Ecology of the Oral Microbiome: Beyond Bacteria

Antimicrobial effects of surface pre-reacted glass-ionomer (S-PRG) eluate against oral microcosm biofilm

This study investigated the antimicrobial activity of surface pre-reacted glass ionomer eluate (S-PRG) against oral microcosm biofilms collected from the oral cavity of patients. Dental biofilm samples were collected from three volunteers to form microcosm biofilms in vitro. Initially, screening tests were carried out to determine the biofilm treatment conditions with S-PRG eluate. The effects of a daily treatment for 5 min using three microcosm biofilms from different patients was then evaluated. For this, biofilms were formed on tooth enamel specimens for 120 h. Biofilms treated with 100% S-PRG for 5 min per day for 5 days showed a reduction in the number of total microorganisms, streptococci and mutans streptococci. SEM images confirmed a reduction in the biofilm after treatment. Furthermore, S-PRG also reduced lactic acid production. It was concluded that S-PRG eluate reduced the microbial load and lactic acid production in oral microcosm biofilms, reinforcing its promising use as a mouthwash agent.

Concordance in bacterial colonization profiles between voice prostheses and oral microbiota post-laryngectomy: An experimental study

OBJECTIVE

Knowledge about voice prosthesis microbial colonization is vital in laryngectomized patients' quality of life (QoL). Herein, we aimed to explore the relationship between oral microbial patterns, demographic variables and voice prosthesis performance.

METHODS

Thirty laryngectomy patients were assessed for microbial colonization in their voice prostheses and oral cavities. Factors like age, proton pump inhibitor (PPI) usage, and alcohol consumption were considered.

RESULTS

Participants' average age was 74.20 ± 7.31 years, with a majority on PPIs. Staphylococcus aureus was the most common bacterium in prostheses (53 %), followed by Pseudomonas aeruginosa (27 %). Candida albicans was the primary fungal colonizer (67 %). A statistically significant moderate correlation was found between fungal species before and after oral rinsing (p = 0.035, Phi=0.588, Cramer's V = 0.416). Voice prosthesis and oral cavity microbiota profiles showed significant concordance (kappa=0.315, p < 0.004). Among subgroup analyses, bacterial patterns of colonization did not significantly influence VHI (p = 0.9555), VrQoL (p = 0.6610), or SF-36 (p = 0.509) scores. Conversely, fungal patterns of VP colonization significantly impacted subjective voice scores, with Candida krusei demonstrating better VHI (35.25 ± 3.63 vs. 44.54 ± 6.33; p = 0.008), VrQoL (7.13 ± 1.69 vs. 10.73 ± 2.00; p = 0.001), and SF-36 (69.36 ± 7.09 vs. 76.50 ± 7.73; p = 0.051) scores compared to C. albicans.

CONCLUSIONS

There was a significant correlation between the oral microbiota and voice prosthesis colonization. These insights can inform improved care strategies for voice prostheses, enhancing patient outcomes.

Altered salivary microbiota associated with high-sugar beverage consumption

The human oral microbiome may alter oral and systemic disease risk. Consuming high sugar content beverages (HSB) can lead to caries development by altering the microbial composition in dental plaque, but little is known regarding HSB-specific oral microbial alterations. Therefore, we conducted a large, population-based study to examine associations of HSB intake with oral microbiome diversity and composition. Using mouthwash samples of 989 individuals in two nationwide U.S. cohorts, bacterial 16S rRNA genes were amplified, sequenced, and assigned to bacterial taxa. HSB intake was quantified from food frequency questionnaires as low (< 1 serving/week), medium (1-3 servings/week), or high (> 3 servings/week). We assessed overall bacterial diversity and presence of specific taxa with respect to HSB intake in each cohort separately and combined in a meta-analysis. Consistently in the two cohorts, we found lower species richness in high HSB consumers (> 3 cans/week) (p = 0.027), and that overall bacterial community profiles differed from those of non-consumers (PERMANOVA p = 0.040). Specifically, presence of a network of commensal bacteria (Lachnospiraceae, Peptostreptococcaceae, and Alloprevotella rava) was less common in high compared to non-consumers, as were other species including Campylobacter showae, Prevotella oulorum, and Mycoplasma faucium. Presence of acidogenic bacteria Bifodobacteriaceae and Lactobacillus rhamnosus was more common in high consumers. Abundance of Fusobacteriales and its genus Leptotrichia, Lachnoanaerobaculum sp., and Campylobacter were lower with higher HSB consumption, and their abundances were correlated. No significant interaction was found for these associations with diabetic status or with microbial markers for caries (S. mutans) and periodontitis (P. gingivalis). Our results suggest that soft drink intake may alter the salivary microbiota, with consistent results across two independent cohorts. The observed perturbations of overrepresented acidogenic bacteria and underrepresented commensal bacteria in high HSB consumers may have implications for oral and systemic disease risk.

EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale

Bacterial communities are often concomitantly present with numerous microorganisms in the human body and other natural environments. Amplicon-based microbiome studies have generally paid skewed attention, that too at a rather shallow genus level resolution, to the highly abundant bacteriome, with interest now forking toward the other microorganisms, particularly fungi. Given the generally sparse abundance of other microbes in the total microbiome, simultaneous sequencing of amplicons targeting multiple microbial kingdoms could be possible even with full multiplexing. Guiding studies are currently needed for performing and monitoring multi-kingdom-amplicon sequencing and data capture at scale. Aiming to address these gaps, amplification of full-length bacterial 16S rRNA gene and entire fungal internal-transcribed spacer (ITS) region was performed for human saliva samples (n = 96, including negative and positive controls). Combined amplicon DNA libraries were prepared for nanopore sequencing using a major fraction of 16S molecules and a minor fraction of ITS amplicons. Sequencing was performed in a single run of an R10.4.1 flow cell employing the latest V14 chemistry. An approach for real-time monitoring of the species saturation using dynamic rarefaction was designed as a guiding determinant of optimal run time. Real-time saturation monitoring for both bacterial and fungal species enabled the completion of sequencing within 30 hours, utilizing less than 60% of the total nanopores. Approximately 5 million high quality (HQ) taxonomically assigned reads were generated (~4.2 million bacterial and 0.7 million fungal), providing a wider (beyond bacteriome) snapshot of human oral microbiota at species-level resolution. Among the more than 400 bacterial and 240 fungal species identified in the studied samples, the species of Streptococcus (e.g., Streptococcus mitis and Streptococcus oralis) and Candida (e.g., Candida albicans and Candida tropicalis) were observed to be the dominating microbes in the oral cavity, respectively. This conformed well with the previous reports of the human oral microbiota. EnsembleSeq provides a proof-of-concept toward the identification of both fungal and bacterial species simultaneously in a single fully multiplexed nanopore sequencing run in a time- and resource-effective manner. Details of this workflow, along with the associated codebase, are provided to enable large-scale application for a holistic species-level microbiome study.

IMPORTANCE

Human microbiome is a sum total of a variety of microbial genomes (including bacteria, fungi, protists, viruses, etc.) present in and on the human body. Yet, a majority of amplicon-based microbiome studies have largely remained skewed toward bacteriome as an assumed proxy of the total microbiome, primarily at a shallow genus level. Cost, time, effort, data quality/management, and importantly lack of guiding studies often limit progress in the direction of moving beyond bacteriome. Here, EnsembleSeq presents a proof-of-concept toward concomitantly capturing multiple-kingdoms of microorganisms (bacteriome and mycobiome) in a fully multiplexed (96-sample) single run of long-read amplicon sequencing. In addition, the workflow captures dynamic tracking of species-level saturation in a time- and resource-effective manner.

