Characterization of the salivary microbiome in people with obesity

Autophagy, a double-edged sword for oral tissue regeneration

BACKGROUND

Oral health is of fundamental importance to maintain systemic health in humans. Stem cell-based oral tissue regeneration is a promising strategy to achieve the recovery of impaired oral tissue. As a highly conserved process of lysosomal degradation, autophagy induction regulates stem cell function physiologically and pathologically. Autophagy activation can serve as a cytoprotective mechanism in stressful environments, while insufficient or over-activation may also lead to cell function dysregulation and cell death.

AIM OF REVIEW

This review focuses on the effects of autophagy on stem cell function and oral tissue regeneration, with particular emphasis on diverse roles of autophagy in different oral tissues, including periodontal tissue, bone tissue, dentin pulp tissue, oral mucosa, salivary gland, maxillofacial muscle, temporomandibular joint, etc. Additionally, this review introduces the molecular mechanisms involved in autophagy during the regeneration of different parts of oral tissue, and how autophagy can be regulated by small molecule drugs, biomaterials, exosomes/RNAs or other specific treatments. Finally, this review discusses new perspectives for autophagy manipulation and oral tissue regeneration.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Overall, this review emphasizes the contribution of autophagy to oral tissue regeneration and highlights the possible approaches for regulating autophagy to promote the regeneration of human oral tissue.

Analysis of the saliva microbiome in patients with immunoglobulin G4-related disease

OBJECTIVES

This article aims to investigate the saliva microbiome in patients with immunoglobulin G4-related disease (IgG4RD) compared with primary Sjögren's syndrome (SS).

METHODS

Saliva samples were collected from 11 IgG4RD and 11 SS patients who visited IMSUT Hospital, The Institute of Medical Science, The University of Tokyo. Deoxyribonucleic acid (DNA) was extracted from the samples, and primers were used to amplify the V3-V4 regions of bacterial and archaeal 16S ribosomal RNA (rRNA) genes, which was then analysed by paired-end sequencing. Amplicon reads were processed using QIIME2 to generate representative sequences. The Greengenes database was used to identify the bacterial flora in each sample and compare them between groups.

RESULTS

The IgG4RD and SS groups exhibited differences in bacterial diversity. Cluster analyses of attributed classification groups by species and disease showed that IgG4RD and SS cases formed individual clusters. Significant differences in relative abundance between IgG4RD and SS were observed for the following organisms: Mogibacterium (P = .0051), Solobacterium moorei (P = .0195), Slackia (P = .0356), and Moryella (P = .0455).

CONCLUSIONS

Salivary microbiome analysis of IgG4RD and SS patients revealed significantly higher relative proportions of Mogibacterium, S. moorei, Slackia, and Moryella bacteria in IgG4RD compared with SS.

Characteristics of Abdominal Visceral Adipose Tissue, Metabolic Health and the Gut Microbiome in Adults

CONTEXT

Compared with the relatively benign effects of increased subcutaneous adipose tissue (SAT), increased visceral adipose tissue (VAT) volume is a causal risk factor for hypertension, hyperlipidemia, type 2 diabetes, and cardiovascular disease. In rodents, increased VAT volume and triglyceride density and ectopic lipid accumulation in kidneys and liver have been induced by alterations in the gut microbiome. However, few studies have characterized these relationships in humans.

OBJECTIVE

To evaluate the tissue triglyceride content of VAT and SAT, liver, kidneys, and pancreas in male and female adults and assess associations with markers of glucose tolerance, serum insulin, and lipids and characteristics of the gut microbiome.

METHODS

Cross-sectional observational study of healthy human adults (n = 60) at a clinical research center. Body mass index (BMI), body composition, and oral glucose tolerance were assessed. Microbiome analysis was conducted on stool samples using 16S rRNA v3 amplicon sequencing. The triglyceride content of VAT, SAT, liver, kidney and pancreas were determined by assessing proton density fat fraction (PDFF) with magnetic resonance imaging (MRI).

