Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized.

Background: Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remains less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called 'vanishing microbiomes' potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. Results: Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the United States within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain source. Conclusion: Our findings demonstrate that by controlling for geography, we can isolate an important role for lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.

A preliminary report on the exploration of salivary bacterial diversity by the multiplex SNaPshot assay.

Salivary bacterial community composition is associated with the host's internal and environmental factors, which have potential applications in forensic practice. The 16S rRNA gene sequencing is the most commonly used strategy for detecting salivary bacterial diversity; however, its platforms are not compatible with capillary electrophoresis (CE) platforms commonly used for forensic applications. Therefore, we attempted to detect the salivary bacterial diversity using a single nucleotide polymorphism (SNP) assay. Salivary bacterial diversity varies among diverse geographic locations, making it a potential supplementary biomarker for forensic geographic sourcing. To evaluate the performance of the multiplex SNaPshot assay, saliva samples from three geographic locations in China were analyzed using the multiplex SNaPshot assay and 16S rRNA gene sequencing. We screened SNPs from two high-relative-abundance salivary genera (Streptococcus and Veillonella) to construct a multiplex SNaPshot system that can be used on the CE platform. The stability and sensitivity of the multiplex SNaPshot system were also tested. A random forest classification model was used to classify samples from different regions to explore the ability of salivary bacteria to discriminate between geographic sources. Six bacterial SNPs were screened and a multiplex SNaPshot system was constructed. The stability results showed that the typing of salivary stains that were placed indoors for different days was not affected in this study. Two-thirds of mocked salivary stain samples showed more than 90% of typing results obtained for salivary stain samples with an input of 0.1 µl saliva. The results of principal coordinate analysis based on salivary bacterial diversity showed significant differences between samples from the three different geographic locations. The accuracy of the random forest classification was 66.67% based on the multiplex SNaPshot assay and 83.33% based on the 16S rRNA gene sequencing. In conclusion, this is the first attempt to detect salivary bacterial diversity using a multiplex SNaPshot bacterial SNP assay. The geographic difference in human salivary bacterial community composition was significant, as revealed by the multiplex SNaPshot assay; however, its performance in discriminating geographic sources was lower than that of 16S rRNA gene sequencing. This strategy based on bacterial SNP loci may favor the detection of human bacterial diversity in common forensic laboratories but requires further exploration in larger sample sizes and more bacterial SNP loci.

Oral manifestations in women using hormonal contraceptive methods: a systematic review.

OBJECTIVES: To investigate the oral manifestations in women of reproductive age using hormonal contraceptive methods. MATERIALS AND METHODS: This review is based on the PRISMA statement. A literature search incorporated observational studies from the last 21 years. An investigative question was formulated using the PICO model, studies were selected, and a quality analysis was performed using the modified STROBE guidelines. A bibliometric analysis was performed, and the data were examined. RESULTS: Thirteen articles were included, with the majority evaluating periodontal status. Others analyzed factors such as the presence of alveolar osteitis, oral candidiasis, and salivary microbiome dysbiosis. Ten articles were deemed to have a low risk of bias. CONCLUSIONS: Hormonal contraceptives may increase the risk of alveolar osteitis following tooth extraction and increase the presence of the Candida species in the oral cavity. They also affect the periodontium, such as the frequent development of gingivitis, but do not lead to changes in the salivary microbiome. CLINICAL RELEVANCE: The increasing number of women using hormonal contraceptives and the knowledge that these contraceptives can produce oral cavity alterations underscore the need to evaluate the oral manifestations found in these women.

Response of salivary microbiome to temporal, environmental, and surface characteristics under in vitro exposure.