Fungi and bacteria occupy distinct spatial niches within carious dentin

The role of bacteria in the etiology of dental caries is long established, while the role of fungi has only recently gained more attention. The microbial invasion of dentin in advanced caries especially merits additional research. We evaluated the fungal and bacterial community composition and spatial distribution within carious dentin. Amplicon 16S rRNA gene sequencing together with quantitative PCR was used to profile bacterial and fungal species in caries-free children (n = 43) and 4 stages of caries progression from children with severe early childhood caries (n = 32). Additionally, healthy (n = 10) and carious (n = 10) primary teeth were decalcified, sectioned, and stained with Grocott's methenamine silver, periodic acid Schiff (PAS) and calcofluor white (CW) for fungi. Immunolocalization was also performed using antibodies against fungal β-D-glucan, gram-positive bacterial lipoteichoic acid, gram-negative endotoxin, Streptococcus mutans, and Candida albicans. We also performed field emission scanning electron microscopy (FESEM) to visualize fungi and bacteria within carious dentinal tubules. Bacterial communities observed included a high abundance of S. mutans and the Veillonella parvula group, as expected. There was a higher ratio of fungi to bacteria in dentin-involved lesions compared to less severe lesions with frequent preponderance of C. albicans, C. dubliniensis, and in one case C. tropicalis. Grocott's silver, PAS, CW and immunohistochemistry (IHC) demonstrated the presence of fungi within carious dentinal tubules. Multiplex IHC revealed that fungi, gram-negative, and gram-positive bacteria primarily occupied separate dentinal tubules, with rare instances of colocalization. Similar findings were observed with multiplex immunofluorescence using anti-S. mutans and anti-C. albicans antibodies. Electron microscopy showed monomorphic bacterial and fungal biofilms within distinct dentin tubules. We demonstrate a previously unrecognized phenomenon in which fungi and bacteria occupy distinct spatial niches within carious dentin and seldom co-colonize. The potential significance of this phenomenon in caries progression warrants further exploration.

A review and new perspective on oral bacteriophages: manifestations in the ecology of oral diseases

Objective

To explore the manifestations of bacteriophages in different oral disease ecologies, including periodontal diseases, dental caries, endodontic infections, and oral cancer, as well as to propel phage therapy for safer and more effective clinical application in the field of dentistry.

Methods

In this literature review, we outlined interactions between bacteriophages, bacteria and even oral cells in the oral ecosystem, especially in disease states. We also analyzed the current status and future prospects of phage therapy in the perspective of different oral diseases.

Results

Various oral bacteriophages targeting at periodontal pathogens as Porphyromonas gingivalis, Fusobacterium nucleatum, Treponema denticola and Aggregatibacter actinomycetemcomitans, cariogenic pathogen Streptococcus mutans, endodontic pathogen Enterococcus faecalis were predicted or isolated, providing promising options for phage therapy. In the realm of oral cancer, aside from displaying tumor antigens or participating in tumor-targeted therapies, phage-like particle vaccines demonstrated the potential to prevent oral infections caused by human papillomaviruses (HPVs) associated with head-and-neck cancers.

Conclusion

Due to their intricate interactions with bacteria and oral cells, bacteriophages are closely linked to the progression and regression of diverse oral diseases. And there is an urgent need for research to explore additional possibilities of bacteriophages in the management of oral diseases.

Comparison of the performance of MiSeq and NovaSeq in oral microbiome study

Objective

Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study.

Methods

Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens.

Results

NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades.

Conclusion

Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.

Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence

Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.

Exploring the Efficacy of Novel Therapeutic Strategies for Periodontitis: A Literature Review

Periodontitis, a prevalent oral condition, is facing difficulties in therapeutic approaches, sometimes leading to failure. This literature review was conducted to investigate the diversity of other therapeutic approaches and their potential contributions to the successful management of the disease. This research scrutinized the alterations in microbial diversity and imbalances in crucial microbial species, which contribute significantly to the pathogenesis of periodontitis. Within the limitations of this study, we highlight the importance of understanding the treatment plan's role in periodontitis disease, opening the way for further research and innovative treatment plans to mitigate the impact of periodontitis on oral health. This will aid both healthcare professionals and patients in preventing and effectively treating periodontitis, ultimately improving oral health outcomes and overall systemic health and well-being.

Interactions among microorganisms open up a new world for anti-infectious therapy

The human microbiome, containing bacteria, fungi, and viruses, is a community that coexists peacefully with humans most of the time, but with the potential to cause disease under certain conditions. When the environment changes or certain stimuli are received, microbes may interact with each other, causing or increasing the severity of disease in a host. With the appropriate methods, we can make these microbiota work for us, creating new applications for human health. This review discusses the wide range of interactions between microorganisms that result in an increase in susceptibility to, severity of, and mortality of diseases, and also briefly introduces how microorganisms interact with each other directly or indirectly. The study of microbial interactions and their mechanisms has revealed a new world of treatments for infectious disease. The regulation of the balance between intestinal flora, the correct application of probiotics, and the development of effective drugs by symbiosis all demonstrate the great contributions of the microbiota to human health and its powerful potential value. Consequently, the study of interactions between microorganisms plays an essential role in identifying the causes of diseases and the development of treatments.

Ectopic colonization by oral bacteria as an emerging theme in health and disease

The number of research papers published on the involvement of the oral microbiota in systemic diseases has grown exponentially over the last 4 years clearly demonstrating the growing interest in this field. Indeed, accumulating evidence highlights the central role of ectopic colonization by oral bacteria in numerous noncommunicable diseases including inflammatory bowel diseases (IBDs), undernutrition, preterm birth, neurological diseases, liver diseases, lung diseases, heart diseases, or colonic cancer. There is thus much interest in understanding the molecular mechanisms that lead to the colonization and maintenance of ectopic oral bacteria. The aim of this review is to summarize and conceptualize the current knowledge about ectopic colonization by oral bacteria, highlight wherever possible the underlying molecular mechanisms and describe its implication in health and disease. The focus lies on the newly discovered molecular mechanisms, showcasing shared pathophysiological mechanisms across different body sites and syndromes and highlighting open questions in the field regarding the pathway from oral microbiota dysbiosis to noncommunicable diseases.

Oral bacteriophages: metagenomic clues to interpret microbiomes

Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases.

Measurement and analysis of microbial fluoride resistance in dental biofilm models

The interactions between communities of microorganisms inhabiting the dental biofilm is a major determinant of oral health. These biofilms are periodically exposed to high concentrations of fluoride, which is present in almost all oral healthcare products. The microbes resist fluoride through the action of membrane export proteins. This chapter describes the culture, growth and harvest conditions of model three-species dental biofilm comprised of cariogenic pathogens Streptococcus mutans and Candida albicans and the commensal bacterium Streptococcus gordonii. In order to examine the role of fluoride export by S. mutans in model biofilms, procedures for generating a strain of S. mutans with a genetic knockout of the fluoride exporter are described. We present a case study examining the effects of this mutant strain on the biofilm mass, acid production and mineral dissolution under exposure to low levels of fluoride. These general approaches can be applied to study the effects of any gene of interest in physiologically realistic multispecies oral biofilms.