RESULTS

Higher VAT PDFF and the ratio of VAT to SAT PDFF were related to higher BMI, HbA1c, HOMA-IR, non-high-density lipoprotein cholesterol, plasma triglycerides, low-density lipoprotein (LDL) cholesterol, and lower high-density lipoprotein (HDL) cholesterol. A higher VAT PDFF and VAT to SAT PDFF ratio were associated with lower alpha diversity and altered beta diversity of the gut microbiome. Differences in VAT were associated with higher relative abundance of the phylum Firmicutes, lower relative abundance of the phylum Bacteroidetes, and enrichment of the bacterial genera Dorea, Streptococcus, and Solobacterium.

CONCLUSION

VAT PDFF measured with MRI is related to impaired glucose homeostasis, dyslipidemia, and differences in the gut microbiome, independently of the total body fat percentage.

Dynamic changes in the gut microbiota during three consecutive trimesters of pregnancy and their correlation with abnormal glucose and lipid metabolism

INTRODUCTION

During normal pregnancy, changes in the gut microbiota (GM) in response to physiological alterations in hormonal secretion, immune functions and homeostasis have received extensive attention. However, the dynamic changes in the GM during three consecutive trimesters of pregnancy and their relationship with glucose and lipid metabolism have not been reported. In this study, we aimed to investigate the dynamic changes in the diversity and species of the GM during three consecutive trimesters in women who naturally conceived, and their relationships with abnormal fasting blood glucose (FBG) and serum lipid levels.

METHODS

A total of 30 pregnant women without any known chronic or autoimmune inflammatory disease history before pregnancy were enrolled during the first trimester. Serum and stool samples were collected during the first trimester, the second trimester, and the third trimester. Serum samples were tested for FBG and blood lipid levels, and stool specimens were analyzed by 16S rDNA sequencing.

RESULTS

The abundance ratio of bacteroidetes/firmicutes showed an increasing tendency in most of the subjects (19/30, 63.3%) from the first to the third trimester. LEfSe analysis showed that the abundance of Bilophila was significantly increased from the first to the third trimester. In addition, at the genus level, the increased relative abundance of Mitsuokella, Clostridium sensu stricto and Weissella were potentially involved in the development of high FBG during pregnancy. The raised relative abundance of Corynebacterium, Rothia and Granulicatella potentially contributed to the occurrence of dyslipidemia during pregnancy.

CONCLUSIONS

There are dynamic changes in the GM during the three trimesters, and the alterations in some bacterium abundance may contribute to the development of high FBG and dyslipidemia during pregnancy. Monitoring enterotypes and correcting dysbiosis in the first trimester may become new strategies for predicting and preventing glucolipid metabolism disorders during pregnancy.

Preliminary exploratory research on the application value of oral and intestinal meta-genomics in predicting subjects' occupations-A case study of the distinction between students and migrant workers

Background

In the field of forensic science, accurately determining occupation of an individual can greatly assist in resolving cases such as criminal investigations or disaster victim identifications. However, estimating occupation can be challenging due to the intricate relationship between occupation and various factors, including gender, age, living environment, health status, medication use, and lifestyle habits such as alcohol consumption and smoking. All of these factors can impact the composition of oral or gut microbial community of an individual.

Methods and results

In this study, we collected saliva and feces samples from individuals representing different occupational sectors, specifically students and manual laborers. We then performed metagenomic sequencing on the DNA extracted from these samples to obtain data that could be analyzed for taxonomic and functional annotations in five different databases. The correlation between occupation with microbial information was assisted from the perspective of α and β diversity, showing that individuals belonging to the two occupations hold significantly different oral and gut microbial communities, and that this correlation is basically not affected by gender, drinking, and smoking in our datasets. Finally, random forest (RF) models were built with recursive feature elimination (RFE) processes. Models with 100% accuracy in both training and testing sets were constructed based on three species in saliva samples or on a single pathway annotated by the KEGG database in fecal samples, namely, "ko04145" or Phagosome.

Conclusion

Although this study may have limited representativeness due to its small sample size, it provides preliminary evidence of the potential of using microbiome information for occupational inference.

Can medication-related osteonecrosis of the jaw be attributed to specific microorganisms through oral microbiota analyses? A preliminary study

BACKGROUND

Medication-related osteonecrosis of the jaw (MRONJ) can cause significant pain and loss of aesthetics and function if not treated properly. However, diagnosis still relies on detailed intraoral examinations and imaging. Prognosis varies even among patients with similar stages or conditions of MRONJ, emphasizing the need for a deeper understanding of its complex mechanisms. Thus, this study aimed to identify the oral microbiota of patients with MRONJ.

