Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis

Identification of Aerobic Salivary Microorganisms in Patients With Oral Squamous Cell Carcinoma Using MALDI-TOF MS: Preliminary Findings From a Pilot Study

RATIONALE

Oral squamous cell carcinoma (OSCC) is a multifactorial disease, and emerging evidence links the oral microbiome to its development. Rapid, noninvasive identification of salivary microorganisms may offer novel diagnostic and prognostic insights into oral cancer.

METHODS

Salivary microbiota from OSCC patients and healthy individuals were analyzed using MALDI Biotyper. Saliva samples were cultured, and microbial identification was performed based on protein spectral profiles using an UltrafleXtreme MALDI-TOF mass spectrometer.

RESULTS

Thirteen OSCC patients (mean age 55 ± 11 years; 69% male) and nineteen healthy controls (mean age 55 ± 10 years; 79% male) were analyzed. Distinct microbial profiles were observed in OSCC patients, including pathogenic species previously associated with carcinogenesis, suggesting potential biomarkers for oral cancer.

CONCLUSIONS

The MALDI Biotyper is an effective, noninvasive tool for identifying salivary microbiota. Its application may support early diagnosis and prognosis of OSCC, reinforcing the significance of the oral microbiome in cancer etiology.

Mycobiome: an underexplored kingdom in cancer

SUMMARYThe human microbiome, including bacteria, fungi, archaea, and viruses, is intimately linked to both health and disease. The relationship between bacteria and disease has received much attention and intensive investigation, while that of the fungal microbiome, also known as mycobiome, has lagged far behind bacteria. There is growing evidence showing mycobiome dysbiosis in cancer patients, and certain cancer-specific fungi may contribute to cancer progression by interacting with both host and bacteria. It was also demonstrated that the role of fungi-derived products in cancer should also not be underestimated. Therefore, investigating how fungal pathogenesis contributes to the onset and spread of cancer would yield crucial information for cancer diagnosis, prevention, and anti-cancer therapy.

Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types

The relationship between the oral microbiome and oral squamous cell carcinoma (OSCC) has been extensively investigated. Nonetheless, most previous studies were single-center, resulting in the absence of systematic evaluations. To address this gap, we performed a comprehensive meta-analysis on 1,255 samples from OSCC-related 16S rRNA gene data sets, representing a diverse range of OSCC phenotypes. It is recognized that the progression of cancer is related to the alterations in the microbiome among different phenotypes. Our findings revealed distinct microbiome characteristics among different sample types, with Biopsy (Bios) and Swab samples exhibiting significant differences between phenotypes. In Bios samples, the microbiomes of the Cancer group and the normal tissue adjacent to the tumor (NAT) group display a higher similarity, while both differ from the microbiome of the Fibroepithelial polyp (FEP) group. Moreover, the identified differential genera and pathways corresponded with these observations. We developed a diagnostic model using the random forest algorithm on Swab samples, achieving an area under the receiver operating characteristic curve (AUC) of 0.918. Importantly, this model exhibited considerable effectiveness (AUC = 0.849) when applied to another sequencing platform. Taken together, our study provides a comprehensive overview of the oral microbiome during various OSCC progression stages, potentially enhancing early detection and treatment.IMPORTANCEThis study answers key questions regarding the universal microbial characteristics and comprehensive oral microbiome dynamics during oral squamous cell carcinoma (OSCC) progression. By integrating multiple data sets, we examine the following critical aspects: (1) Do different sample types harbor distinct microbial communities within the oral cavity? (2) Which sample types offer greater potential for investigating OSCC progression? (3) How are the oral microbiomes of the Cancer group, normal tissue adjacent to the tumor group, and Fibroepithelial polyp group related, and what is their potential association with OSCC development? (4) Can a diagnostic model based on microbial signatures effectively distinguish between Cancer and Health groups using Swab samples?

The Role of Oral Yeasts in the Development and Progression of Oral Squamous Cell Carcinoma: A Scoping Review

The role of oral yeasts in oral squamous cell carcinoma (OSCC) has gained attention due to evidence linking fungal dysbiosis to carcinogenesis. While Candida albicans has been the primary focus, emerging studies highlight the importance of non-Candida species yeast genera. This scoping review synthesises the evidence on the role of oral yeasts, including Candida spp. and non-Candida species, in the development and progression of OSCC. A PRISMA-ScR-guided search was conducted in Medline, Embase, EBM Reviews, and CINAHL. Observational and experimental studies involving humans with OSCC, oral potentially malignant disorders (OPMDs), or oral epithelial dysplasia (OED) were included. This review analysed 75 studies. Research on oral yeast in OSCC has progressed since the 1970s, with advancements in identification techniques-from conventional culture methods to metagenomic sequencing and multi-omics approaches-alongside improved animal and cellular models of OSCC. These methodological advancements have identified notable distinctions in the oral mycobiome between carcinomatous and healthy states. Clinical findings reinforce the hypothesis that oral yeasts, particularly Candida spp., actively contribute to the dysplasia-carcinoma sequence. Emerging evidence suggests that oral yeasts may significantly modulate events contributing to OSCC progression. However, further mechanistic studies and robust clinical evidence are essential to establish causality and clarify their role in OSCC.