A bibliometric and visualized in oral microbiota and cancer research from 2013 to 2022

Numerous studies have highlighted the implication of oral microbiota in various cancers. However, no bibliometric analysis has been conducted on the relationship between oral microbiota and cancer. This bibliometric analysis aimed to identify the research hotspots in oral microbiota and cancer research, as well as predict future research trends. The literature published relating to oral microbiota and cancer was searched from the Web of Science Core Collection database (WoSCC) from 2013 to 2022. VOSviewer or Citespace software was used to perform the bibliometric analysis, focusing on countries, institutions, authors, journals, keywords and references. A total of 1516 publications were included in the analysis. The number of publications related oral microbiota and cancer increased annually, reaching its peak in 2022 with 287 papers. The United States (456) and China (370) were the countries with the most publications and made significant contributions to the field. Sears CL and Zhou XD were the most productive authors. The high frequency of keywords revealed key topics, including cancer (colorectal cancer, oral cancer), oral microbiota (Fusobacterium nucleatum, Porphyromonas gingivalis), and inflammation (periodontal disease). The latest trend keywords were F. nucleatum, dysbiosis, prognosis, tumor microenvironment, gastric microbiota, complications and survival, suggesting a new hotspot in the field of oral microbiota and cancer. Our study provides a comprehensive analysis of oral microbiota and cancer research, revealing an increase in publications in recent years. Future research directions will continue to focus on the diversity of oral microbiota impacted by cancers and the underlying mechanism connecting them, providing new ideas for targeted therapy of tumorigenesis.

The oral microbiome: diversity, biogeography and human health

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

Herpesviruses and SARS-CoV-2: Viral Association with Oral Inflammatory Diseases

The oral cavity is a niche for diverse microbes, including viruses. Members of the Herpesviridae family, comprised of dsDNA viruses, as well as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an ssRNA virus, are among the most prevalent viruses infecting the oral cavity, and they exhibit clinical manifestations unique to oral tissues. Viral infection of oral mucosal epithelia triggers an immune response that results in prolonged inflammation. The clinical and systemic disease manifestations of HHV have been researched extensively, and several recent studies have illuminated the relationship between HHV and oral inflammatory diseases. Burgeoning evidence suggests the oral manifestation of SARS-CoV-2 infection includes xerostomia, dysgeusia, periodontal disease, mucositis, and opportunistic viral and bacterial infections, collectively described as oral post-acute sequelae of COVID-19 (PASC). These diverse sequelae could be a result of intensified immune responses initially due to the copious production of proinflammatory cytokines: the so-called "cytokine storm syndrome", facilitating widespread oral and non-oral tissue damage. This review explores the interplay between HHV, SARS-CoV-2, and oral inflammatory diseases such as periodontitis, endodontic disease, and peri-implantitis. Additionally, the review discusses proper diagnostic techniques for identifying viral infection and how viral diagnostics can lead to improved overall patient health.

Comparison of the main pathogenic microorganisms of various common oral diseases in children and adults

The microorganisms in the human body gradually change and maintain a dynamic balance with the development of physiology and pathology. Oral microbiota is one of the most important microbiota in human body. It is not only closely related to the occurrence and development of oral diseases, but also plays an important role in the overall health. In childhood, the population of oral microorganisms is relatively small, but with the growth of age and tooth development, the species and quantity of oral microorganisms are gradually increasing. Different oral diseases also have their corresponding main microorganisms, and these dominant microorganisms change at different stages of the disease. In this review, we summarized and compared the main pathogenic microorganisms of several common oral diseases in children and adults. In addition, the possible association and difference between adults and children of the main pathogenic microorganisms in different stages of the same or different diseases are also discussed in order to provide research data for the development and diagnosis of common oral diseases in children and adults.

Acid tolerance of Lactobacillus spp. on root carious lesions: A complex and multifaceted response

Lactobacillus spp. are acidogenic and aciduric bacteria and are among the main cariogenic microorganisms associated with the carious process.

OBJECTIVE

This study aimed to identify genes involved in the acid-tolerance of Lactobacillus spp. and potential functions attributed to these genes within the metatranscriptome of sound root surfaces and carious root surfaces.

DESIGN

Genomic libraries were built from mRNA isolated from the biofilm samples (10 from sound root and 9 from carious root using Illumina HiSeq 2500). Reads generated by RNA-seq were mapped against 162 oral microbial genomes and genes potentially related to acid tolerance were manually extracted from the Lactobacillus spp. genomes using L. paracasei ATCC 344 as reference genome. The R package DESeq2 was used to calculate the level of differential gene expression between those two clinical conditions.

RESULTS

Fifteen Lactobacillus spp. genomes were identified and a total of 653 acid tolerance genes were overexpressed in carious root surfaces. Multiple functions, as translation, ribosomal structure and biogenesis, transport of nucleotides and amino acids, are involved in Lactobacillus spp. acid tolerance. Species-specific functions also seem to be related to the fitness of Lactobacillus spp. in acidified environments such as that of the cariogenic biofilm associated with carious root lesions.

CONCLUSIONS

The response of Lactobacillus spp. to an acidic environment is complex and multifaceted. This finding suggests several possible avenues for further research into the adaptive mechanisms of these bacteria.

Oral microbiota disorder in GC patients revealed by 2b-RAD-M

BACKGROUND

Microbiota alterations are linked with gastric cancer (GC). However, the relationship between the oral microbiota (especially oral fungi) and GC is not known. In this study, we aimed to apply 2b-RAD sequencing for Microbiome (2b-RAD-M) to characterize the oral microbiota in patients with GC.

METHODS

We performed 2b-RAD-M analysis on the saliva and tongue coating of GC patients and healthy controls. We carried out diversity, relative abundance, and composition analyses of saliva and tongue coating bacteria and fungi in the two groups. In addition, indicator analysis, the Gini index, and the mean decrease accuracy were used to identify oral fungal indicators of GC.

RESULTS

In this study, fungal imbalance in the saliva and tongue coating was observed in the GC group. At the species level, enriched Malassezia globosa (M. globosa) and decreased Saccharomyces cerevisiae (S. cerevisiae) were observed in saliva and tongue coating samples of the GC group. Random forest analysis indicated that M. globosa in saliva and tongue coating samples could serve as biomarkers to diagnose GC. The Gini index and mean decreases in accuracy for M. globosa in saliva and tongue coating samples were the largest. In addition, M. globosa in saliva and tongue coating samples classified GC from the control with areas under the receiver operating curve (AUCs) of 0.976 and 0.846, respectively. Further ecological analysis revealed correlations between oral bacteria and fungi.

CONCLUSION

For the first time, our data suggested that changes in oral fungi between GC patients and controls may help deepen our understanding of the complex spectrum of the different microbiotas involved in GC development. Although the cohort size was small, this study is the first to use 2b-RAD-M to reveal that oral M. globosa can be a fungal biomarker for detecting GC.

Staphylococcus aureus Adaptation to the Skin in Health and Persistent/Recurrent Infections

Staphylococcus aureus is a microorganism with an incredible capability to adapt to different niches within the human body. Approximately between 20 and 30% of the population is permanently but asymptomatically colonized with S. aureus in the nose, and another 30% may carry S. aureus intermittently. It has been established that nasal colonization is a risk factor for infection in other body sites, including mild to severe skin and soft tissue infections. The skin has distinct features that make it a hostile niche for many bacteria, therefore acting as a strong barrier against invading microorganisms. Healthy skin is desiccated; it has a low pH at the surface; the upper layer is constantly shed to remove attached bacteria; and several host antimicrobial peptides are produced. However, S. aureus is able to overcome these defenses and colonize this microenvironment. Moreover, this bacterium can very efficiently adapt to the stressors present in the skin under pathological conditions, as it occurs in patients with atopic dermatitis or suffering chronic wounds associated with diabetes. The focus of this manuscript is to revise the current knowledge concerning how S. aureus adapts to such diverse skin conditions causing persistent and recurrent infections.

