which leads to paracrine signaling to subjacent bone cells. Sustained chronic periodontal inflammation disrupts "coupled" osteoclast-osteoblast actions, which ultimately result in alveolar bone destruction. This chapter will provide an overview of alveolar bone physiology and will highlight why the oral microbiota is a critical regulator of alveolar bone remodeling. The ecology of dental plaque biofilms will be discussed in the context that periodontitis is a polymicrobial disruption of host homeostasis. The pathogenesis of periodontal bone loss will be explained from both a historical and current perspective, providing the opportunity to revisit the role of fibrosis in alveolar bone destruction. Periodontal immune cell interactions with bone cells will be reviewed based on our current understanding of osteoimmunological mechanisms influencing alveolar bone remodeling. Lastly, probiotic and prebiotic interventions in the oral microbiota will be evaluated as potential noninvasive therapies to support alveolar bone homeostasis and prevent periodontal bone loss.

Acquisition and establishment of the oral microbiota

Acquisition and establishment of the oral microbiota occur in a dynamic process over various stages and involve close and continuous interactions with the host and its environment. In the present review, we discuss the stages of this process in chronological order. We start with the prenatal period and address the following questions: ‘Is the fetus exposed to maternal microbiota during pregnancy?’ and ‘If so, what is the potential role of this exposure?’ We comment on recent reports of finding bacterial DNA in placenta during pregnancies, and provide current views on the potential functions of prenatal microbial encounters. Next, we discuss the physiological adaptations that take place in the newborn during the birth process and the effect of this phase of life on the acquisition of the oral microbiota. Is it really just exposure to maternal vaginal microbes that results in the difference between vaginally and Cesarian section‐born infants? Then, we review the postnatal phase, in which we focus on transmission of microbes, the intraoral niche specificity, the effects of the host behavior and environment, as well as the role of genetic background of the host on shaping the oral microbial ecosystem. We discuss the changes in oral microbiota during the transition from deciduous to permanent dentition and during puberty. We also address the finite knowledge on colonization of the oral cavity by microbes other than the bacterial component. Finally, we identify the main outstanding questions that limit our understanding of the acquisition and establishment of a healthy microbiome at an individual level.

The oralome and its dysbiosis: New insights into oral microbiome-host interactions

The oralome is the summary of the dynamic interactions orchestrated between the ecological community of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorganisms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this review, we discuss the composition of the oralome and inter-species and host-microbial interactions that take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to disease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and caries and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer's disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, probiotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) disruption, and host response modulators.

Dynamic Alterations of Oral Microbiota Related to Halitosis in Preschool Children

Objective

This longitudinal study was aimed to evaluate the dynamic shift in oral microbiota during the process of halitosis progression among preschool children.

Methods

The oral examinations, questionnaires and tongue coating specimens were collected at the baseline and 12-month follow-up. All children were oral healthy at the enrollment. At the 12-month follow-up, children who developed halitosis were included to the halitosis group (n = 10). While children who matched the age, gender, kindergarten and without halitosis were included to the control group (n = 10). 16S rRNA gene sequencing was used to reveal the shift of the tongue coating microbiome in these children during the 12- month period with the Human Oral Microbiome Database.

Results

A remarkable shift in relative abundance of specific bacteria was observed prior to halitosis development. The principal coordinates and alpha diversity analyses revealed different shifting patterns of halitosis and the healthy participants’ microbiome structures and bacterial diversity over the 12-month follow-up. Both groups showed variable microbiota community structures before the onset of halitosis. Halitosis-enriched species Prevotella melaninogenica, Actinomyces sp._HMT_180 and Saccharibacteria TM7_G-1_bacterium_HMT_352 were finally selected as biomarkers in the halitosis-onset prediction model after screening, with a prediction accuracy of 91.7%.

Conclusions

The microbiome composition and relative abundance of the tongue coatings in the halitosis and control groups remarkably differed, even prior to the onset of the clinical manifestations of halitosis. The halitosis prediction model constructed on the basis of tongue coating microbiome biomarkers indicated the microbial shifts before the halitosis onset. Therefore, this can be considered for the timely detection and intervention of halitosis in children.

Characterization of Salivary Microbiota in Patients with Atherosclerotic Cardiovascular Disease: A Case-Control Study

Aims: Oral bacteria have been reported to be associated with the pathogenesis of atherosclerosis; however, the relationship between the oral microbiota and atherosclerosis remains unclear. The present study aimed to investigate whether or not salivary microbiota of patients with atherosclerotic cardiovascular disease (ACVD) differs from that of subjects without ACVD, and to characterize the salivary microbiota of patients with ACVD.