METHODS

This single-center prospective cohort study included patients with confirmed MRONJ who visited the Department of Oral and Maxillofacial Surgery at Yonsei University Dental Hospital between 2021 and 2022. Oral swab samples were collected from the affected and unaffected sides of each patient. The composition and enumeration of the microbial communities were analyzed, and the diversity was compared to verify ecological changes in the groups using a next-generation sequencing-based 16S metagenomic analysis. A statistical analysis was performed using Wilcoxon signed-rank test with SPSS version 22, and values of P less than 0.05 were considered statistically significant.

RESULTS

The final study sample included 12 patients. The mean age was 82.67 ± 5.73 (range, 72-90) years. Changes in microbial composition were observed at different taxonomic levels (phylum, genus, and species). The identified microorganisms were commonly associated with periodontitis, gingival disease, and endodontic infection, suggesting a multifactorial etiology of MRONJ.

CONCLUSIONS

Although this study is based on a small number of cases, it shows that MRONJ is not caused by a specific microorganism but can rather be caused by a variety of factors. By addressing these findings in large-scale studies, the significance of oral microbiome in pathogenesis can be further elucidated and can facilitate the development of effective therapeutic interventions for patients with MRONJ.

Analysis of the influence of host lifestyle (coffee consumption, drinking, and smoking) on Korean oral microbiome

If a DNA sample collected in the field is old or degraded, short tandem repeat analysis is difficult to perform, a representative analysis method currently used for individual identification. Given that microorganisms exist everywhere and within the human body, in similar amounts to human cells, microbial analysis could be used to identify individuals even in cases in which human DNA-based identification is difficult. Research has demonstrated that the types of microorganisms within the human body differ depending on various internal or external factors, such as body part or bodily fluid type, lifestyle, geographical area of residence, sex, and age. In this study, we aimed to examine the relationship between lifestyle factors and the composition and diversity of the oral microbiome in individuals living in Korea. We collected 43 saliva samples from Korean individuals and analyzed the oral microbiome and its variations due to external factors, such as coffee consumption, drinking, and smoking. Linear discriminant analysis effect size revealed that Oribacterium, Campylobacter, and Megasphaera were abundant in coffee consumers, whereas Saccharimonadales, Clostridia, and Catonella were abundant in alcohol non-drinkers. We found increased levels of Stomatobaculum in the saliva of smokers, compared with that of non-smokers. Thus, our analysis revealed characteristic microorganisms for each parameter that was evaluated (coffee consumption, smoking, drinking). Consequently, our study provides insight into the oral microbiome in the Korean population and lays the foundation for developing the Korean Forensic Microbiome Database.

A New Landscape of Human Dental Aging: Causes, Consequences, and Intervention Avenues

Aging is accompanied by physical dysfunction and physiologic degeneration that occurs over an individual's lifetime. Human teeth, like many other organs, inevitably undergo chronological aging and age-related changes throughout the lifespan, resulting in a substantial need for preventive, restorative as well as periodontal dental care. This is particularly the case for seniors at 65 years of age and those older but economically disadvantaged. Dental aging not only interferes with normal chewing and digestion, but also affects daily appearance and interpersonal communications. Further dental aging can incur the case of multiple disorders such as oral cancer, encephalitis, and other systemic diseases. In the next decades or even hundreds of years, the proportion of the elderly in the global population will continue to rise, a tendency that attracts increasing attention across multiple scientific and medical disciplines. Dental aging will bring a variety of problems to the elderly themselves and poses serious challenges to the medical profession and social system. A reduced, but functional dentition comprising 20 teeth in occlusion has been proposed as a measurement index of successful dental aging. Healthy dental aging is critical to healthy aging, from both medical and social perspectives. To date, biomedical research on the causes, processes and regulatory mechanisms of dental aging is still in its infancy. In this article, updated insights into typical manifestations, associated pathologies, preventive strategies and molecular changes of dental aging are provided, with future research directions largely projected.