Rhamnolipid 89 Biosurfactant Is Effective against Streptococcus oralis Biofilm and Preserves Osteoblast Behavior: Perspectives in Dental Implantology

Biofilm-related peri-implant diseases represent the major complication for osteointegrated dental implants, requiring complex treatments or implant removal. Microbial biosurfactants emerged as new antibiofilm coating agents for implantable devices thanks to their high biocompatibility. This study aimed to assess the efficacy of the rhamnolipid 89 biosurfactant (R89BS) in limiting Streptococcus oralis biofilm formation and dislodging sessile cells from medical grade titanium, but preserving adhesion and proliferation of human osteoblasts. The inhibitory activity of a R89BS coating on S. oralis biofilm formation was assayed by quantifying biofilm biomass and microbial cells on titanium discs incubated up to 72 h. R89BS dispersal activity was addressed by measuring residual biomass of pre-formed biofilms after rhamnolipid treatment up to 24 h. Adhesion and proliferation of human primary osteoblasts on R89BS-coated titanium were evaluated by cell count and adenosine-triphosphate quantification, while cell differentiation was studied by measuring alkaline phosphatase activity and observing mineral deposition. Results showed that R89BS coating inhibited S. oralis biofilm formation by 80% at 72 h and dislodged 63-86% of pre-formed biofilms in 24 h according to concentration. No change in the adhesion of human osteoblasts was observed, whereas proliferation was reduced accompanied by an increase in cell differentiation. R89BS effectively counteracts S. oralis biofilm formation on titanium and preserves overall osteoblasts behavior representing a promising preventive strategy against biofilm-related peri-implant diseases.

SVep1, a temperate phage of human oral commensal Streptococcus vestibularis

Introduction

Bacteriophages play a vital role in the human oral microbiome, yet their precise impact on bacterial physiology and microbial communities remains relatively understudied due to the limited isolation and characterization of oral phages. To address this gap, the current study aimed to isolate and characterize novel oral phages.

Methods

To achieve this, oral bacteria were isolated using a culture-omics method from 30 samples collected from healthy individuals. These bacteria were then cultured in three different types of media under both aerobic and anaerobic conditions. The samples were subsequently subjected to full-length 16S rRNA gene sequencing for analysis. Subsequently, we performed the isolation of lytic and lysogenic phages targeting all these bacteria.

Results

In the initial step, a total of 75 bacterial strains were successfully isolated, representing 30 species and 9 genera. Among these strains, Streptococcus was found to have the highest number of species. Using a full-length 16S rRNA gene similarity threshold of 98.65%, 14 potential novel bacterial species were identified. In the subsequent phase, a temperate phage, which specifically targets the human oral commensal bacterium S. vestibularis strain SVE8, was isolated. The genome of S. vestibularis SVE8 consists of a 1.96-megabase chromosome, along with a 43,492-base pair prophage designated as SVep1. Annotation of SVep1 revealed the presence of 62 open reading frames (ORFs), with the majority of them associated with phage functions. However, it is worth noting that no plaque formation was observed in S. vestibularis SVE8 following lytic induction using mitomycin C. Phage particles were successfully isolated from the supernatant of mitomycin C-treated cultures of S. vestibularis SVE8, and examination using transmission electron microscopy confirmed that SVep1 is a siphovirus. Notably, phylogenetic analysis suggested a common ancestral origin between phage SVep1 and the cos-type phages found in S. thermophilus.

Discussion

The presence of SVep1 may confer immunity to S. vestibularis against infection by related phages and holds potential for being engineered as a genetic tool to regulate oral microbiome homeostasis and oral diseases.

Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research

The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.

Oral microbiota in human health and disease: A perspective

The evolution of medical knowledge about oral microbiota has increased awareness of its important role for the entire human body health. A wide range of microbial species colonizing the oral cavity interact both with each other and with their host through complex pathways. Usually, these interactions lead to a harmonious coexistence (i.e. eubiosis). However, several factors - including diet, poor oral hygiene, tobacco smoking, and certain medications, among others - can disrupt this weak homeostatic balance (i.e. dysbiosis) with potential implications on both oral (i.e. development of caries and periodontal disease) and systemic health. This article is thus aimed at providing an overview on the importance of oral microbiota in mediating several physiological and pathological conditions affecting human health. In this context, strategies based on oral hygiene and diet as well as the role of probiotics supplementation are discussed.

Living together: The role of Candida albicans in the formation of polymicrobial biofilms in the oral cavity

The oral cavity of humans is colonized by diversity of microbial community, although dominated by bacteria, it is also constituted by a low number of fungi, often represented by Candida albicans. Although in the vast minority, this usually commensal fungus under certain conditions of the host (e.g., immunosuppression or antibiotic therapy), can transform into an invasive pathogen that adheres to mucous membranes and also to medical or dental devices, causing mucosal infections. This transformation is correlated with changes in cell morphology from yeast-like cells to hyphae and is supported by numerous virulence factors exposed by C. albicans cells at the site of infection, such as multifunctional adhesins, degradative enzymes, or toxin. All of them affect the surrounding host cells or proteins, leading to their destruction. However, at the site of infection, C. albicans can interact with different bacterial species and in its filamentous form may produce biofilms-the elaborated consortia of microorganisms, that present increased ability to host colonization and resistance to antimicrobial agents. In this review, we highlight the modification of the infectious potential of C. albicans in contact with different bacterial species, and also consider the mutual bacterial-fungal relationships, involving cooperation, competition, or antagonism, that lead to an increase in the propagation of oral infection. The mycofilm of C. albicans is an excellent hiding place for bacteria, especially those that prefer low oxygen availability, where microbial cells during mutual co-existence can avoid host recognition or elimination by antimicrobial action. However, these microbial relationships, identified mainly in in vitro studies, are modified depending on the complexity of host conditions and microbial dominance in vivo.

Bacterial exclusion and wound healing potential of horizontal platelet-rich fibrin (H-PRF) membranes when compared to 2 commercially available collagen membranes

OBJECTIVES

The aim of the present study was to compare the barrier function during bacterial invasion and wound healing properties of 3 commonly used membranes including horizontal platelet-rich fibrin (H-PRF) against two commercially available resorbable collagen membranes.

MATERIALS AND METHODS

H-PRF membranes were prepared by collecting venous blood from 3 healthy volunteers using a 700 g for 8-min centrifugation protocol followed by compression into membranes. To evaluate their barrier function, 3 groups (H-PRF membrane, collagen membrane A (Bio-Gide, Geistlich), collagen membrane B (Megreen, Shanxi Ruisheng Biotechnology Co) were placed between an inner chamber and outer chamber and inoculated with S. aureus. At 2 h, 24 h, and 48 h post-inoculation, cultures from the inner and outer chambers were assessed for bacterial CFUs. Then, scanning electron microscope (SEM) was utilized to visualized the morphological destruction by bacteria of the inner and outer surfaces of the membranes. To assess the wound healing properties of each membrane, leachates from each group were applied to human gingival fibroblasts (HGF) and a scratch assay was performed at 24 h and 48 h.

RESULTS

S. aureus showed a minimal bacterial attachment or invasion rate through either collagen membranes at 2 h post-inoculation, yet over time demonstrated rapid degradation, especially on the rougher surface. While PRF demonstrated higher number of CFUs after 2 h, no significant penetration/degradation of the H-PRF membranes was observed at 24 h and 48 h in the H-PRF group. Both collagen membranes demonstrated significant morphological changes 48 h post-bacterial innoculation, while minimal obvious morphological changes were observed in the H-PRF group. The wound healing assay also demonstrated significantly better wound closure rates in the H-PRF group.