Methods: This study included 43 patients with ACVD and 86 age- and sex-matched non-ACVD individuals. 16S rRNA metagenomic analysis were performed using DNA isolated from the saliva samples of the participants. To select unique operational taxonomic unit (OTU) sets of ACVD, we conducted the random forest algorithm in machine learning, followed by confirmation via 10-fold cross-validation

Results: There was no difference in richness or evenness between the ACVD and non-ACVD groups (alpha diversity; observed OTU index, p =0.503; Shannon’s index, p =0.478). However, significant differences were found in the overall salivary microbiota structure (beta diversity; unweighted UniFrac distances, p =0.001; weighted UniFrac distances, p =0.001). The Actinobacteria phylum was highly abundant in patients with ACVD, while the Bacteroidetes phylum was less abundant. The random forest classifier identified 43 OTUs as an optimal marker set of ACVD. In a 10-fold cross validation using the validation data, an area under the curve (AUC) of 0.933 (95% CI, 0.855–1.000) was obtained.

Conclusions: The salivary microbiota in patients with ACVD was distinct from that of non-ACVD individuals, indicating that the salivary microbiota may be related to ACVD.

Study of oral microorganisms contributing to non-carious cervical lesions via bacterial interaction and pH regulation

There is a lack of evidence about the relationship between microorganisms and non‐carious cervical lesions (NCCLs) due to limited technologies. A group of 78 patients was enrolled for microbial 16S rRNA sequencing of dental plaques on normal and defective cervical surfaces. Parallel data from 39 patients were analysed with paired t tests, and Fusobacteriales exhibited significantly less distribution on NCCLs than on normal surfaces. As a result, Fusobacterium nucleatum, the most common oral bacterial strain belonging to the order Fusobacteriales, was selected for further research. From a scanning electron microscopy (SEM) scan, the tooth surface with Fusobacterium nucleatum and Streptococcus mutans culture was more intact than that without Fusobacterium nucleatum. Furthermore, the calcium contents in groups with Fusobacterium nucleatum were significantly higher than that without it. In further mechanistic research, Fusobacterium nucleatum was demonstrated to adhere to and disturb other organisms as well as producing alkaline secretions to neutralize the deleterious acidic environment, protecting the tooth structure. In conclusion, microorganisms and NCCLs were confirmed directly related through adherent bacterial interactions and pH regulation. The research provides a new perspective and experimental evidence for the relation between microorganisms and NCCLs, which guides clinical treatment and preventive dentistry in the future.

Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria

Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conduct a long-read metagenomic study of human saliva using PromethION. Our analyses, which integrate both PromethION and HiSeq data of >30 Gb per sample with low human DNA contamination, identify hundreds of viral contigs; 0-43.8% and 12.5-56.3% of the confidently predicted phages and prophages, respectively, do not cluster with those reported previously. Our analyses demonstrate enhanced scaffolding, and the ability to place a prophage in its host genomic context and enable its taxonomic classification. Our analyses also identify a Streptococcus phage/prophage group and nine jumbo phages/prophages. 86% of the phage/prophage group and 67% of the jumbo phages/prophages contain remote homologs of antimicrobial resistance genes. Pan-genome analysis of the phages/prophages reveals remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Furthermore, our study suggests that oral phages present in human saliva are under selective pressure to escape CRISPR immunity. Our study demonstrates the power of long-read metagenomics utilizing PromethION in uncovering bacteriophages and their interaction with host bacteria.

Quantitative interactions between Candida albicans and the mutans streptococci in patients with Down Syndrome

BACKGROUND

Oral microorganisms produce damage through the transfer to bloodstream, colonizing other tissues or direct damage in the oral cavity. Aim to study the quantitative interactions between C. albicans and the mutans streptococci and ms serotypes in the saliva of the oral cavity of patients with Down syndrome (DS).

MATERIAL AND METHODS

Included 120 patients of both genders, 60 patients with Down syndrome (DS) and 60 pa- tients as a control group (CG). Samples of saliva were taken, and bacteria and fungi were grown on TYCSB and Saboureaud agar. Microbiological, serological and quantitative analyses were performed to determine the kind of isolated of microorganisms corresponding to the ms c, e, f and k for species S. mutans and d and g for S. sobrinus and C. albicans. Electronic scanning microscopy was employed to visualize and confirm the colonies under study. Statistics analysis included t-test proofs for matched data test, Scheffé and ANOVA.

RESULTS

Forming units (CFU) per mL of saliva of C. albicans a significant difference was observed among DS<CG groups. A correlation of the C. albicans quantity and the ms count was found by age intervals however, tendencies were different in SD and CG. Also, the CFU of C. albicans was different among the serotypes of ms (c, e, f, k <d, g, h, <notyped).

CONCLUSIONS

These results show a significant non-random association between these two commensal microorganisms in different patient groups.