The microbiome of saliva stains deposited at crime scenes and in everyday settings is valuable for forensic investigations and environmental ecology. However, the dynamics and applications of microbial communities in these saliva stains have not been fully explored. In this study, we analyzed saliva samples that were exposed to indoor conditions for up to 1 year and to different carriers (cotton, sterile absorbent cotton swab, woolen, dacron) in both indoor and outdoor environments for 1 month using high-throughput sequencing. The analysis of microbial composition and Mfuzz clustering showed that the salivary flora, specifically Streptococcus (cluster7), which was associated with microbial contamination, remained stable over short periods of time. However, prolonged exposure led to significant differences due to the invasion of environmental bacteria such as Pseudomonas and Achromobacter. The growth and colonization of environmental flora were promoted by humidity. The neutral model predictions indicated that the assembly of salivary microbial communities in outdoor environments was significantly influenced by stochastic processes, with environmental characteristics having a greater impact on community change compared to surface characteristics. By incorporating data from previous studies on fecal and vaginal secretion microbiology, we developed RF and XGBoost classification models that achieved high accuracy (>98 %) and AUC (>0.8). Additionally, a RF regression model was created to determine the time since deposition (TsD) of the stains. Time inference models yielded a mean absolute error (MAE) of 7.1 days for stains exposed for 1 year and 14.2 h for stains exposed for 14 days. These findings enhance our understanding of the changes in the microbiome of saliva stains over time, in different environments, and on different surfaces. They also have potential applications in assessing potential microbial contamination, identifying body fluids, and inferring the time of deposition.

Impact of waterpipe smoking on the salivary microbiome.

Background: While oral mirobial dysbiosis due to tobacco smoking has been studied thoroughly, there is limited data on the effect of waterpipe smoking on the oral microbiome. This study aims to compare the salivary microbiome between waterpipe smokers and non-smokers. Materials and methods: Unstimulated saliva samples were collected from 60 participants, 30 smokers and 30 non-smokers in Kuala Lumpur and Klang Valley, Malaysia. DNA extraction was performed using the Qiagen DNA mini kit, and the 16S rRNA bacterial gene was amplified and sequenced using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and the alpha and beta diversity of the bacterial community was assessed. Significantly differentiated taxa were identified using LEfSe analysis, while differentially expressed pathways were identified using MaAsLin2. Results: A significant compositional change (beta diversity) was detected between the two groups (PERMANOVA P < 0.05). Specifically, the levels of phylum Firmicutes and genus Streptococcus were elevated in smokers, whereas phylum Proteobacteria and genus Haemophilus were depleted compared to non-smokers. At the species level, Streptococcus oralis, Streptococcus salivarius, and Streptococcus gingivalis were enriched in smokers. We observed significant differences in the abundance of thirty-seven microbial metabolic pathways between waterpipe smokers and non-smokers. The microbial pathways enriched in smokers were those implicated in polymer degradation and amino acid metabolism. Conclusion: The taxonomic and metabolic profile of the salivary microbiome in waterpipe smokers compared to healthy controls exhibited a paradigm shift, thus, implying an alteration in the homeostatic balance of the oral cavity posing unique challenges for oral health.

Salivary microbiome in kidney diseases: A narrative review.

Many research has been conducted since the microbiota's discovery that have focused on the role it plays in health and disease. Microbiota can be divided into categories like intestinal, oral, respiratory, and skin microbiota based on the specific localized areas. To maintain homeostasis and control immunological response, the microbial populations live in symbiosis with the host. On the other hand, dysbiosis of the microbiota can cause diseases including kidney diseases and the deregulation of body functioning. We discuss the current understanding of how various kidney diseases are caused by the salivary microbiome (SM) in this overview. First, we review the studies on the salivary microbiota in diverse clinical situations. The importance of the SM in diabetic kidney disease, chronic kidney disease, membranous nephropathy, and IgA nephropathy is next highlighted. We conclude that the characteristics of the SM of patients with various kidney diseases have revealed the potential of salivary microbial markers as noninvasive tool for the detection of various kidney diseases.

Salivary microbiome of healthy women of reproductive age.