CONCLUSION

H-PRF membranes exhibited better barrier function towards S. aureus over 2 days of innoculation and better wound healing ability when compared to two commercially available collagen membranes.

CLINICAL RELEVANCE

This study provides further evidence for the application of H-PRF membranes during guided bone regeneration by minimizing bacterial invasion. Furthermore, H-PRF membranes have significantly better ability to promote wound healing.

Exploring the Potential of Bee-Derived Antioxidants for Maintaining Oral Hygiene and Dental Health: A Comprehensive Review

Honey bee products comprise various compounds, including honey, propolis, royal jelly, bee pollen, bee wax and bee venom, which have long been recognized for their pharmacological and health-promoting benefits. Scientists have discovered that periodontal disorders stem from dental biofilm, an inflammatory response to bacterial overgrowth produced by dysbiosis in the oral microbiome. The bee products have been investigated for their role in prevention of oral diseases, which are attributed to a myriad of biologically active compounds including flavonoids (pinocembrin, catechin, caffeic acid phenethyl ester (CAPE) and galangin), phenolic acids (hydroxybenzoic acid, hydroxycinnamic acid, p-coumaric, ellagic, caffeic and ferulic acids) and terpenoids. This review aims to update the current understanding of role of selected bee products, namely, honey, propolis and royal jelly, in preventing oral diseases as well as their potential biological activities and mechanism of action in relation to oral health have been discussed. Furthermore, the safety of incorporation of bee products is also critically discussed. To summarize, bee products could potentially serve as a therapy option for people suffering from a variety of oral disorders.

The Role of IL-17 in the Pathogenesis of Oral Squamous Cell Carcinoma

Elucidating the inflammatory mechanisms underlying formation and progression of oral squamous cell carcinoma (OSCC) is crucial for discovering new targeted therapeutics. The proinflammatory cytokine IL-17 has proven roles in tumor formation, growth, and metastasis. The presence of IL-17 is demonstrated in both in vitro and in vivo models, and in OSCC patients, is mostly accompanied by enhanced proliferation and invasiveness of cancer cells. Here we review the known facts regarding the role of IL-17 in OSCC pathogenesis, namely the IL-17 mediated production of proinflammatory mediators that mobilize and activate myeloid cells with suppressive and proangiogenic activities and proliferative signals that directly induce proliferation of cancer cells and stem cells. The possibility of a potential IL-17 blockade in OSCC therapy is also discussed.

Impact of Nystatin Oral Rinse on Salivary and Supragingival Microbial Community among Adults with Oral Candidiasis

This study aimed to evaluate the impact of Nystatin oral rinse on salivary and supragingival microbiota in adults with oral candidiasis and identify predictive factors related to individuals' responses to Nystatin. The trial involved twenty participants who used 600,000 International Units/application of Nystatin oral rinse for seven days, four times a day, and were followed up at one week and three months after the rinse. The salivary and plaque microbiome of the participants were assessed via 16S rDNA amplicon sequencing. Overall, salivary and plaque microbiomes remained stable. However, among the participants (53 percent) who responded to Nystatin rinse (defined as free of oral Candida albicans post treatment), Veillonella emerged as a core genus alongside Streptococcus and Actinomyces in supragingival plaque at the 3-month follow-up. Furthermore, statistical models were fit to identify predictive factors of Nystatin rinse success (elimination of C. albicans) or failure (remaining C. albicans). The results revealed that an increased level of salivary Interferon (IFN)-γ-inducible protein (IP-10), also known as C-X-C motif chemokine ligand 10 (CXCL10), was an indicator of a failure of responding to Nystatin rinse. Future clinical trials are warranted to comprehensively assess the impact of antifungal treatment on the oral flora.

Simultaneous Analysis of Bacterial and Fungal Communities in Oral Samples from Intubated Patients in Intensive Care Unit

Intubated patients in intensive care units (ICUs) too frequently contract ventilator-associated pneumonia or Candida infections. Oropharyngeal microbes are believed to play an important etiologic role. This study was undertaken to determine whether next-generation sequencing (NGS) can be used to simultaneously analyze bacterial and fungal communities. Buccal samples were collected from intubated ICU patients. Primers targeting the V1-V2 region of bacterial 16S rRNA and the internal transcribed spacer 2 (ITS2) region of fungal 18S rRNA were used. V1-V2, ITS2, or mixed V1-V2/ITS2 primers were used to prepare an NGS library. Bacterial and fungal relative abundances were comparable for V1-V2, ITS2, or mixed V1-V2/ITS2 primers, respectively. A standard microbial community was used to adjust the relative abundances to theoretical abundance, and NGS and RT-PCR-adjusted relative abundances showed a high correlation. Using mixed V1-V2/ITS2 primers, bacterial and fungal abundances were simultaneously determined. The constructed microbiome network revealed novel interkingdom and intrakingdom interactions, and the simultaneous detection of bacterial and fungal communities using mixed V1-V2/ITS2 primers enabled analysis across two kingdoms. This study provides a novel approach to simultaneously determining bacterial and fungal communities using mixed V1-V2/ITS2 primers.

A decade of progress: bibliometric analysis of trends and hotspots in oral microbiome research (2013-2022)

Background

Over the past decade, a plethora of studies have delved into the oral microbiome. Our objective was to evaluate the trends in oral microbiome research employing a quantitative approach.

Materials and methods

We extracted clinical studies on the oral microbiome published between 2013 and 2022 from the Web of Science database, yielding 3024 articles. The assembled literature was visually scrutinized using VOSviewer 1.6.18, Citespace 6.1.6, Pajek, Scimago Graphica, and other specialized software to assess authors, institutions, countries, journals, co-cited literature, keywords, genes, and diseases.

Results

Our analysis identified a total of 3024 articles. The volume and rate of annual publications steadily increased, with research interest in the oral microbiome progressively intensifying. The United States, China, and the UK contributed the highest number of publications. Growth rates of publications varied among countries over time. The Forsyth Institute emerged as the most collaborative institution, boasting the highest number of relevant papers (135) and securing the top rank, followed by Sichuan University and Harvard University. Paster Bruce J, Zhou Xuedong, and He Xuesong were pioneers in the field of oral microbiome research. This analysis demonstrates that the homeostatic balance of the oral microbiome, advanced microbial sequencing technology, connections with gut microbiota, and tumorigenesis, including oral cancer, have become emerging topics in the oral microbiome field.

Conclusions

This study delineated a comprehensive landscape of hotspots and frontiers in oral microbiome research, thus facilitating the identification of interdisciplinary advancements. We sincerely hope that our bibliometric analysis will enable researchers to leverage the oral microbiome to ultimately improve human oral health.