The human virome: assembly, composition and host interactions

The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 10³¹ particles on Earth. The human virome is similarly vast and complex, consisting of approximately 10¹³ particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.

Recombinant bacteriophage T4 Rnl1 impacts Streptococcus mutans biofilm formation

Bacteriophage T4 RNA ligase 1 (T4 Rnl1) can be stably expressed in many bacteria and has been reported to affect the bioactivity of the host bacteria. Recently, we constructed bacteriophage T4 Rnl1 expressing system in Streptococcus mutans, a crucial biofilm-forming and dental caries-causing oral pathogen. Here, we characterized the function of recombinant bacteriophage T4 Rnl1 in biofilm formation of S. mutans. The T4 Rnl1 mutant exhibited similar growth phenotype but resulted in a significant reduction of biofilm biomass compared to wild type strain and empty plasmid carrying strain. The abnormal biofilm of the T4 Rnl1 mutant harbored loose bacterial clusters with defective production and distribution of exopolysaccharides. Moreover, the expression of several biofilm formation-associated genes was dysregulated at mRNA level in the T4 Rnl1 mutant. These results reveal that the bacteriophage T4 Rnl1 exert antibiofilm activities against the cariogenic bacterium S. mutans, which impacts the spatial organization of the exopolysaccharides and further impairs the three-dimensional biofilm architecture. These findings implicate that manipulation of bacteriophage T4 Rnl1, a biological tool used for RNA ligation, will provide a promising approach to cariogenic biofilm control.

Bacterial diversity and functional analysis of severe early childhood caries and recurrence in India

Dental caries is the most prevalent oral disease affecting nearly 70% of children in India and elsewhere. Micro-ecological niche based acidification due to dysbiosis in oral microbiome are crucial for caries onset and progression. Here we report the tooth bacteriome diversity compared in Indian children with caries free (CF), severe early childhood caries (SC) and recurrent caries (RC). High quality V3–V4 amplicon sequencing revealed that SC exhibited high bacterial diversity with unique combination and interrelationship. Gracillibacteria_GN02 and TM7 were unique in CF and SC respectively, while Bacteroidetes, Fusobacteria were significantly high in RC. Interestingly, we found Streptococcus oralis subsp. tigurinus clade 071 in all groups with significant abundance in SC and RC. Positive correlation between low and high abundant bacteria as well as with TCS, PTS and ABC transporters were seen from co-occurrence network analysis. This could lead to persistence of SC niche resulting in RC. Comparative in vitro assessment of biofilm formation showed that the standard culture of S. oralis and its phylogenetically similar clinical isolates showed profound biofilm formation and augmented the growth and enhanced biofilm formation in S. mutans in both dual and multispecies cultures.

Heme Competition Triggers an Increase in the Pathogenic Potential of Porphyromonas gingivalis in Porphyromonas gingivalis-Candida albicans Mixed Biofilm

As one of the main pathogens of periodontitis, Porphyromonas gingivalis often forms mixed biofilms with other bacteria or fungi under the gingiva, such as Candida albicans. Heme is an important iron source for P. gingivalis and C. albicans that supports their growth in the host. From the perspective of heme competition, this study aims to clarify that the competition for heme enhances the pathogenic potential of P. gingivalis during the interaction between P. gingivalis and C. albicans. Porphyromonas gingivalis single-species biofilm and P. gingivalis-C. albicans dual-species biofilm were established in a low- and high-heme environment. The results showed that the vitality of P. gingivalis was increased in the dual-species biofilm under the condition of low heme, and the same trend was observed under a laser confocal microscope. Furthermore, the morphological changes in P. gingivalis were observed by electron microscope, and the resistance of P. gingivalis in dual-species biofilm was stronger against the killing effect of healthy human serum and antibiotics. The ability of P. gingivalis to agglutinate erythrocyte was also enhanced in dual-species biofilm. These changes disappeared when heme was sufficient, which confirmed that heme competition was the cause of thepathogenicy change in P. gingivalis. Gene level analysis showed that P. gingivalis was in a superior position in the competition relationship by increasing the expression of heme utilization-related genes, such as HmuY, HmuR, HusA, and Tlr. In addition, the expression of genes encoding gingipains (Kgp, RgpA/B) was also significantly increased. They not only participate in the process of utilizing heme, but also are important components of the virulence factors of P. gingivalis. In conclusion, our results indicated that the pathogenic potential of P. gingivalis was enhanced by C. albicans through heme competition, which ultimately promoted the occurrence and development of periodontitis and, therefore, C. albicans subgingival colonization should be considered as a factor in assessing the risk of periodontitis.

The saccharibacterium TM7x elicits differential responses across its host range

Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces, thirteen strains, including XH001, could host TM7x, and further classified into "permissive" and "nonpermissive" based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.