IMPORTANCE: The salivary microbiome has been proven to play a crucial role in local and systemic diseases. Moreover, the effects of biological and lifestyle factors such as oral hygiene and smoking on this microbial community have already been explored. However, what was not yet well understood was the natural variation of the saliva microbiome in healthy women and how this is associated with specific use of hormonal contraception and with the number of different sexual partners with whom microbiome exchange is expected regularly. In this paper, we characterized the salivary microbiome of 255 healthy women of reproductive age using an in-depth questionnaire and self-sampling kits. Using the large metadata set, we were able to investigate the associations of several host-related and lifestyle variables with the salivary microbiome profiles. Our study shows a high preservation between individuals.

Novel bacterial proteolytic and metabolic activity associated with dental erosion-induced oral dysbiosis.

BACKGROUND: Dental erosion is a disease of the oral cavity where acids cause a loss of tooth enamel and is defined as having no bacterial involvement. The tooth surface is protected from acid attack by salivary proteins that make up the acquired enamel pellicle (AEP). Bacteria have been shown to readily degrade salivary proteins, and some of which are present in the AEP. This study aimed to explore the role of bacteria in dental erosion using a multi-omics approach by comparing saliva collected from participants with dental erosion and healthy controls. RESULTS: Salivary proteomics was assessed by liquid-chromatography mass spectrometry (LC-MS) and demonstrated two altered AEP proteins in erosion, prolactin inducible protein (PIP), and zinc-alpha-2 glycoprotein (ZAG). Immunoblotting further suggested that degradation of PIP and ZAG is associated with erosion. Salivary microbiome analysis was performed by sequencing the bacterial 16S rRNA gene (V1-V2 region, Illumina) and showed that participants with dental erosion had a significantly (p < 0.05) less diverse microbiome than healthy controls (observed and Shannon diversity). Sequencing of bacterial mRNA for gene expression (Illumina sequencing) demonstrated that genes over-expressed in saliva from erosion participants included H + proton transporter genes, and three protease genes (msrAB, vanY, and ppdC). Salivary metabolomics was assessed using nuclear magnetic resonance spectrometry (NMR). Metabolite concentrations correlated with gene expression, demonstrating that the dental erosion group had strong correlations between metabolites associated with protein degradation and amino acid fermentation. CONCLUSIONS: We conclude that microbial proteolysis of salivary proteins found in the protective acquired enamel pellicle strongly correlates with dental erosion, and we propose four novel microbial genes implicated in this process. Video Abstract.

Ecological shifts of salivary microbiota associated with metabolic-associated fatty liver disease.

Introduction: Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease related to metabolic syndrome. However, ecological shifts in the saliva microbiome in patients with MAFLD remain unknown. This study aimed to investigate the changes to the salivary microbial community in patients with MAFLD and explore the potential function of microbiota. Methods: Salivary microbiomes from ten MAFLD patients and ten healthy participants were analyzed by 16S rRNA amplicon sequencing and bioinformatics analysis. Body composition, plasma enzymes, hormones, and blood lipid profiles were assessed with physical examinations and laboratory tests. Results: The salivary microbiome of MAFLD patients was characterized by increased α-diversity and distinct ß-diversity clustering compared with control subjects. Linear discriminant analysis effect size analysis showed a total of 44 taxa significantly differed between the two groups. Genera Neisseria, Filifactor, and Capnocytophaga were identified as differentially enriched genera for comparison of the two groups. Co-occurrence networks suggested that the salivary microbiota from MAFLD patients exhibited more intricate and robust interrelationships. The diagnostic model based on the salivary microbiome achieved a good diagnostic power with an area under the curve of 0.82(95% CI: 0.61-1). Redundancy analysis and spearman correlation analysis revealed that clinical variables related to insulin resistance and obesity were strongly associated with the microbial community. Metagenomic predictions based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States revealed that pathways related to metabolism were more prevalent in the two groups. Conclusions: Patients with MAFLD manifested ecological shifts in the salivary microbiome, and the saliva microbiome-based diagnostic model provides a promising approach for auxiliary MAFLD diagnosis.