Alteration of taste perception, food neophobia and oral microbiota composition in children with food allergy

Currently, the mechanisms underlying sensory perception and sensory performance in children with food allergies are far from being understood. As well, only recently, single research afforded the oral host-commensal milieu, addressing oral microbial communities in children with peanut allergies. To bridge the current gaps in knowledge both in the sensory and microbial fields, a psychophysiological case-control study was performed in allergic children (n = 29) and a healthy sex-age-matched control group (n = 30). Taste perception, food neophobia, and liking were compared in allergic and non-allergic children. The same subjects were characterized for their oral microbiota composition by addressing saliva to assess whether specific profiles were associated with the loss of oral tolerance in children with food allergies. Our study evidenced an impaired ability to correctly identify taste qualities in the allergic group compared to controls. These results were also consistent with anatomical data related to the fungiform papillae on the tongue, which are lower in number in the allergic group. Furthermore, distinct oral microbial profiles were associated with allergic disease, with significant down-representations of the phylum Firmicutes and of the genera Veillonella spp., Streptococcus spp., Prevotella spp., and Neisseria spp. For the first time, this study emphasizes the link between sensory perception and food allergy, which is a novel and whole-organism view of this pathology. Our data indicated that an impaired taste perception, as regards both functionality and physiologically, was associated with food allergy, which marginally influences the food neophobia attitude. It is also accompanied by compositional shifts in oral microbiota, which is, in turn, another actor of this complex interplay and is deeply interconnected with mucosal immunity. This multidisciplinary research will likely open exciting new approaches to therapeutic interventions.

Underestimated microbial infection of resorbable membranes on guided regeneration

Barrier membranes are critical in creating tissuecompartmentalization for guided tissue (GTR) and bone regeneration (GBR) therapies. More recently, resorbable membranes have been widely used for tissue and bone regeneration due to their improved properties and the dispensable re-entry surgery for membrane removal. However, in cases with membrane exposure, this may lead to microbial contamination that will compromise the integrity of the membrane, surrounding tissue, and bone regeneration, resulting in treatment failure. Although the microbial infection can negatively influence the clinical outcomes of regenerative therapy, such as GBR and GTR, there is a lack of clinical investigations in this field, especially concerning the microbial colonization of different types of membranes. Importantly, a deeper understanding of the mechanisms of biofilm growth and composition and pathogenesis on exposed membranes is still missing, explaining the mechanisms by which bone regeneration is reduced during membrane exposure. This scoping review comprehensively screened and discussed the current in vivo evidence and possible new perspectives on the microbial contamination of resorbable membranes. Results from eligible in vivo studies suggested that different bacterial species colonized exposed membranes according to their composition (collagen, expanded polytetrafluoroethylene (non-resorbable), and polylactic acid), but in all cases, it negatively affected the attachment level and amount of bone gain. However, limited models and techniques have evaluated the newly developed materials, and evidence is scarce. Finally, new approaches to enhance the antimicrobial effect should consider changing the membrane surface or incorporating long-term released antimicrobials in an effort to achieve better clinical success.

Oral polymicrobial communities: Assembly, function, and impact on diseases

Oral microbial communities assemble into complex spatial structures. The sophisticated physical and chemical signaling systems underlying the community enable their collective functional regulation as well as the ability to adapt by integrating environmental information. The combined output of community action, as shaped by both intra-community interactions and host and environmental variables, dictates homeostatic balance or dysbiotic disease such as periodontitis and dental caries. Oral polymicrobial dysbiosis also exerts systemic effects that adversely affect comorbidities, in part due to ectopic colonization of oral pathobionts in extra-oral tissues. Here, we review new and emerging concepts that explain the collective functional properties of oral polymicrobial communities and how these impact health and disease both locally and systemically.

Mechanochemical Properties of Mucoadhesive Tablets Based on PVP/HPβCD Electrospun Nanofibers as Local Delivery of Polygoni cuspidati Extract for Treating Oral Infections

This study investigated the ability of PVP/HPβCD-based electrospun nanofibers to enhance the dissolution rate of poorly soluble polydatin and resveratrol, the main active components of Polygoni cuspidati extract. To make a solid unit dosage form that would be easier to administer, extract-loaded nanofibers were ground. SEM examination was used to analyze the nanostructure of the fibers, and the results of the cross-section of the tablets showed that they had maintained their fibrous structure. The release of the active compounds (polydatin and resveratrol) in the mucoadhesive tablets was complete and prolonged in time. Additionally, the possibility of staying on the mucosa for a prolonged time has also been proven for both tablets from PVP/HPβCD-based nanofibers and powder. The appropriate physicochemical properties of the tablets, along with the proven antioxidant, anti-inflammatory, and antibacterial properties of P. cuspidati extract, highlight the particular benefits of the mucoadhesive formulation for use as a drug delivery system for periodontal diseases.

Both live and heat-killed Bifidobacterium animalis J-12 alleviated oral ulcers in LVG golden Syrian hamsters by gavage by directly intervening in the intestinal flora structure

Live and heat-killed Bifidobacterium has been proven to have anti-inflammatory and antioxidant effects. In this study, we evaluated the effects of live and heat-killed Bifidobacterium animalis J-12 (J-12) on the oral ulceration of LVG golden Syrian hamsters after buccal membrane injection with methyl viologen dichloride. Results showed that interleukin-1β, glutathione, and malondialdehyde in serum were downregulated by the gavage of live and heat-killed J-12 bacteria. The J-12 live and heat-killed bacteria can reduce the expression of matrix metalloproteinase-9 by reducing the expression of nuclear factor kappa-B, thus reducing the expression of anti-inflammatory factors lipoxin A4 and prostaglandin E2. Reducing the expression of caspase-3 and adenosine diphosphate ribose polymerase resulted in a reduction of ulcer tissue DNA damage. In addition, regulating the structure of the intestinal flora prevented the process of oral ulcer formation. This study shows that J-12 can reduce the risk of oral ulcer formation while also having a positive effect on inhibiting existing oral ulcer growth.

The Effects of Drug Addiction and Detoxification on the Human Oral Microbiota

Drug addiction can powerfully and chronically damage human health. Detoxification contributes to health recovery of the body. It is well established that drug abuse is associated with poor oral health in terms of dental caries and periodontal diseases. We supposed that drug addiction and detoxification might have significant effects on the oral microbiota. To test the hypothesis, we assessed the effects of drug (heroin and methylamphetamine) addiction/detoxification on the oral microbiota based on 16S rRNA gene sequencing by an observational investigation, including 495 saliva samples from participants. The oral microbial compositions differed between non-users, current and former drug users. Lower alpha diversities were observed in current drug users, with no significant differences between non-users and former drug users. Heroin and METH addiction can cause consistent variations in several specific phyla, such as the enrichment of Acidobacteria and depletion of Proteobacteria and Tenericutes. Current drug users had significantly lower relative abundances of Neisseria subflava and Haemophilus parainfluenzae compared to non-users and former drug users. The result of random forest prediction model suggested that the oral microbiota has a powerful classification potential for distinguishing current drug users from non-users and former drug users. A cooccurrence network analysis showed that current drug users had more complex oral microbial networks and lower functional modularity. Overall, our study suggested that drug addiction may damage the balance of the oral microbiota. These results may have benefits for further understanding the effects of addiction-related oral microbiota on the health of drug users and promoting the microbiota to serve as a potential tool for accurate forensic identification. IMPORTANCE Drug addiction has serious negative consequences for human health and public security. The evidence indicates that drug abuse can cause poor oral health. In the current study, we observed that drug addiction caused oral microbial dysbiosis. Detoxication have positive effects on the recovery of oral microbial community structures to some extent. Understanding the effects of drug addiction and detoxification on oral microbial communities will promote a more rational approach for recovering the oral function and health of drug users. Furthermore, specific microbial species might be considered biomarkers that could provide information regarding drug abuse status for saliva left at crime scenes. To the best of our knowledge, this is the first report on the role of the oral microbiota in drug addiction and detoxification. Our findings give new clues to understand the association between drug addiction and oral health.