Keystone salivary mycobiome in postpartum period in health and disease conditions

Despite of known pathogenic potential of human mycobiome in initiation and progression of oral disorders, it is poorly characterized and understudied due to its small number in oral cavity. In the present study, salivary mycobiome of three postpartum females along with one healthy non-pregnant female was investigated by targeting ITS region. A total of 55 genera and 92 species were detected with predominant genera: Candida (12.2%) followed by Saccharomyces (9.27%), Phialosimplex (9.19%), Termitomyces (6.96%), Penicillium (6.85%), Aspergillus (6.56%), Olpidium (5.15%), Cochliobolus (4.78%), Malassezia (4.61%), Neurospora (4.3%), and Cristinia (3.04%) in all samples. Diversity increase was observed in postpartum group as compared to non-pregnant female. Stachybotrys, Geotrichum, Talaromyces, Leucosporidium, Acremonium, Wallemia, Eupenicillium, Septoria, Zymoseptoria, Coniosporium, Phialophora, and Mycosphaerella were genera detected only in postpartum group. Postpartum female with gingivitis and dental caries showed greater abundance of genus Saccharomyces, Phialosimplex, Candida, Olpidium, Cochliobolus, Malaseezia, Hyphodontia, Debaryomyces, Mrakia, and Nakaseomyces as compared to those postpartum females with good oral health. Among postpartum group female with oral health issues as well as who had preterm low weight birth (PLWB), showed reduced richness, evenness with elevated levels of Saccharomyces, Candida, Hyphodontia and Malassezia compared to the female having full term birth (FTB). These findings showed that, pregnancy with or without oral health issues is associated with oral microbial diversity change and there might be an association of changing fungal diversity with adverse pregnancy outcomes (APOs) like pre-term birth (PTB) and low weight birth (LWB).

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. Forty-two of these species had no genomes in public repositories, thereby representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understood to be obligate epibionts, which are dependent on host bacteria. These data suggest that the various Saccharibacteria clades may rely on their hosts for highly distinct metabolic requirements, which would have significant evolutionary and ecological implications. Across the study group, Rothia, Neisseria, and Haemophilus spp. were associated with good dental health, whereas Prevotella spp., Streptococcus mutans, and Human herpesvirus 4 (Epstein-Barr virus [EBV]) were more prevalent in children with caries. Finally, 10 of the host immunological markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential relationships between microbes and host immunological molecules. Overall, this study illustrated the oral microbiome at an unprecedented resolution and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.

Oral Neutrophils: Underestimated Players in Oral Cancer

The composition of the oral milieu reflects oral health. Saliva provides an environment for multiple microorganisms, and contains soluble factors and immune cells. Neutrophils, which rapidly react on the changes in the microenvironment, are a major immune cell population in saliva and thus may serve as a biomarker for oral pathologies. This review focuses on salivary neutrophils in the oral cavity, their phenotype changes in physiological and pathological conditions, as well as on factors regulating oral neutrophil amount, activation and functionality, with special emphasis on oral cancer and its risk factors.

Role of Oral Bacteria in the Development of Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is an invasive epithelial neoplasm that is influenced by various risk factors, with a low survival rate and an increasing death rate. In the past few years, with the verification of the close relationship between different types of cancers and the microbiome, research has focused on the compositional changes of oral bacteria and their role in OSCC. Generally, oral bacteria can participate in OSCC development by promoting cell proliferation and angiogenesis, influencing normal apoptosis, facilitating invasion and metastasis, and assisting cancer stem cells. The study findings on the association between oral bacteria and OSCC may provide new insight into methods for early diagnosis and treatment development.

Oral microbiota alteration associated with oral cancer and areca chewing

Oral cancer is among most common neoplasm of oral cavity; in many cases, it develops at the site of premalignant lesion. Areca nut has been identified as a carcinogen, which was proved to promote the inflammation level and contributes to oral malignancy. Chewing areca nut is the main cause of the premalignant disease oral submucous fibrosis (OSF). Bacterial alterations were suggested to be assonated with oral cancer progression. Therefore, the present study was carried out to determine the changes of microbiota in the mucosa along stage of development of oral cancer with areca nut chewing. 162 participants, reporting to department of oral medical center, were enrolled into the study which includes 45 patients each of OSF, 42 of oral cancer, 29 healthy controls (HC) with areca nut chewing, and 46 healthy controls (HC) never chewing areca nut. Oral swabbing of tongue dorsum, buccal mucosa, and gingiva was evaluated by MiSeq platform of the V3-V4 region of the 16S rRNA gene. These data revealed microbial changes that may mirror oral cancer progression and reflect clinical preconditions such as areca nut chewing. Consequently, revealing microbial changes in patients with oral squamous cell carcinomas and the premalignant disease oral submucous fibrosis (OSF) with areca nut chewing might improve our understanding of the pathobiology of the disease and help in the design of novel diagnostic and treatment strategies.