Microbial Signatures in Oral Submucous Fibrosis and Oral Squamous Cell Carcinoma: Implications of Tobacco and Betel Quid Consumption

OBJECTIVES

We compared the oral bacteriome and mycobiome of patients with oral submucosal fibrosis (OSMF) and oral squamous cell carcinoma (OSCC) who consumed tobacco/betel quid with those of healthy individuals.

METHODS

Targeted amplicon sequencing coupled with bioinformatics analysis was performed to assess the bacterial and fungal communities in the oral cavity.

RESULTS

Distinct variations in the microbial communities were observed among the healthy, OSMF, and OSCC samples. Firmicutes was dominant at the phylum level: 21.71%, 21.73%, and 24.56% in the healthy control, OSMF, and OSCC samples, respectively. Lactobacillus (9.6%, 9.04%, and 8.9%) and Streptococcus (7.3%, 7.55%, and 6.1%) showed minimal variation among the healthy, OSMF, and OSCC samples, respectively, at the genus level. Rothia (2.73%) and Veillonella (1.52%) were prominent in those with OSMF, and Gemella (2.2%) and Fusobacterium (1.5%) were prominent in the OSCC samples. The oral mycobiome was dominated by Ascomycota and Basidiomycota in all samples, with Ascomycota accounting for 18.95%, 16.05%, and 15.87%, and Basidiomycota for 13.55%, 15.79%, and 15.96% in the OSCC, OSMF, and healthy samples, respectively. PICRUSt2 analysis revealed the key metabolic pathways linked to disease and xenobiotic degradation, related to the harmful compounds from tobacco, highlighting the clinical relevance of tobacco and betel quid associated microbial communities as well as the differences between OSCC and OSMF.

CONCLUSIONS

Microbial signatures associated with OSCC and OSMF could serve as biomarkers for early cancer detection. These findings highlight how tobacco and betel quid consumption promote cancer and alter the oral microbome.

Systematic analyses uncover robust salivary microbial signatures and host-microbiome perturbations in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is a prevalent malignancy in the oral-maxillofacial region with a poor prognosis. Oral microbiomes play a potential role in the pathogenesis of this disease. However, findings from individual studies have been inconsistent, and a comprehensive understanding of OSCC-associated microbiome dysbiosis remains elusive. Here, we conducted a large-scale meta-analysis by integrating 11 publicly available data sets comprising salivary microbiome profiles of OSCC patients and healthy controls. After correcting for batch effects, we observed significantly elevated alpha diversity and distinct beta-diversity patterns in the OSCC salivary microbiome compared to healthy controls. Leveraging random effects models, we identified robust microbial signatures associated with OSCC across data sets, including enrichment of taxa such as Streptococcus, Lactobacillus, Prevotella, Bulleidia moorei, and Haemophilus in OSCC samples. The machine learning models constructed from these microbial markers accurately predicted OSCC status, highlighting their potential as non-invasive diagnostic biomarkers. Intriguingly, our analyses revealed that the age- and gender-associated signatures in normal saliva microbiome were disrupted in the OSCC, suggesting perturbations in the intricate host-microbe interactions. Collectively, our findings uncovered complex alterations in the oral microbiome in OSCC, providing novel insights into disease etiology and paving the way for microbiome-based diagnostic and therapeutic strategies. Given that the salivary microbiome can reflect the overall health status of the host and that saliva sampling is a safe, non-invasive approach, it may be worthwhile to conduct broader screening of the salivary microbiome in high-risk OSCC populations as implications for early detection.

IMPORTANCE

The oral cavity hosts a diverse microbial community that plays a crucial role in systemic and oral health. Accumulated research has investigated significant differences in the saliva microbiota associated with oral cancer, suggesting that microbiome dysbiosis may contribute to the pathogenesis of oral squamous cell carcinoma (OSCC). However, the specific microbial alterations linked to OSCC remain controversial. This meta-analysis reveals robust salivary microbiome alterations. Machine learning models using differential operational taxonomic units accurately predicted OSCC status, highlighting the potential of the salivary microbiome as a non-invasive diagnostic biomarker. Interestingly, age- and gender-associated signatures in the normal salivary microbiome were disrupted in OSCC, suggesting perturbations in host-microbe interactions.