The Contribution of the Human Oral Microbiome to Oral Disease: A Review

The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human microbiome project. This article reviews the current literature surrounding the oral microbiome, briefly highlighting most recent methods of microbiome characterization including cutting edge omics, databases for the microbiome, and areas with current gaps in knowledge. This article also describes reports on microorganisms contained in the oral microbiome which include viruses, archaea, fungi, and bacteria, and provides an in-depth analysis of their significant roles in tissue homeostasis. Finally, we detail key bacteria involved in oral disease, including oral cancer, and the current research surrounding their role in stimulation of inflammatory cytokines, the role of gingival crevicular fluid in periodontal disease, the creation of a network of interactions between microorganisms, the influence of the planktonic microbiome and cospecies biofilms, and the implications of antibiotic resistance. This paper provides a comprehensive literature analysis while also identifying gaps in knowledge to enable future studies to be conducted.

The fecal and oropharyngeal eukaryotic viromes of healthy infants during the first year of life are personal

Using a metagenomic sequencing approach, we described and compared the diversity and dynamics of the oropharyngeal and fecal eukaryotic virome of nine asymptomatic children in a semi-rural community setting located in the State of Morelos, Mexico. Ninety oropharyngeal swabs and 97 fecal samples were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In both niches, more than 95% of the total sequence reads were represented by viruses that replicate either in humans or in plants. Regarding human viruses, three families were most abundant and frequent in the oropharynx: Herpesviridae, Picornaviridae, and Reoviridae; in fecal samples, four virus families predominated: Caliciviridae, Picornaviridae, Reoviridae, and Anelloviridae. Both niches showed a high abundance of plant viruses of the family Virgaviridae. Differences in the frequency and abundance of sequence reads and diversity of virus species were observed in both niches and throughout the year of study, with some viruses already present in the first months of life. Our results suggest that the children's virome is dynamic and likely shaped by the environment, feeding, and age. Moreover, composition analysis suggests that the virome composition is mostly individual. Whether this constant exposition to different viruses has a long-term impact on children's health or development remains to be studied.

An Outlook on Dental Practices to Avoid the Oral Transmission of COVID-19

The oral microbiome plays an important role in the maintenance of immune homeostasis, whereas its association with SARS-CoV-2 infection remains under investigation. Since the oral path is one of the transmission routes for COVID-19, we attempt to show the relationship between the oral microbiome, COVID-19 infection, and oral hygiene. We highlight the importance of oral hygiene to control the infection, especially for ICU cases with COVID-19. Moreover, we present the current strategies adapted by in-person dental clinics to overcome the spread of COVID-19. New emerging policies and protocols suggested during the pandemic and their future implementation to minimize virus transmission are also summarized in this review.

Metaproteomic Analysis of an Oral Squamous Cell Carcinoma Dataset Suggests Diagnostic Potential of the Mycobiome

Oral squamous cell carcinoma (OSCC) is the most common head and neck malignancy, with an estimated 5-year survival rate of only 40-50%, largely due to late detection and diagnosis. Emerging evidence suggests that the human microbiome may be implicated in OSCC, with oral microbiome studies putatively identifying relevant bacterial species. As the impact of other microbial organisms, such as fungi and viruses, has largely been neglected, a bioinformatic approach utilizing the Trans-Proteomic Pipeline (TPP) and the R statistical programming language was implemented here to investigate not only bacteria, but also viruses and fungi in the context of a publicly available, OSCC, mass spectrometry (MS) dataset. Overall viral, bacterial, and fungal composition was inferred in control and OSCC patient tissue from protein data, with a range of proteins observed to be differentially enriched between healthy and OSCC conditions, of which the fungal protein profile presented as the best potential discriminator of OSCC within the analysed dataset. While the current project sheds new light on the fungal and viral spheres of the oral microbiome in cancer in silico, further research will be required to validate these findings in an experimental setting.

Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a phenotype of liver diseases associated with metabolic syndrome. The pathogenesis MAFLD remains unclear. The liver maintains is located near the intestine and is physiologically interdependent with the intestine via metabolic exchange and microbial transmission, underpinning the recently proposed "oral-gut-liver axis" concept. However, little is known about the roles of commensal fungi in the disease development. This study aimed to characterize the alterations of oral and gut mycobiota and their roles in MAFLD. Twenty-one MAFLD participants and 20 healthy controls were enrolled. Metagenomics analyses of saliva, supragingival plaques, and feces revealed significant alterations in the gut fungal composition of MAFLD patients. Although no statistical difference was evident in the oral mycobiome diversity within MAFLD and healthy group, significantly decreased diversities were observed in fecal samples of MAFLD patients. The relative abundance of one salivary species, five supragingival species, and seven fecal species was significantly altered in MAFLD patients. Twenty-two salivary, 23 supragingival, and 22 fecal species were associated with clinical parameters. Concerning the different functions of fungal species, pathways involved in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and carbon metabolism were abundant both in the oral and gut mycobiomes. Moreover, different fungal contributions in core functions were observed between MAFLD patients and the healthy controls, especially in the supragingival plaque and fecal samples. Finally, correlation analysis between oral/gut mycobiome and clinical parameters identified correlations of certain fungal species in both oral and gut niches. Particularly, Mucor ambiguus, which was abundant both in saliva and feces, was positively correlated with body mass index, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase, providing evidence of a possible "oral-gut-liver" axis. The findings illustrate the potential correlation between core mycobiome and the development of MAFLD and could propose potential therapeutic strategies.

Impact of oral microbiota on pathophysiology of GVHD

Allogeneic transplantation of hematopoietic cells is the only curative therapy for several hematopoietic disease in which patients receive cytotoxic conditioning regimens followed by infusion of hematopoietic stem cells. Although the outcomes have improved over the past decades, graft-versus-host-disease (GVHD), the most common life-threatening complication, remains a major cause of non-relapse morbidity and mortality. Pathophysiology of acute GVHD characterized by host antigen-presenting cells after tissue damage and donor T-cells is well studied, and additionally the importance of recipient microbiota in the intestine is elucidated in the GVHD setting. Oral microbiota is the second most abundant bacterial flora in the body after the intestinal tract, and it is related to chronic inflammation and carcinogenesis. Recently, composition of the oral microbiome in GVHD related to transplantation has been characterized and several common patterns, dysbiosis and enrichment of the specific bacterial groups, have been reported. This review focuses on the role of the oral microbiota in the context of GVHD.

Inhibitory effects of Stevioside on Streptococcus mutans and Candida albicans dual-species biofilm

Introduction

Streptococcus mutans is the most prevalent biofilm-forming pathogen in dental caries, while Candida albicans is often detected in the presence of S. mutans.

Methods

We aimed to evaluate the anti-caries effect of stevioside in medium trypticase soy broth (TSB) with or without sucrose supplementation compared with the same sweetness sucrose and xylitol in a dual-species model of S. mutans and C. albicans, based on planktonic growth, crystal violet assay, acid production, biofilm structural imaging, confocal laser scanning microscopy, and RNA sequencing.

Results

Our results showed that compared with sucrose, stevioside significantly inhibited planktonic growth and acid production, changed the structure of the mixed biofilm, and reduced the viability of biofilm and the production of extracellular polysaccharides in dual-species biofilm. Through RNA-seq, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway impact analysis showed that stevioside decreased sucrose metabolism and increased galactose and intracellular polysaccharide metabolism in S. mutans, and decreased genes related to GPI-modified proteins and secreted aspartyl proteinase (SAP) family in C. albicans. In contrast to xylitol, stevioside also inhibited the transformation of fungal morphology of C. albicans, which did not form mycelia and thus had reduced pathogenicity. Stevioside revealed a superior suppression of dual-species biofilm formation compared to sucrose and a similar anti-caries effect with xylitol. However, sucrose supplementation diminished the suppression of stevioside on S. mutans and C. albicans.