Investigation of putative roles of smoking-associated salivary microbiome alterations on carcinogenesis by integrative in silico analysis.

Growing evidence suggests that cigarette smoking alters the salivary microbiome composition and affects the risk of various complex diseases including cancer. However, the potential role of the smoking-associated microbiome in cancer development remains unexplained. Here, the putative roles of smoking-related microbiome alterations in carcinogenesis were investigated by in silico analysis and suggested evidence can be further explored by experimental methodologies. The Disbiome database was used to extract smoking-associated microbial taxa in saliva and taxon set enrichment analysis (TSEA) was conducted to identify the gene sets associated with extracted microbial taxa. We further analyzed the expression profiles of identified genes by using RNA-sequencing data from TCGA and GTEx projects. Associations of the genes with smoking-related phenotypes in cancer datasets were analyzed to prioritize genes for their interplay between smoking-related microbiome and carcinogenesis. Thirty-eight microbial taxa associated with smoking were included in the TSEA and this revealed sixteen genes that were significantly associated with smoking-associated microbial taxa. All genes were found to be differentially expressed in at least one cancer dataset, yet the ELF3 and CTSH were the most common differentially expressed genes giving significant results for several cancer types. Moreover, C2CD3, CTSH, DSC3, ELF3, RHOT2, and WSB2 showed statistically significant associations with smoking-related phenotypes in cancer datasets. This study provides in silico evidence for the potential roles of the salivary microbiome on carcinogenesis. The results shed light on the importance of smoking cessation strategies for cancer management and interventions to stratify smokers for their risk of smoking-induced carcinogenesis.

Dysbiosis in Head and Neck Cancer: Determining Optimal Sampling Site for Oral Microbiome Collection.

Recent research suggests that dysbiosis of the oral microbial community is associated with head and neck cancer (HNC). It remains unclear whether this dysbiosis causes chemo-radiotherapy (CRT)-related complications. However, to address this question, it is essential to determine the most representative oral site for microbiome sampling. In this study, our purpose was to determine the optimal site for oral sample collection and whether the presence of HNC is associated with altered oral microbiome from this site. In 21 newly diagnosed HNC patients and 27 healthy controls, microbiome samples were collected from saliva, swabs from buccal mucosa, tongue, hard palate, faucial pillars and all mucosal sites combined. Microbial DNA was extracted and underwent 16S rRNA amplicon gene sequencing. In healthy controls, analysis of observed taxonomic units detected differences in alpha- and beta-diversity between sampling sites. Saliva was found to have the highest intra-community microbial diversity and lowest within-subject (temporal) and between-subject variance. Feature intersection showed that most species were shared between all sites, with saliva demonstrating the most unique species as well as highest overlap with other sites. In HNC patients, saliva was found to have the highest diversity but differences between sites were not statistically significant. Across all sites, HNC patients had lower alpha diversity than healthy controls. Beta-diversity analysis showed HNC patients' microbiome to be compositionally distinct from healthy controls. This pattern was confirmed when the salivary microbiome was considered alone. HNC patients exhibited reduced diversity of the oral microbiome. Salivary samples demonstrate temporal stability, have the richest diversity and are sufficient to detect perturbation due to presence of HNC. Hence, they can be used as representative oral samples for microbiome studies in HNC patients.

Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota.