Aspergillus flavus with Mycovirus as an Etiologic Factor for Acute Leukemias in Susceptible Individuals: Evidence and Discussion

Several etiologic factors for the development of acute leukemias have been suggested; however, none is applicable to all cases. We isolated a certain mycovirus-containing Aspergillus flavus (MCAF) from the home of a patient with acute lymphoblastic leukemia. Repeated electron microscopic evaluations proved the existence of mycovirus in this organism. According to chemical analysis, this organism does not produce any aflatoxin, possibly due to its infestation with mycoviruses. We reported that using the ELISA technique, forty pediatric patients with acute lymphoblastic leukemia (ALL) uniformly had antibodies to the products of MCAF. In contrast, three separate groups of controls, consisting of normal blood donors, individuals with solid tumors, and patients with sickle cell disease, were negative. In vitro exposure of mononuclear blood cells from patients with ALL, in full remission, to the products of MCAF induced redevelopment of cell surface phenotypes and genetic markers characteristic of ALL. The controls were negative. The incubation of normal and ALL cell lines with the products of MCAF resulted in significant cellular apoptosis, changes in the cell cycle, and the downregulation of transcription factors, including PAX-5 and Ikaros (75 and 55 kDa). Fungi are widespread in nature, and many contain mycoviruses. Normally, an individual inhales 1 to 10 fungal spores per minute, while farmers can inhale up to 75,000 spores per minute. It is known that farmers and foresters, who are more exposed to fungi, have a higher rate of acute leukemia. In contrast, asthmatics, most of whom are allergic to fungal agents, and individuals working in office settings have a lower rate. One of the theories for the development of acute leukemia suggests a genetic predisposition followed by exposure to an infectious agent. With the above findings, we propose that mycovirus-containing Aspergillus flavus may have an etiological role in leukemogenesis in immune-depressed and genetically susceptible individuals.

Oral Leukoplakia Microbiome Predicts the Degree of Dysplasia and is Shaped by Smoking and Tooth Loss

OBJECTIVE

This study aimed to determine if the oral potentially malignant disorder, oral leukoplakia (OLK), exhibited microbiome changes that predict the degree of dysplasia and the risk of malignant progression.

RESULTS

We examined the microbiome in 216 swabs of OLK from 177 patients. Compared to healthy controls (n = 120 swabs from 61 patients), who were less likely to smoke and had better oral health, OLK patients exhibited an increased abundance of Rothia mucilaginosa, Streptococcus parasanguinis and S. salivarius, resembling acetaldehyde generating communities described previously. Compared to the patients' healthy contralateral normal (CLN) mucosa (n = 202), which acts as a matched control for oral health parameters, OLK exhibited increased S. infantis, Leptotrichia spp., Bergeyella spp., Porphyromonas spp. and F. nucleatum. Machine learning with clinical and microbiome data could discriminate high-risk dysplasia (moderate to severe) from low-risk dysplasia (none or mild) (sensitivity 87.4%; specificity 76.5%). Follow-up swabs were recovered from 58 patients, eight of whom progressed to a higher grade of dysplasia or OSCC and these eight patients exhibited a higher abundance of Fusobacterium species at their initial presentation.

CONCLUSIONS

Our study suggests that the OLK microbiome has potential to be an aid to the prediction of dysplasia grade and the risk of malignant transformation.

Impact of oral flora in tongue coating and saliva on oral cancer risk and the regulatory role of Interleukin-8

BACKGROUND

Oral flora and inflammatory factors play a crucial role in oral cancer, but the relationship between them and oral cancer has not been clearly established.

METHODS

Oral flora served as exposure factor, oral cancer as outcome factor, and inflammatory factors as mediating factor. Mendelian randomization (MR) analysis was used to analyze the relationship between oral flora and oral cancer, and the potential mediating effect of inflammatory factors was explored through mediation analysis.

RESULTS

29 kinds of oral flora in tongue coating and 22 kinds of oral flora in saliva were associated with increased risk of oral cancer. 18 species of oral flora in tongue coating and 25 species in saliva were associated with a reduced risk of oral cancer. Interleukin-8 (IL8) played a mediating role in the relationship between oral flora and oral cancer, and it was associated with an increased risk of oral cancer. Granulicatella, Streptococcus mitis, Saccharimonadaceae and Haemophilus in oral flora caused oral cancer indirectly through IL8. IL8 expression increased in oral cancer, which has good diagnostic value. IL8-related genes in oral cancer are closely associated with immune cell infiltration. What's more, IL8 has potential medicinal properties.

CONCLUSION

Oral flora of tongue coating and saliva is closely related to oral cancer, and IL8 plays a mediating role in the causal relationship between oral flora and oral cancer.