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.

The Role of Oral Microbiota in Intra-Oral Halitosis

Halitosis is a common ailment concerning 15% to 60% of the human population. Halitosis can be divided into extra-oral halitosis (EOH) and intra-oral halitosis (IOH). The IOH is formed by volatile compounds, which are produced mainly by anaerobic bacteria. To these odorous substances belong volatile sulfur compounds (VSCs), aromatic compounds, amines, short-chain fatty or organic acids, alcohols, aliphatic compounds, aldehydes, and ketones. The most important VSCs are hydrogen sulfide, dimethyl sulfide, dimethyl disulfide, and methyl mercaptan. VSCs can be toxic for human cells even at low concentrations. The oral bacteria most related to halitosis are Actinomyces spp., Bacteroides spp., Dialister spp., Eubacterium spp., Fusobacterium spp., Leptotrichia spp., Peptostreptococcus spp., Porphyromonas spp., Prevotella spp., Selenomonas spp., Solobacterium spp., Tannerella forsythia, and Veillonella spp. Most bacteria that cause halitosis are responsible for periodontitis, but they can also affect the development of oral and digestive tract cancers. Malodorous agents responsible for carcinogenesis are hydrogen sulfide and acetaldehyde.

Role of the oral microbiota in cancer evolution and progression

Bacteria identified in the oral cavity are highly complicated. They include approximately 1000 species with a diverse variety of commensal microbes that play crucial roles in the health status of individuals. Epidemiological studies related to molecular pathology have revealed that there is a close relationship between oral microbiota and tumor occurrence. Oral microbiota has attracted considerable attention for its role in in‐situ or distant tumor progression. Anaerobic oral bacteria with potential pathogenic abilities, especially Fusobacterium nucleatum and Porphyromonas gingivalis, are well studied and have close relationships with various types of carcinomas. Some aerobic bacteria such as Parvimonas are also linked to tumorigenesis. Moreover, human papillomavirus, oral fungi, and parasites are closely associated with oropharyngeal carcinoma. Microbial dysbiosis, colonization, and translocation of oral microbiota are necessary for implementation of carcinogenic functions. Various underlying mechanisms of oral microbiota‐induced carcinogenesis have been reported including excessive inflammatory reaction, immunosuppression of host, promotion of malignant transformation, antiapoptotic activity, and secretion of carcinogens. In this review, we have systemically described the impact of oral microbial abnormalities on carcinogenesis and the future directions in this field for bringing in new ideas for effective prevention of tumors.

The mycobiota of the human body: a spark can start a prairie fire

Mycobiota are inseparable from human health, shaking up the unique position held by bacteria among microorganisms. What is surprising is that this seemingly small species can trigger huge changes in the human body. Dysbiosis and invasion of mycobiota are confirmed to cause disease in different parts of the body. Meanwhile, our body also produces corresponding immune changes upon mycobiota infection. Several recent studies have made a connection between intestinal mycobiota and the human immune system. In this review, we focus on questions related to mycobiota, starting with an introduction of select species, then we summarize the typical diseases caused by mycobiota in different parts of the human body. Moreover, we constructed a framework for the human anti-fungal immune system based on genetics and immunology. Finally, the progression of fungal detection methods is also reviewed.

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts

Oral microbiome research has moved from asking "Who's there?" to "What are they doing?" Understanding what microbes "do" involves multiple approaches, including obtaining genomic information and examining the interspecies interactions. Recently we isolated a human oral Saccharibacteria (TM7) bacterium, HMT-952, strain TM7x, which is an ultrasmall parasite of the oral bacterium Actinomyces odontolyticus. The host-parasite interactions, such as phage-bacterium or Saccharibacteria-host bacterium, are understudied areas with large potential for insight. The Saccharibacteria phylum is a member of Candidate Phyla Radiation, a large lineage previously devoid of cultivated members. However, expanding our understanding of Saccharibacteria-host interactions requires examining multiple phylogenetically distinct Saccharibacteria-host pairs. Here we report the isolation of 3 additional Saccharibacteria species from the human oral cavity in binary coculture with their bacterial hosts. They were obtained by filtering ultrasmall Saccharibacteria cells free of other larger bacteria and inoculating them into cultures of potential host bacteria. The binary cocultures obtained could be stably passaged and studied. Complete closed genomes were obtained and allowed full genome analyses. All have small genomes (<1 Mb) characteristic of parasitic species and dramatically limited de novo synthetic pathway capabilities but include either restriction modification or CRISPR-Cas systems as part of an innate defense against foreign DNA. High levels of gene synteny exist among Saccharibacteria species. Having isolates growing in coculture with their hosts allowed time course studies of growth and parasite-host interactions by phase contrast, fluorescence in situ hybridization, and scanning electron microscopy. The cells of the 4 oral Saccharibacteria species are ultrasmall and could be seen attached to their larger Actinobacteria hosts. Parasite attachment appears to lead to host cell death and lysis. The successful cultivation of Saccharibacteria species has significantly expanded our understanding of these ultrasmall Candidate Phyla Radiation bacteria.