Axial spondyloarthritis (axSpA) is an inflammatory arthritis involving the spine and the sacroiliac joint with extra-articular manifestations in the eye, gut, and skin. The intestinal microbiota has been implicated as a central environmental component in the pathogenesis of various types of spondyloarthritis including axSpA. Additionally, alterations in the oral microbiota have been shown in various rheumatological conditions, such as rheumatoid arthritis (RA). Therefore, the aim of this study was to investigate whether axSpA patients have an altered immunoglobulin A (IgA) response in the gut and oral microbial communities. We performed 16S rRNA gene (16S) sequencing on IgA positive (IgA+) and IgA negative (IgA-) fractions (IgA-SEQ) from feces (n=17 axSpA; n=14 healthy) and saliva (n=14 axSpA; n=12 healthy), as well as on IgA-unsorted fecal and salivary samples. PICRUSt2 was used to predict microbial metabolic potential in axSpA patients and healthy controls (HCs). IgA-SEQ analyses revealed enrichment of several microbes in the fecal (Akkermansia, Ruminococcaceae, Lachnospira) and salivary (Prevotellaceae, Actinobacillus) microbiome in axSpA patients as compared with HCs. Fecal microbiome from axSpA patients showed a tendency towards increased alpha diversity in IgA+ fraction and decreased diversity in IgA- fraction in comparison with HCs, while the salivary microbiome exhibits a significant decrease in alpha diversity in both IgA+ and IgA- fractions. Increased IgA coating of Clostridiales Family XIII in feces correlated with disease severity. Inferred metagenomic analysis suggests perturbation of metabolites and metabolic pathways for inflammation (oxidative stress, amino acid degradation) and metabolism (propanoate and butanoate) in axSpA patients. Analyses of fecal and salivary microbes from axSpA patients reveal distinct populations of immunoreactive microbes compared to HCs using the IgA-SEQ approach. These bacteria were not identified by comparing their relative abundance alone. Predictive metagenomic analysis revealed perturbation of metabolites/metabolic pathways in axSpA patients. Future studies on these immunoreactive microbes may lead to better understanding of the functional role of IgA in maintaining microbial structure and human health.

Integrated analysis of the salivary microbiome and metabolome in chronic and aggressive periodontitis: A pilot study.

This pilot study was designed to identify the salivary microbial community and metabolic characteristics in patients with generalized periodontitis. A total of 36 saliva samples were collected from 13 patients with aggressive periodontitis (AgP), 13 patients with chronic periodontitis (ChP), and 10 subjects with periodontal health (PH). The microbiome was evaluated using 16S rRNA gene high-throughput sequencing, and the metabolome was accessed using gas chromatography-mass spectrometry. The correlation between microbiomes and metabolomics was analyzed by Spearman's correlation method. Our results revealed that the salivary microbial community and metabolite composition differed significantly between patients with periodontitis and healthy controls. Striking differences were found in the composition of salivary metabolites between AgP and ChP. The genera Treponema, Peptococcus, Catonella, Desulfobulbus, Peptostreptococcaceae_[XI] ([G-2], [G-3] [G-4], [G-6], and [G-9]), Bacteroidetes_[G-5], TM7_[G-5], Dialister, Eikenella, Fretibacterium, and Filifactor were present in higher levels in patients with periodontitis than in the healthy participants. The biochemical pathways that were significantly different between ChP and AgP included pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; beta-alanine metabolism; citrate cycle; and arginine and proline metabolism. The differential metabolites between ChP and AgP groups, such as urea, beta-alanine, 3-aminoisobutyric acid, and thymine, showed the most significant correlations with the genera. These differential microorganisms and metabolites may be used as potential biomarkers to monitor the occurrence and development of periodontitis through the utilization of non-invasive and convenient saliva samples. This study reveals the integration of salivary microbial data and metabolomic data, which provides a foundation to further explore the potential mechanism of periodontitis.

The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease.

Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders that fall into two main categories: Crohn's disease (CD) and ulcerative colitis (UC). The gastrointestinal tract extends from the mouth to the anus and harbors diverse bacterial communities. Several sequencing-based studies have identified an intestinal enrichment of oral-associated bacteria and demonstrated their ability to induce intestinal inflammation in mice, suggesting that intestinal pathobionts originate from the oral cavity, particularly members of the genus Streptococcus. This study aimed to investigate the composition of the salivary and fecal microbiome of IBD patients (n = 14) compared to healthy controls (n = 12) and to determine the abundance of common bacterial taxa in both niches. Metagenomic DNA was extracted from saliva and fecal samples, and the 16S rRNA gene was targeted for sequencing. Our results revealed that the overall microbial composition of saliva was significantly altered in the IBD patients compared to the control subjects (p = 0.038). At the genus level, Veillonella and Prevotella were highly abundant in IBD (median: 25.4% and 22.2%, respectively) compared to the control group (17.9% and 13.4%, respectively). In contrast, Neisseria, Streptococcus, Haemophilus, and Fusobacterium were associated with a healthy gut state. Regarding the fecal microbiome, the IBD group had a significantly higher abundance of Clostridium sensu stricto 1 and Escherichia-Shigella (both comprising pathogenic bacteria) compared with the control group. Members of both bacterial groups have previously been shown to positively correlate with intestinal inflammation and high expression of pro-inflammatory cytokines that disrupt intestinal barrier integrity. In addition, we demonstrate that the increased abundance of Clostridium sensu stricto 1 and Escherichia-Shigella has also been associated with significant upregulation of certain metabolic pathways in the feces of the IBD group, including bacterial invasion of epithelial cells. Streptococcus was the only common genus detected in both the salivary and fecal microbiome and represented the oral-gut axis in our study. Using culture-based methods, we isolated 57 and 91 Streptococcus strains from saliva as well as 40 and 31 strains from fecal samples of the controls and IBD patients, respectively. The phylogenetic tree of streptococci based on sodA sequences revealed several patient-specific clusters comprising salivary and fecal streptococcal isolates from the same patient and belonging to the same species, suggesting that the oral cavity is an endogenous reservoir for intestinal strains.

Salivary microbiome in chronic kidney disease: what is its connection to diabetes, hypertension, and immunity?

BACKGROUND: The association between oral dysbiosis and chronic kidney disease (CKD) has gained increasing attention in recent years. Diabetes and hypertension are the most common conditions in CKD. However, a case-control study with matched confounding variables on the salivary microbiome in CKD and the influence of diabetes and hypertension on the microbiome has never been reported. METHODS: In our study, we compared the salivary microbiome profile between patients with CKD and healthy controls (HC) using 16S ribosomal DNA sequencing and examine its association with diabetes, hypertension, and immunity. RESULTS: We observed that the bacterial community was skewed in the saliva of CKD, with increased Lautropia and Pseudomonas, and decreased Actinomyces, Prevotella, Prevotella 7, and Trichococcus. No difference in the bacterial community between the CKD patients complicated with and without diabetes, and between those with and without hypertension. Prevotella 7 declined in CKD patients with/without hypertension with respect to HC, while Pseudomonas increased in CKD patients with/without hypertension. Pseudomonas was negatively associated with immunoglobin G in CKD patients. Both CKD patients with positive and negative antistreptolysin O had declined Prevotella 7 and Trichococcus compared to HC, whereas increased Pseudomonas. CONCLUSIONS: Our study identifies a distinct bacterial saliva microbiome in CKD patients characterized by alteration in composition. We unravel here that the co-occurrence diseases of diabetes and hypertension are not associated with specific bacterial alterations, suggesting that bacterial dysbiosis in saliva plays a role in renal damage regardless of the occurrence of diabetes and hypertension.

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference.