From Skin and Gut to the Brain: The Infectious Journey of the Human Commensal Fungus Malassezia and Its Neurological Consequences

The human mycobiome encompasses diverse communities of fungal organisms residing within the body and has emerged as a critical player in shaping health and disease. While extensive research has focused on the skin and gut mycobiome, recent investigations have pointed toward the potential role of fungal organisms in neurological disorders. Among those fungal organisms, the presence of the commensal fungus Malassezia in the brain has created curiosity because of its commensal nature and primary association with the human skin and gut. This budding yeast is responsible for several diseases, such as Seborrheic dermatitis, Atopic dermatitis, Pityriasis versicolor, Malassezia folliculitis, dandruff, and others. However recent findings surprisingly show the presence of Malassezia DNA in the brain and have been linked to diseases like Alzheimer's disease, Parkinson's disease, Multiple sclerosis, and Amyotrophic lateral sclerosis. The exact role of Malassezia in these disorders is unknown, but its ability to infect human cells, travel through the bloodstream, cross the blood-brain barrier, and reside along with the lipid-rich neuronal cells are potential mechanisms responsible for pathogenesis. This also includes the induction of pro-inflammatory cytokines, disruption of the blood-brain barrier, gut-microbe interaction, and accumulation of metabolic changes in the brain environment. In this review, we discuss these key findings from studies linking Malassezia to neurological disorders, emphasizing the complex and multifaceted nature of these cases. Furthermore, we discuss potential mechanisms through which Malassezia might contribute to the development of neurological conditions. Future investigations will open up new avenues for our understanding of the fungal gut-brain axis and how it influences human behavior. Collaborative research efforts among microbiologists, neuroscientists, immunologists, and clinicians hold promise for unraveling the enigmatic connections between human commensal Malassezia and neurological disorders.

Review Article: Disrupted Oral Microbiota and Its Implications in Cancer Onset and Progression: A Narrative Review

The oral microbiota plays a pivotal role in maintaining oral health, but its dysbiosis has been increasingly implicated in the development of systemic diseases, including cancer. Emerging evidence highlights the potential contribution of oral microorganisms to carcinogenesis in the oral cavity and distant organs, such as the lungs, pancreas, and genitourinary tract. This review explores the mechanisms through which the oral microbiota influences cancer development and treatment response, mainly driven by microbial translocation, systemic inflammation, immune modulation, and the release of carcinogenic metabolites. Additionally, the review discusses how oral microbiota perturbations interact with host factors, such as diet, systemic diseases, genetics, and cancer therapies, to influence tumor initiation, progression, and response to treatment. A critical analysis of past and emerging literature shows that specific microbial taxa potentially influence tumor progression and immune responses, including Fusobacterium, Porphyromonas, Aggregatibacter and Treponema. The detection of these microorganisms and the study of oral microbiome profiling in cancer care may offer new diagnostic and therapeutic strategies; however, further studies with homogeneous patient populations are needed to fully understand the contributions of oral dysbiosis in cancer development and treatment responses.

The oral microbiome and its role in oral squamous cell carcinoma: a systematic review of microbial alterations and potential biomarkers

Background

Oral squamous cell carcinoma (OSCC) is one of the most common cancers worldwide. Despite advances in diagnosis and treatment, the incidence of OSCC is increasing, and the mortality rate remains high. This systematic review aims to examine the potential association between the composition of the oral microbiota and OSCC.

Materials and methods

This study's protocol was developed according to the PRISMA guidelines. Several search engines, including Medline-PubMed, Scopus (via Elsevier), and Google Scholar, were used to identify original studies that analyzed differences in the oral microbiome between OSCC patients and controls. Twenty-seven studies were identified that reported significant differences in microbial abundance between OSCC and controls.

Results

The systematic review highlights a complex relationship between the oral microbiome and the pathogenesis of OSCC. Significant changes in the microbial composition were identified, with a predominance of phyla such as Bacteroidetes and Fusobacteria, which are associated with inflammatory mechanisms facilitating tumor progression. A remarkable variability in microbial profiles emerged based on the different stages of the disease and the types of samples analyzed, demonstrating the complexity of the oral microbial ecosystem.

Conclusion

Although alterations in the oral cavity microbiome composition are evident in patients with OSCC, identifying a specific pattern remains challenging. However, the integration of advanced analytical techniques, such as artificial intelligence, could overcome this problem, allowing the identification of crucial biomarkers and improving the understanding of the role of the microbiome in carcinogenesis. This approach could transform microbiome analysis into a useful tool for screening and monitoring patients with OSCC.