Colonization by Pseudomonas aeruginosa and Staphylococcus aureus of Antral Biopsy Specimens from Gastritis Patients Uninfected with Helicobacter Pylori

Purpose

Roles and incidence of some microorganisms that transiently or permanently colonize the human stomach are still unknown despite advances in gastroenterology. We aimed to examine the incidence of four microorganisms, Helicobacter pylori, Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis, in the antral biopsy specimens of patients with gastroduodenal conditions.

Patients and Methods

Patients (67 females, 33 males; mean age = 49.5 years) were initially examined and diagnosed by a gastroenterologist at the Mehrad Hospital, Tehran, Iran. We enrolled those who underwent the upper gastrointestinal endoscopy because of gastroduodenal conditions. Two antral biopsy samples were taken by endoscopy; the first sample was used for the “rapid urease test” to confirm H. pylori. The second was used for DNA extraction and PCR analyses with specific, corresponding primer sets to establish the presence of the four microorganisms. Our study was approved by the Ethics Committee at the Tarbiat Modares University, Tehran.

Results

Based on pathology and endoscopy findings, we divided the patients into three groups: 62 presented with gastritis, 18 with duodenal ulcer, and 20 gastric ulcer. The number of patients with P. aeruginosa but without H. pylori significantly differed from the number of those co-infected with both microorganisms (P = 0.03). Additionally, a similar significance was found between the incidence of S. aureus in patients without H. pylori and those with both infections (P = 0.04). Our results indicated that a significant number of patients with gastritis were colonized with P. aeruginosa or S. aureus without being co-infected with H. pylori (P < 0.001). Interestingly, the incidence of colonization by P. aeruginosa of patients without H. pylori (45/49, 91.8%) was higher than that by S. aureus (28/49, 57%).

Conclusion

The number of patients without H. pylori but with P. aeruginosa or with S. aureus infection significantly differed from that with both infections, respectively. Our study thus shows that patients without H. pylori infection are prone to be colonized by P. aeruginosa or S. aureus, indicating that targeted antibiotic regimens are necessary for clinically treating them.

Mucosal microbial parasites/symbionts in health and disease: an integrative overview

Microbial parasites adapted to thrive at mammalian mucosal surfaces have evolved multiple times from phylogenetically distant lineages into various extracellular and intracellular life styles. Their symbiotic relationships can range from commensalism to parasitism and more recently some host-parasites interactions are thought to have evolved into mutualistic associations too. It is increasingly appreciated that this diversity of symbiotic outcomes is the product of a complex network of parasites-microbiota-host interactions. Refinement and broader use of DNA based detection techniques are providing increasing evidence of how common some mucosal microbial parasites are and their host range, with some species being able to swap hosts, including from farm and pet animals to humans. A selection of examples will illustrate the zoonotic potential for a number of microbial parasites and how some species can be either disruptive or beneficial nodes in the complex networks of host-microbe interactions disrupting or maintaining mucosal homoeostasis. It will be argued that mucosal microbial parasitic diversity will represent an important resource to help us dissect through comparative studies the role of host-microbe interactions in both human health and disease.

Mouth-Watering Results: Clinical Need, Current Approaches, and Future Directions for Salivary Gland Regeneration

Permanent damage to the salivary glands and resulting hyposalivation and xerostomia have a substantial impact on patient health, quality of life, and healthcare costs. Currently, patients rely on lifelong treatments that alleviate the symptoms, but no long-term restorative solutions exist. Recent advances in adult stem cell enrichment and transplantation, bioengineering, and gene transfer have proved successful in rescuing salivary gland function in a number of animal models that reflect human diseases and that result in hyposalivation and xerostomia. By overcoming the limitations of stem cell transplants and better understanding the mechanisms of cellular plasticity in the adult salivary gland, such studies provide encouraging evidence that a regenerative strategy for patients will be available in the near future.

The antifungal pipeline: the need is established. Are there new compounds?