Saliva is a common body fluid with significant forensic value used to investigate criminal cases such as murder and assault. In the past, saliva identification often relied on the α-amylase test; however, this method has low specificity and is prone to false positives. Accordingly, forensic researchers have been working to find new specific molecular markers to refine the current saliva identification approach. At present, research on immunological methods, mRNA, microRNA, circRNA, and DNA methylation is still in the exploratory stage, and the application of these markers still has various limitations. It has been established that salivary microorganisms exhibit good specificity and stability. In this study, 16S rDNA sequencing technology was used to sequence the V3-V4 hypervariable regions in saliva samples from five regions to reveal the role of regional location on the heterogeneity in microbial profile information in saliva. Although the relative abundance of salivary flora was affected to a certain extent by geographical factors, the salivary flora of each sample was still dominated by Streptococcus, Neisseria, and Rothia. In addition, the microbial community in the saliva samples in this study was significantly different from that in the vaginal secretions, semen, and skin samples reported in our previous studies. Accordingly, saliva can be distinguished from the other three body fluids and tissues. Moreover, we established a prediction model based on the random forest algorithm that could distinguish saliva between different regions at the genus level even though the model has a certain probability of misjudgment which needs more in-depth research. Overall, the microbial community information in saliva stains might have prospects for potential application in body fluid identification and biogeographic inference.

Salivary bacterial community profile in normal-weight and obese adolescent patients prior to orthodontic treatment with fixed appliances.

OBJECTIVES: The aim of this study was to compare the intra-oral bacterial profile of normal-weight and obese adolescents prior to orthodontic treatment with fixed appliances. MATERIALS AND METHODS: Nineteen adolescent patients were recruited into two groups based upon body mass index (BMI) and classified as normal-weight or obese. Unstimulated whole mouth saliva was obtained for 5 minutes. Bacterial DNA extraction was performed from saliva, and 16S rRNA gene sequencing of the V1-2 variable regions was undertaken followed by analysis using the mothur pipeline. RESULTS: Saliva from a total of 19 adolescent patients with mean (SD) age 15.6 (1.8) years were divided into 10 normal-weight with mean BMI of 19.4 (2.2) kg/m2 and 9 obese with mean BMI of 30.2 (3.5) kg/m2 . A total of 156 783 sequences were obtained from the 19 samples with no significant differences in richness or diversity between sample groups by obesity status or gender (AMOVA). The bacterial community in both groups was dominated by bacterial genera characteristic of the human mouth, which included Streptococcus, Porphyromonas, Veillonella, Gemella, Prevotella, Fusobacterium and Rothia. CONCLUSION: There were no differences in alpha or beta diversity of oral bacterial communities between normal-weight and obese orthodontic patients. Obese adolescents attending for orthodontic treatment had a similar microflora to their normal-weight counterparts.

Rifaximin-α reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial.

BACKGROUND & AIMS: Rifaximin-α is efficacious for the prevention of recurrent hepatic encephalopathy (HE), but its mechanism of action remains unclear. We postulated that rifaximin-α reduces gut microbiota-derived endotoxemia and systemic inflammation, a known driver of HE. METHODS: In a placebo-controlled, double-blind, mechanistic study, 38 patients with cirrhosis and HE were randomised 1:1 to receive either rifaximin-α (550 mg BID) or placebo for 90 days. PRIMARY OUTCOME: 50% reduction in neutrophil oxidative burst (OB) at 30 days. SECONDARY OUTCOMES: changes in psychometric hepatic encephalopathy score (PHES) and neurocognitive functioning, shotgun metagenomic sequencing of saliva and faeces, plasma and faecal metabolic profiling, whole blood bacterial DNA quantification, neutrophil toll-like receptor (TLR)-2/4/9 expression and plasma/faecal cytokine analysis. RESULTS: Patients were well-matched: median MELD (11 rifaximin-α vs. 10 placebo). Rifaximin-α did not lead to a 50% reduction in spontaneous neutrophil OB at 30 days compared to baseline (p = 0.48). However, HE grade normalised (p = 0.014) and PHES improved (p = 0.009) after 30 days on rifaximin-α. Rifaximin-α reduced circulating neutrophil TLR-4 expression on day 30 (p = 0.021) and plasma tumour necrosis factor-α (TNF-α) (p <0.001). Rifaximin-α suppressed oralisation of the gut, reducing levels of mucin-degrading sialidase-rich species, Streptococcus spp, Veillonella atypica and parvula, Akkermansia and Hungatella. Rifaximin-α promoted a TNF-α- and interleukin-17E-enriched intestinal microenvironment, augmenting antibacterial responses to invading pathobionts and promoting gut barrier repair. Those on rifaximin-α were less likely to develop infection (odds ratio 0.21; 95% CI 0.05-0.96). CONCLUSION: Rifaximin-α led to resolution of overt and covert HE, reduced the likelihood of infection, reduced oralisation of the gut and attenuated systemic inflammation. Rifaximin-α plays a role in gut barrier repair, which could be the mechanism by which it ameliorates bacterial translocation and systemic endotoxemia in cirrhosis. CLINICAL TRIAL NUMBER: ClinicalTrials.gov NCT02019784. LAY SUMMARY: In this clinical trial, we examined the underlying mechanism of action of an antibiotic called rifaximin-α which has been shown to be an effective treatment for a complication of chronic liver disease which effects the brain (termed encephalopathy). We show that rifaximin-α suppresses gut bacteria that translocate from the mouth to the intestine and cause the intestinal wall to become leaky by breaking down the protective mucus barrier. This suppression resolves encephalopathy and reduces inflammation in the blood, preventing the development of infection.