Oral fungal dysbiosis and systemic immune dysfunction in Chinese patients with schizophrenia

Oral microbial dysbiosis contributes to the development of schizophrenia (SZ). While numerous studies have investigated alterations in the oral bacterial microbiota among SZ patients, investigations into the fungal microbiota, another integral component of the oral microbiota, are scarce. In this cross-sectional study, we enrolled 118 Chinese patients with SZ and 97 age-matched healthy controls (HCs) to evaluate the oral fungal microbiota from tongue coating samples using internal transcribed spacer 1 amplicon sequencing and assess host immunity via multiplex immunoassays. Our findings revealed that SZ patients exhibited reduced fungal richness and significant differences in β-diversity compared to HCs. Within the oral fungal communities, we identified two distinct fungal clusters (mycotypes): Candida and Malassezia, with SZ patients showing increased Malassezia and decreased Candida levels. These key functional oral fungi may serve as potential diagnostic biomarkers for SZ. Furthermore, SZ patients displayed signs of immunological dysfunction, characterized by elevated levels of pro-inflammatory cytokines such as IL-6 and TNF-α, and chemokines including MIP-1α and MCP-1. Importantly, Malassezia mycotype correlated positively with peripheral pro-inflammatory cytokines, while Candida mycotype exhibited a negative correlation with these cytokines. In conclusion, we have demonstrated, for the first time, the presence of altered oral fungal communities and systemic immune dysfunction in Chinese SZ patients compared to HCs, providing novel insights into the potential role of oral fungi as biomarkers and the broader implications for understanding SZ pathogenesis.

Bacteriome and mycobiome dysbiosis in oral mucosal dysplasia and oral cancer

It has long been considered that the oral microbiome is tightly connected to oral health and that dysbiotic changes can be detrimental to the occurrence and progression of dysplastic oral mucosal lesions or oral cancer. Improved understanding of the concepts of microbial dysbiosis together with advances in high-throughput molecular sequencing of these pathologies have charted in greater microbiological detail the nature of their clinical state. This review discusses the bacteriome and mycobiome associated with oral mucosal lesions, oral candidiasis, and oral squamous cell carcinoma, aiming to delineate the information available to date in pursuit of advancing diagnostic and prognostic utilities for oral medicine.

Is Short-Read 16S rRNA Sequencing of Oral Microbiome Sampling a Suitable Diagnostic Tool for Head and Neck Cancer?

The oral microbiome, studied by sampling the saliva or by oral rinse, has been long thought to have diagnostic capacity for head and neck cancers (HNC). However, previous reports on the HNC oral microbiome provide inconsistent results. The aim of this study is to consolidate these datasets and determine the oral microbial composition between HNC patients to healthy and premalignant individuals. We analyzed 16 published head and neck cancer (HNC) short-read 16S rRNA sequencing datasets, specifically targeting the V3V4, V4 and V4V5 regions. These datasets included saliva and oral rinse samples from donors with HNC, as well as from healthy and premalignant donors. Differences in diversities and microbial abundance were determined. HNC saliva displayed lower alpha diversity than healthy donors. In contrast, the opposite trend was observed for oral rinse samples. Beta diversity scores were largely similar across different patient types. Similar oral phyla were detected for all samples, but proportions were largely dependent on sample type (i.e., saliva or oral rinse) and primer set utilized for 16S rRNA sequencing. Neisseria, Leptotrichia and Megasphaera were elevated in healthy saliva, while Mycoplasma was elevated in HNC saliva. Oral rinse and saliva displayed similar enrichment for Fusobacterium, while Veillonella, Alloprevotella, and Campylobacter showed conflicting results. The sparse partial least squares discriminant analysis model performed effectively in discriminating HNC from healthy or premalignant patients using V3V4 saliva (AUC = 0.888) and V3V4 oral rinse (AUC = 0.928), while poor discriminative capacity was observed for V4 saliva (AUC = 0.688). In conclusion, our meta-analysis highlighted the limitations of 16S rRNA sequencing, particularly due to variations across study batches, primer sets (i.e., V3V4, V4), and sample types. Hence, caution should be exercised when interpreting 16S rRNA sequencing results across studies, especially when different primer sets and sample types are used.

Application of Natural Medicinal Plants Active Ingredients in Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is the most common malignant cancer of the head and neck, with high morbidity and mortality, ranking as the sixth most common cancer in the world. The treatment of OSCC is mainly radiotherapy, chemotherapy and surgery, however, the prognosis of patients is still poor and the recurrence rate is high. This paper reviews the range of effects of natural medicinal plant active ingredients (NMPAIs) on OSCC cancer, including the types of NMPAIs, anti-cancer mechanisms, involved signaling pathways, and clinical trials. The NMPAIs include terpenoids, phenols, flavonoids, glycosides, alkaloids, coumarins, and volatile oils. These active ingredients inhibit proliferation, induce apoptosis and autophagy, inhibit migration and invasion of OSCC cells, and regulate cancer immunity to exert anti-cancer effects. The mechanism involves signaling pathways such as mitogen-activated protein kinase, phosphatidylinositol 3 kinase/protein kinase B, nuclear factor kappa B, miR-22/WNT1/β-catenin and Nrf2/Keap1. Clinically, NMPAIs can inhibit the growth of OSCC, and the combined drug is more effective. Natural medicinal plants are promising candidates for the treatment of OSCC.