Our review summarizes and compares the temporal development (eras) of antifungal drug discovery as well as antibacterial ventures. The innovation gap that occurred in antibacterial discovery from 1960 to 2000 was likely due to tailoring of existing compounds to have better activity than predecessors. Antifungal discovery also faced innovation gaps. The semi-synthetic antibiotic era was followed closely by the resistance era and the heightened need for new compounds and targets. With the immense contribution of comparative genomics, antifungal targets became part of the discovery focus. These targets by definition are absolutely required to be fungal- or even lineage (clade) specific. Importantly, targets need to be essential for growth and/or have important roles in disease and pathogenesis. Two types of antifungals are discussed that are mostly in the FDA phase I–III clinical trials. New antifungals are either modified to increase bioavailability and stability for instance, or are new compounds that inhibit new targets. One of the important developments in incentivizing new antifungal discovery has been the prolific number of publications of global and country-specific incidence. International efforts that champion global antimicrobial drug discovery are discussed. Still, interventions are needed. The current pipeline of antifungals and alternatives to antifungals are discussed including vaccines.

An optimised saliva collection method to produce high-yield, high-quality RNA for translational research

Saliva represents an ideal matrix for diagnostic biomarker development as it is readily available and requires no invasive collection procedures. However, salivary RNA is labile and rapidly degrades. Previous attempts to isolate RNA from saliva have yielded poor quality and low concentrations. Here we compare collection and processing methods and propose an approach for future studies. The effects of RNA stabilisers, storage temperatures, length of storage and fasting windows were investigated on pooled saliva samples from healthy volunteers. Isolated RNA was assessed for concentration and quality. Bacterial growth was investigated through RT-PCR using bacterial and human primers. Optimal conditions were implemented and quality controlled in a clinical setting. The addition of RNAlater increased mean RNA yield from 4912 ng/μl to 15,473 ng and RNA Integrity Number (RIN) from 4.5 to 7.0. No significant changes to RNA yield were observed for storage at room temperature beyond 1 day or at -80 °C. Bacterial growth did not occur in samples stored at ambient temperature for up to a week. There was a trend towards higher RNA concentration when saliva was collected after overnight fasting but no effect on RIN. In the clinic, RNA yields of 6307 ng and RINs of 3.9 were achieved, improving on previous reports. The method we describe here is a robust, clinically feasible saliva collection method using preservative that gives high concentrations and improved RINs compared to saliva collected without preservative.

Single-Cell Genomics and the Oral Microbiome

The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems

Abstract: The human oral cavity is home to an abundant and diverse microbial community (i.e., the oral microbiome), whose composition and roles in health and disease have been the focus of intense research in recent years. Thanks to developments in sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore the diversity and roles of oral microbes, even if unculturable. Recent sequencing-based studies have charted oral ecosystems and how they change due to lifestyle or disease conditions. As studies progress, there is increasing evidence of an important role of the oral microbiome in diverse health conditions, which are not limited to diseases of the oral cavity. This, in turn, opens new avenues for microbiome-based diagnostics and therapeutics that benefit from the easy accessibility of the oral cavity for microbiome monitoring and manipulation. Yet, many challenges remain ahead. In this review, we survey the main sequencing-based methodologies that are currently used to explore the oral microbiome and highlight major findings enabled by these approaches. Finally, we discuss future prospects in the field.

Balanced oral pathogenic bacteria and probiotics promoted wound healing via maintaining mesenchymal stem cell homeostasis

Objectives

The homeostasis of oral pathogenic bacteria and probiotics plays a crucial role in maintaining the well-being and healthy status of human host. Our previous study confirmed that imbalanced oral microbiota could impair mesenchymal stem cell (MSC) proliferation capacity and delay wound healing. However, the effects of balanced oral pathogenic bacteria and probiotics on MSCs and wound healing are far from clear. Here, the balance of pathogenic bacteria Porphyromonas gingivalis and probiotics Lactobacillus reuteri extracts was used to investigate whether balanced oral microbiota modulate the physiological functions of MSCs and promote wound healing.

Methods

The effects of balanced pathogenic bacteria P. gingivalis and probiotics L. reuteri extracts on gingival MSCs (GMSCs) were tested using the migration, alkaline phosphatase activity, alizarin red staining, cell counting kit-8, real-time PCR, and western blot assays. To investigate the role of balanced pathogenic bacteria P. gingivalis and probiotics L. reuteri extracts in the wound of mice, the wounds were established in the mucosa of palate and were inoculated with bacteria every 2 days.

Results

We found that the balance between pathogenic bacteria and probiotics enhanced the migration, osteogenic differentiation, and cell proliferation of MSCs. Additionally, local inoculation of the mixture of L. reuteri and P. gingivalis promoted the process of wound healing in mice. Mechanistically, we found that LPS in P. gingivalis could activate NLRP3 inflammasome and inhibit function of MSCs, thereby accelerating MSC dysfunction and delaying wound healing. Furthermore, we also found that reuterin was the effective ingredient in L. reuteri which maintained the balance of pathogenic bacteria and probiotics by neutralizing LPS in P. gingivalis, thus inhibiting inflammation and promoting wound healing.