Conclusions

Our study is the first to confirm that stevioside has anticariogenic effects on S. mutans and C. albicans in a dual-species biofilm. As a substitute for sucrose, it may help reduce the risk of developing dental caries.

Oral Candidiasis of Tobacco Smokers: A Literature Review

The mouth is a vital point of entry into the human body, the health of the mouth entails mental, physical as well as social well-being. Studying diseases, microbiota and environmental conditions of the mouth is important to maintain oral health and all body. The smoke of tobacco cigarettes is one of the worst habits that affect the health of the mouth and the body. Therefore, this review has been conducted to study the effect of smoking on the balance of the oral microbiota and the opportunistic organisms, one of the most important of them &lt;i&gt;Candida&lt;/i&gt;. Although a few studies have found that cigarette smoking does not influence carriage by &lt;i&gt;Candida&lt;/i&gt; significantly. However, most of the studies had results completely contrary to that, smoking cigarettes affect &lt;i&gt;Candida&lt;/i&gt; pathogenic characteristics such as a transition from yeast to hyphal form, biofilm formation and, virulence-related gene expressions. Tobacco is not only an inducer of the transition process but it considers an excellent medium for this process. Furthermore, smoking was significantly associated with &lt;i&gt;Candida&lt;/i&gt; pathogenicity in patients with clinically suspected oral leukoplakia and smoking worsens oral candidiasis and dampens epithelial cell defense response. Nicotine significantly altered the composition and proportion of yeast cells, as well as the extracellular polysaccharide amounts which increase biofilm matrix and thickness which could promote oral candidiasis. Smoking has the potential to alter the oral condition and cause severe oxidative stress, thereby damaging the epithelial barrier of the mouth. These oxidative molecules during smoking activate epithelial cells proteins called oxidative stress-sensing proteins. If some of these proteins induced, widely thought to have anti-inflammatory properties, inhibit the secretion of pro-inflammatory cytokines and are linked to inflammation and oxidative stress is thought to be a possible therapeutic objective and a crucial regulator for smoking-related oral diseases and mouth candidiasis for instance leukoplakia. Also, it is transported into the cell nucleus in the existence of additional electrophilic chemicals to activate antioxidant enzyme gene expression. Therefore, smoking cigarettes destroys oral health and consequently destroys the health of the whole body.

Dental caries and their microbiomes in children: what do we do now?

The oral cavity is an unique ecosystem formed by different structures, tissues, and a complex microbial community formed by hundreds of different species of bacteria, fungi, viruses, phages, and the candidate phyla radiation (CPR) group, all living in symbiosis with healthy individuals. In an opposite state, dental caries is a biofilm-mediated dysbiosis that involves changes in the core microbiome composition and function, which leads to the demineralization of tooth tissues due to the fermentation of dietary carbohydrates, producing acid by select oral bacteria. The cariogenic biofilm is typically characterized by bacterial species with the ability of adhering to the saliva-coated tooth surface, production of exopolysaccharides-rich matrix (which will limit the diffusion of acidic products of carbohydrate fermentation), and the ability of surviving in this acidic environment. Besides years of research and dental treatment, dental caries remains the most common chronic disease in children worldwide. This article aims to bring an insightful discussion about important questions that remain unanswered in the Cariology and Oral Microbiology fields, to move Science forward, characterize the interrelationships of these communities, and understand mechanistic functions between microorganisms and the host, therefore leading to translatable knowledge that benefits the provision of care to our pediatric patients.

Insights into oral microbiome and colorectal cancer - on the way of searching new perspectives

Microbiome is a keystone polymicrobial community that coexist with human body in a beneficial relationship. These microorganisms enable the human body to maintain homeostasis and take part in mechanisms of defense against infection and in the absorption of nutrients. Even though microbiome is involved in physiologic processes that are beneficial to host health, it may also cause serious detrimental issues. Additionally, it has been proven that bacteria can migrate to other human body compartments and colonize them even although significant structural differences with the area of origin exist. Such migrations have been clearly observed when the causes of genesis and progression of colorectal cancer (CRC) have been investigated. It has been demonstrated that the oral microbiome is capable of penetrating into the large intestine and cause impairments leading to dysbiosis and stimulation of cancerogenic processes. The main actors of such events seem to be oral pathogenic bacteria belonging to the red and orange complex (regarding classification of bacteria in the context of periodontal diseases), such as Porphyromonas gingivalis and Fusobacterium nucleatum respectively, which are characterized by significant amount of cancerogenic virulence factors. Further examination of oral microbiome and its impact on CRC may be crucial on early detection of this disease and would allow its use as a precise non-invasive biomarker.

Application of Fluorescence In Situ Hybridization (FISH) in Oral Microbial Detection

Varieties of microorganisms reside in the oral cavity contributing to the occurrence and development of microbes associated with oral diseases; however, the distribution and in situ abundance in the biofilm are still unclear. In order to promote the understanding of the ecosystem of oral microbiota and the diagnosis of oral diseases, it is necessary to monitor and compare the oral microorganisms from different niches of the oral cavity in situ. The fluorescence in situ hybridization (FISH) has proven to be a powerful tool for representing the status of oral microorganisms in the oral cavity. FISH is one of the most routinely used cytochemical techniques for genetic detection, identification, and localization by a fluorescently labeled nucleic acid probe, which can hybridize with targeted nucleic acid sequences. It has the advantages of rapidity, safety, high sensitivity, and specificity. FISH allows the identification and quantification of different oral microorganisms simultaneously. It can also visualize microorganisms by combining with other molecular biology technologies to represent the distribution of each microbial community in the oral biofilm. In this review, we summarized and discussed the development of FISH technology and the application of FISH in oral disease diagnosis and oral ecosystem research, highlighted its advantages in oral microbiology, listed the existing problems, and provided suggestions for future development..

The Pivotal Role of the Gut Microbiome in Colorectal Cancer

Simple Summary

Colorectal cancer is a common form of cancer observed globally. It is thought that the gut microbiome may play a pivotal role in the development and progression of colorectal cancer in patients. Furthermore, current treatment strategies may lead to a variety of side effects, and chemotherapeutic resistance is observed. Consequently, new types of treatments should be considered, including post/pre/synbiotics and fecal microbiota transfer, which may be able to restore gut microbial dysbiosis.

Abstract

Colorectal cancer is the third most diagnosed cancer worldwide and the second most prevalent cause of cancer-related mortality. It is believed that alterations within the gut microbiome may impact the development and progression of cancer. Additionally, the diet an individual maintains and the amount of alcohol consumed can alter the microbiome, thus impacting the development of colorectal cancer. A diet focused on fiber intake is considered beneficial, as it contains short-chain fatty acids such as butyrate, which have antitumor properties. Furthermore, current treatment strategies, such as chemotherapy, have various side effects. In this review, we discuss the role of the gut microbiome and oral bacteria in relation to colorectal cancer. We also deliberate on the role of diet and alcohol consumption in the development of colorectal cancer. Moreover, the influence of the various metabolites within the gut and the importance of gut inflammation in the development of colorectal cancer are explained. Finally, potential therapies such as fecal microbiota transfer and post/prebiotics are elaborated on. To further comprehend risk factors in the development of colorectal cancer, future studies are warranted to determine the precise mechanisms of action between the gut microbiome and carcinogenesis in order to develop therapies that may target gut microbial dysbiosis.