Diversity and compositional differences in the oral microbiome of oral squamous cell carcinoma patients and healthy controls: a scoping review

Objectives

The human oral microbiome may play a role in the development of oral squamous cell carcinoma. The aim of this scoping review was to examine microbial diversity and differences in the composition of the oral microbiome between OSCC patients and healthy controls.

Methods

A literature search (in PubMed and Embase.com) was performed on January 9, 2023. The outcome variables used from the included studies of this review were alpha- and beta diversity and oral microbiome composition profiles for each taxonomic level (phylum-, class-, order-, genus- and species level).

Results

Thirteen out of 423 studies were included in this review compromising 1,677 subjects, of which 905 (54.0%) were OSCC patients and 772 (46.0%) were healthy controls. Most studies found a higher alpha diversity in the OSCC patient group and significantly different beta diversities between OSCC patient samples and healthy control samples. Studies reported more abundant Fusobacteria (on phylum level), Fusobacterium (on genus level), Fusobacterium nucleatum, Porphyromonas endodontalis and Prevotella intermedia (on species level) in OSCC patients. The healthy control group had more abundant Actinobacteria (on phylum level), Streptococcus and Veilonella (on genus level) and Veilonella parvula (on species level) according to most studies.

Conclusions

Our findings show differences in oral microbiome diversity and composition in OSCC patients. Clinical implications demand continuing study. Development of internationally accepted standard procedures for oral sample collection and oral microbiota analysis is needed for more conclusive and clinically relevant comparisons in future research.

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.

Prevotella intermedia boosts OSCC progression through ISG15 upregulation: a new target for intervention

PURPOSE

Periodontitis-associated bacteria, such as Porphyromonas gingivalis and Fusobacterium nucleatum, are closely linked to the risk of oral squamous cell carcinoma (OSCC). Emerging studies have indicated that another common periodontal pathogen, Prevotella intermedia (P. intermedia), is enriched in OSCC and could affect the occurrence and progression of OSCC. Our aim is to determine the effects of P. intermedia on the progression of OSCC and the role of antibiotics in reversing these effects.

METHODS

In this study, a murine xenograft model of OSCC was established, and the mice were injected intratumorally with PBS (control group), P. intermedia (P.i group), or P. intermedia combined with an antibiotic cocktail administration (P.i + ABX group), respectively. The effects of P. intermedia and ABX administration on xenograft tumor growth, invasion, angiogenesis, and metastasis were investigated by tumor volume measurement and histopathological examination. Enzyme-linked immunosorbent assay (ELISA) was used to investigate the changes in serum cytokine levels. Immunohistochemistry (IHC) was adopted to analyze the alterations in the levels of inflammatory cytokines and infiltrated immune cells in OSCC tissues of xenograft tumors. Transcriptome sequencing and analysis were conducted to determine differential expression genes among various groups.

RESULTS

Compared with the control treatment, P. intermedia treatment significantly promoted tumor growth, invasion, angiogenesis, and metastasis, markedly affected the levels of inflammatory cytokines, and markedly altered M2 macrophages and regulatory T cells (Tregs) infiltration in the tumor microenvironment. However, ABX administration clearly abolished these effects of P. intermedia. Transcriptome and immunohistochemical analyses revealed that P. intermedia infection increased the expression of interferon-stimulated gene 15 (ISG15). Correlation analysis indicated that the expression level of ISG15 was positively correlated with the Ki67 expression level, microvessel density, serum concentrations and tissue expression levels of inflammatory cytokines, and quantities of infiltrated M2 macrophages and Tregs. However, it is negatively correlated with the quantities of infiltrated CD4+ and CD8+ T cells.

CONCLUSION

In conclusion, intratumoral P. intermedia infection aggravated OSCC progression, which may be achieved through upregulation of ISG15. This study sheds new light on the possible pathogenic mechanism of intratumoral P. intermedia in OSCC progression, which could be a prospective target for OSCC prevention and treatment.

Oral Mycobiota: A Narrative Review

Numerous studies have proven the important role of the oral microbiota in health and disease. The dysfunctionality of the oral microbiota, known as dysbiosis, is incriminated in dental caries, periodontal disease, oral infectious diseases, oral cancer, and systemic disease. The lesser-known component of the oral microbiota, the mycobiota, is now assiduously investigated. Recent technological developments have helped foster the identification of new fungal species based on genomic research. Next-generation sequencing has expanded our knowledge about the diversity, architecture, and relationships of oral microorganisms within the oral cavity. The mycobiome structure and relationships with the bacteriome have been studied to identify a mycobiotic signature. This review aimed to emphasize the latest knowledge of the oral mycobiome.