A probabilistic approach to evaluate salivary microbiome in forensic science when the Defense says: `It is my twin brother'.

Salivary microbiota profiles may represent a valid contribution to forensic investigation when standard DNA genotyping methods fail. Starting from questioned and control materials in the form of saliva, the evidence can be expressed by means of a distance between those materials taking into account specific aspects of the microbiota composition. The value of the evidence for forensic discrimination purposes is quantified by means of a Bayes' factor, that allows one to overcome the major limitations and pitfalls of intuition connected to the use of cut-off values as a mean of decision.

Dysbiosis of the Salivary Microbiome is Associated with Hypertension and Correlated with Metabolic Syndrome Biomarkers.

BACKGROUND: Hypertension (HT) is an idiopathic disease with severe complications and a high incidence of global mortality. Although the disease shares characteristic features with diabetes and obesity, the complex interplay of endogenous and environmental factors is not well characterized. The oral microbiome has recently been studied to better understand the role of commensal microorganisms in metabolic disorders, including HT, although its role in disease etiology is unclear. METHODS: To bridge this gap, we compared the oral microbiome and clinical chemistry of adult subjects enrolled at Qatar Biobank. Clinical chemistry was performed using Roche Cobas-6000 analyzer. Saliva samples were subjected to 16S rRNA sequencing using Illumina MiSeq platform. Cross-gender comparisons were made between control (males/females) (C-M and C-F) and HT (HT-M and HT-F) groups. RESULTS: The HT groups had higher (p ≤ 0.05) BMI, plasma glucose, insulin, C-peptide, and alkaline phosphatase (ALP) concentrations. Triglycerides, cholesterol, LDL-cholesterol, and sodium ions were similar among the groups. The microbiome was predominantly occupied by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Firmicutes were higher (p ≤ 0.05) in the HT groups, whereas Proteobacteria was only higher in the C-F group. Prevotella and Veillonella were significantly higher in the HT groups and exhibited a positive correlation with blood pressure and hyperglycemia. In contrast to other studies, the mathematical summation of priori-select microbes reveals that nitrate-reducing microbes were higher in the HT groups compared with the controls. CONCLUSION: In conclusion, these observations suggest a strong association of HT with microbial dysbiosis, where microbial species other than nitrate-reducing microbes contribute to blood pressure regulation. The findings affirm plausible microbial signatures of hypertension and suggest manipulating these microbes as a novel treatment modality. Future experiments are warranted for the mechanistic investigation of hypertension metagenomics and microbial activity.