Conclusions

This study revealed that the homeostasis of oral microbiomes played an indispensable role in maintaining oral heath, provided hopeful methods for the prevention and treatment of oral diseases, and had some referential value for other systemic diseases caused by dysfunction of microbiota and MSCs.

More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment

Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.

Prevalence and Associated-Factors for Entamoeba gingivalis in Adolescents in Southeastern Iran by Culture and PCR, 2017

BACKGROUND

This study aimed to identify the prevalence and potential factors associated with Entamoeba gingivalis in adolescents in the city of Kerman, southeastern Iran, 2017.

METHODS

In this descriptive cross-sectional study, 315 adolescents (mean age; 15 yr) consisting of 189 males and 126 females were randomly selected. For each adolescent, two specimens were collected for culturing and examination by polymerase chain reaction (PCR). Univariate and multivariate logistic regression models were performed to explore any association with demographic and clinical variables.

RESULTS

The prevalence of E. gingivalis was 11.7%. Totally, 30 (15.9%) males and 7 (5.6%) females were infected with E. gingivalis. The rate of infection in males was 2.8 times higher than that in females (P<0.001). Statistical analysis identified 4 major factors including sex (OR=4.12, P<0.001), gingival index with severe inflammation (OR = 50, P<0.001), Candida spp. infection (OR=4.41, P<0.001) and decay-missing-filled teeth [DMFT (OR=3.27, P<0.001)]. In contrast to the aforementioned factors, adolescents with history of antibiotic consumption were significantly protected from E. gingivalis infection (OR= 3.24, P<0.001). Culture media detected 9.2% (n= 29), whilst PCR identified 11.4% (n= 36) of infection.

CONCLUSION

The present findings clearly demonstrate a positive association between E. gingivalis and distinct demographic and clinical risk determinants. Therefore, dental practitioners and health surveillance personnel should be aware of these confounding factors to rigorously detect and critically manage oral health issues in school-age children in order to prevent or at least minimize the eventual periodontal complications in later life.

Influence of delivery and feeding mode in oral fungi colonization - a systematic review

Postnatal acquisition of microorganisms from maternal and environmental sources contributes to the child microbiome development. Several studies showed that the mode of delivery and breastfeeding may have impact on the oral bacterial colonization, however, the influence on oral fungal colonization is still unknown. We performed a systematic literature review on mother to child oral fungi transmission, namely regarding the association between the mode of delivery and breastfeeding in oral yeast colonization. Our analysis revealed no significant differences between the oral mycobiome of breastfed and bottle-fed children. As for the delivery mode, the majority of studies found a relation between fungal colonization and vaginal delivery. Candida albicans was the most commonly isolated fungi species. Our analysis suggests that maternal breastfeeding does not seem to influence oral mycology, but vaginal delivery appears to promote oral yeast colonization in early life.

Exploring the Maternal and Infant Oral Microbiomes: A Pilot Study

Setting the stage for good oral health early in life is critical to long-term oral and overall health. This exploratory study aimed to characterize and compare maternal and newborn oral microbiota among mother-infant pairs. Oral samples were collected from 34 pregnant African American women and their infants at 1 to 3 months of age. Extracted 16SrRNA genes were matched to the Human Oral Microbiome Database. Alpha and beta diversity differed significantly between overall maternal and infant microbiomes. Maternal or infant alpha diversity, however, was not differentiated by maternal gingival status. Several demographic and behavioral variables were associated with, but not predictive of, maternal oral microbiome alpha diversity. There was no association, however, among birth mode, feeding mode, and the infant oral microbiome. Megasphaera micronuciformis was the only periodontal pathogen detected among the infants. Notably, maternal gingival status was not associated with the presence/absence of most periodontal pathogens. This study provides an initial description of the maternal and infant oral microbiomes, laying the groundwork for future studies. The perinatal period presents an important opportunity where perinatal nurses and providers can provide oral assessment, education, and referral to quality dental care.

A brief history of periodontics in the United States of America: Pioneers and thought-leaders of the past, and current challenges

This paper summarizes historical events in periodontology in the United States over the past 200 years. The contributions of some of the key thought-leaders of the past are highlighted. Throughout the 20th century, the evolution of thought, leading to the views currently held regarding the pathogenesis and treatment of periodontal diseases, was significantly influenced by: (1) major changes in health-care education; (2) the emergence of periodontics as a specialty of dentistry; (3) the publication of peer-reviewed journals with an emphasis on periodontology; (4) formation of the National Institute of Dental and Craniofacial Research (NIDCR); and (5) expansion of periodontal research programs by the NIDCR. The two major future challenges facing periodontal research are development of a better understanding of the ecological complexities of host-microbial interactions in periodontal health and disease, and identification of the relevant mechanisms involved in the predictable regeneration of damaged periodontal tissues.