Oral bacteriome and oral potentially malignant disorders: A systematic review of the associations

INTRODUCTION

Periodontal bacteria can infiltrate the epithelium, activate signaling pathways, induce inflammation, and block natural killer and cytotoxic cells, all of which contribute to the vicious circle of carcinogenesis. It is unknown whether oral dysbiosis has an impact on the etiology or prognosis of OPMD.

AIMS

Within this paradigm, this work systemically investigated and reported on the composition of oral microbiota in patients with oral potentially malignant disorders (OPMD) versus healthy controls.

METHODS

Observational studies that reported next generation sequencing analysis of oral tissue or salivary samples and found at least three bacterial species were included. Identification, screening, citation analysis, and graphical synthesis were carried out.

RESULTS

For oral lichen planus (OLP), the bacteria with the highest abundance were Fusobacterium, Capnocytophaga, Gemella, Granulicatella, Porphyromonas, and Rothia; for oral leukoplakia (OLK), Prevotella. Streptococci levels in OLK and OLP were lower. The usage of alcohol or smoke had no effect on the outcomes.

CONCLUSIONS

An increase in periodontal pathogenic bacteria could promote the development and exacerbation of lichen. Effective bacteriome-based biomarkers are worthy of further investigation and application, as are bacteriome-based treatments.

Heat-killed Prevotella intermedia promotes the progression of oral squamous cell carcinoma by inhibiting the expression of tumor suppressors and affecting the tumor microenvironment

BACKGROUND

Oral microbial dysbiosis contributes to the development of oral squamous cell carcinoma (OSCC). Our previous study showed that Prevotella intermedia (P. intermedia) were enriched in the oral mucosal surface, plaque, and saliva of patients with OSCC. Intratumoral microbiome could reshape the immune system and influence the development of various tumors. However, the invasion status of human OSCC tissues by P. intermedia and the pathway through which intratumoral P. intermedia potentiates tumor progression remain unexplored.

METHODS

P. intermedia in human OSCC or normal tissues was detected by FISH. A mouse OSCC cell line SCC7 was adopted to investigate the effects of heat-killed P. intermedia treatment on cell proliferation, invasion, and cytokine release by using CCK-8 assay, transwell invasion assay and ELISA. Moreover, we established a mouse transplanted tumor model by using SCC7 cells, injected heat-killed P. intermedia into tumor tissues, and investigated the effects of heat-killed P. intermedia on tumor growth, invasion, cytokine levels, immune cell infiltrations, and expression levels by using gross observation, H&E staining, ELISA, immunohistochemistry, mRNA sequencing, and transcriptomic analysis.

RESULTS

Our results indicated that P. intermedia were abundant in OSCC and surrounding muscle tissues. Heat-killed P. intermedia promoted SCC7 cell proliferation, invasion and proinflammatory cytokine secretions, accelerated transplanted tumor growth in mice, exacerbate muscle and perineural invasion of OSCC, elevated the serum levels of IL-17A, IL-6, TNF-α, IFN-γ, and PD-L1, induced Treg cells M2 type macrophages in mouse transplanted tumors. The data of transcriptomic analysis revealed that heat-killed P. intermedia increased the expression levels of inflammatory cytokines and chemokines while reduced the expression levels of some tumor suppressor genes in mouse transplanted tumors. Additionally, IL-17 signaling pathway was upregulated whereas GABAergic system was downregulated by heat-killed P. intermedia treatment.

CONCLUSIONS

Taken together, our results suggest that P. intermedia could inhibit the expression of tumor suppressors, alter the tumor microenvironment, and promote the progression of OSCC.

Fungal footprints in oral cancer: unveiling the oral mycobiome

Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer, with a high mortality rate. There is growing evidence supporting a link between oral cancer and the microbiome. The microbiome can impact various aspects of cancer, such as pathogenesis, diagnosis, treatment, and prognosis. While there is existing information on bacteria and its connection to oral cancer, the fungi residing in the oral cavity represent a significant component of the microbiome that remains in its early stages of exploration and understanding. Fungi comprise a minuscule part of the human microbiome called the mycobiome. Mycobiome is ubiquitous in the human body but a weakened immune system offers a leeway space for fungi to showcase its virulence. The role of mycobiome as a colonizer, facilitator, or driver of carcinogenesis is still ambiguous. Reactivating the mycobiome that undergoes collateral damage associated with cancer treatment can be watershed event in cancer research. The coordinated, virulent, non-virulent behavior of the fungi once they reach a critical density must be hacked, considering its diagnostic, prognostic and therapeutic implications in cancer. This review highlights the diversity of the mycobiome and its potential role in oral cancer.

Mechanisms and Potential Clinical Implications of Oral Microbiome in Oral Squamous Cell Carcinoma

Microorganisms in the oral cavity are abundant in the human body. At present, more than 700 species of oral microorganisms have been identified. Recently, a lot of literature has indicated that the oral microbiota plays an important role in the occurrence, development, and prognosis of oral squamous cell carcinoma (OSCC) through various mechanisms. And researchers are now trying to utilize oral microbiota in cancer diagnosis and treatment. However, few articles systematically summarize the effects of oral microbes in the diagnosis, treatment, and disease outcomes of oral cancer. Herein, we made a summary of the microbial changes at cancerous sites and placed more emphasis on the mechanisms by which the oral microbiome promotes cancerization. Moreover, we aimed to find out the clinical value of the oral microbiome in OSCC.

Oral Bacteria, Virus and Fungi in Saliva and Tissue Samples from Adult Subjects with Oral Squamous Cell Carcinoma: An Umbrella Review

Oral squamous cell carcinoma (OSCC) is the most common oral cavity malignancy associated with multiple risk factors. In the last 14 years, oral dysbiosis has attracted the scientific community's attention as a potential oncogenic factor, in parallel with the development of omics technologies that have revolutionized microbiological research. The present umbrella review aimed to investigate the oral microbiological content (bacilli, viruses, and fungi) of tissue and saliva samples from adult (>18 years) patients with OSCC. The secondary objective was to compare the oral microbiome of OSCC subjects with non-OSCC subjects. The study protocol was under the PRISMA statement and registered on PROSPERO (CRD42023448153). Data from 32 systematic reviews were extracted, qualitatively summarized, and analyzed using AMSTAR-2. An increase in oral bacteria of the phylum Fusobacteria, Proteobacteria, and Bacteroidetes and a decrease in Firmicutes and Actinobacteria were observed in OSCC patients. The increased bacterial genera were periodontopathogens. The most common viruses were EBV and HPV, especially the high-risk genotypes. Candida was the most studied oral fungus and was always increased in OSCC subjects. Further studies should investigate the possible carcinogenic mechanisms of oral microorganisms found increased in tissue samples and saliva from adult subjects with OSCC.

A Taxonomy-Agnostic Approach to Targeted Microbiome Therapeutics-Leveraging Principles of Systems Biology

The study of human microbiomes has yielded insights into basic science, and applied therapeutics are emerging. However, conflicting definitions of what microbiomes are and how they affect the health of the "host" are less understood. A major impediment towards systematic design, discovery, and implementation of targeted microbiome therapeutics is the continued reliance on taxonomic indicators to define microbiomes in health and disease. Such reliance often confounds analyses, potentially suggesting associations where there are none, and conversely failing to identify significant, causal relationships. This review article discusses recent discoveries pointing towards a molecular understanding of microbiome "dysbiosis" and away from a purely taxonomic approach. We highlight the growing role of systems biological principles in the complex interrelationships between the gut microbiome and host cells, and review current approaches commonly used in targeted microbiome therapeutics, including fecal microbial transplant, bacteriophage therapies, and the use of metabolic toxins to selectively eliminate specific taxa from dysbiotic microbiomes. These approaches, however, remain wholly or partially dependent on the bacterial taxa involved in dysbiosis, and therefore may not capitalize fully on many therapeutic opportunities presented at the bioactive molecular level. New technologies capable of addressing microbiome-associated diseases as molecular problems, if solved, will open possibilities of new classes and categories of targeted microbiome therapeutics aimed, in principle, at all dysbiosis-driven disorders.

Dysbiosis of the oral microbiota composition is associated with oral squamous cell carcinoma and the impact of radiotherapy: a pilot study

Radiotherapy can potentially influence the diversity and composition of the oral microbiome. We performed a study comparing the composition of oral microbiota in patients with oral squamous cell carcinoma (OSCC) before radiotherapy (n = 6), at three months (n = 6), and six months (n = 6) post-radiotherapy, and controls (n = 6). We profiled the oral microbiome by 16S rRNA gene sequencing using Illumina MiSeq. Alpha diversity (Chao1 index) showed significant differences in species richness between healthy controls and OSCC patients (P = 0.014). Conversely, no noteworthy distinctions were observed in the Chao1 index when comparing the pre-and post-radiation periods at both three and six months. The beta diversity of the oral microbiota differed significantly between the controls and OSCC patients (P = 0.014). However, no significant differences were observed in beta diversity between pre- and post-radiation at three months, whereas a significant difference was observed at six months (P = 0.038). Linear Discriminant Analysis Effect Size (LEfSe) demonstrated lower abundance of Corynebacterium, Actinomyces, Veillonella, and Haemophilus, and higher abundance of Selenomonas and Mycoplasma in OSCC patients than in healthy controls. The oral microbiome composition varied among healthy controls, patients with OSCC, and post-radiation therapy patients with OSCC. The observed recovery in the numerical dominance of specific beneficial oral taxa and the reduction in pathogenic bacteria after radiation therapy highlights the need for further investigations into their clinical implications.

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.