The association of tonsillar microbiota with biochemical indices based on obesity and tonsillar hypertrophy in children

The correlation between tonsil microbiome and tonsillar hypertrophy has not been well established. Given that oral dysbiosis is related to several metabolic diseases and that tonsillar hypertrophy leads to disordered breathing during sleep and obesity in children, it is necessary to investigate the relationship between the oral microbiome and tonsillar hypertrophy. After 16S rRNA amplicon sequencing of tonsillectomy samples, we evaluated the correlation between the tonsil microbiome and biochemical blood indices in pediatric patients who underwent tonsillectomy. Groups are classified into two categories: based on BMI, and grades 2, 3, and 4 based on tonsil size. Children with obesity and tonsillar hypertrophy have similar microbiome compositions and induce comparable changes in microbiome abundance and composition, confirming the association from a metagenomic perspective. In addition, obesity and tonsillar hypertrophy demonstrated a strong correlation with the Proteobacteria to Firmicutes (P/F) ratio, and among various biochemical indicators, alanine aminotransferase (ALT) levels increase with obesity and tonsillar hypertrophy, indicating a possible association of tonsil microbiome and liver metabolism. These novel findings demonstrate the significance of the tonsil microbiome and suggest the need for tonsil regulation, particularly during childhood.

The Effect of Probiotic Supplements on Metabolic Parameters of People with Type 2 Diabetes in Greece-A Randomized, Double-Blind, Placebo-Controlled Study

The role of probiotic supplementation in type 2 diabetes (T2D) treatment is controversial. The present study aimed to assess the effects of a multi-strain probiotic supplement (LactoLevureR (containing Lactobacillus acidophilus, Lactobacillus plantarum, Bifidobacterium lactis, and Saccharomyces boulardii)) over 6 months, primarily on glycemic control as well as on lipid levels and alterations in the gut microbiome, among individuals with T2D residing in Greece. A total of 91 adults with T2D (mean age [±SD] 65.12 ± 10.92 years, 62.6% males) were randomized to receive the probiotic supplement or a matching placebo capsule, once daily, for 6 months. Blood chemistries and anthropometric parameters were conducted every 3 months, and stool samples were collected at baseline and at 6 months. Significant reductions in HbA1c, fasting blood glucose, and total cholesterol were observed in participants treated with the probiotic supplement (n = 46) compared to the controls (n = 45), even after adjustment for a greater decrease in adiposity (waist circumference). Although there were no statistically significant differences in the diversity of the gut microbiome (α and β diversity), the administration of probiotics did influence several genera, metabolites, and key enzymes associated with diabetes. Overall, the administration of the multi-strain probiotic LactoLevureR over a 6-month period in individuals with T2D was well-tolerated and had a positive impact on metabolic parameters, alongside improvements in indices of adiposity.

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.

Salivary microbiome and hypertension in the Qatari population

BACKGROUND

The prevalence of hypertension in Qatar is 33 percent of the adult population. It is postulated that the salivary microbiome can regulate blood pressure (BP). However, limited investigations exist to prove this hypothesis. Therefore, we examined the difference in the salivary microbiome composition between hypertensive and normotensive Qatari subjects.

METHODS

A total of 1190 Qatar Genome Project (QGP) participants (Mean age = 43 years) were included in this study. BP for all participants was classified into Normal (n = 357), Stage1 (n = 336), and Stage2: (n = 161) according to the American Heart Association guidelines. 16S-rRNA libraries were sequenced and analyzed using QIIME-pipeline, and PICRUST was used to predict functional metabolic routes. Machine Learning (ML) strategies were applied to identify salivary microbiome-based predictors of hypertension.

RESULTS

Differential abundant analysis (DAA) revealed that Bacteroides and Atopobium were the significant members of the hypertensive groups. Alpha and beta diversity indices indicated dysbiosis between the normotensive and hypertensive groups. ML-based prediction models revealed that these markers could predict hypertension with an AUC (Area under the curve) of 0.89. Functional predictive analysis disclosed that Cysteine and Methionine metabolism and the sulphur metabolic pathways involving the renin-angiotensin system were significantly higher in the normotensive group. Therefore, members of Bacteroides and Atopobium can serve as predictors of hypertension. Likewise, Prevotella, Neisseria, and Haemophilus can be the protectors that regulate BP via nitric acid synthesis and regulation of the renin-angiotensin system.

CONCLUSION

It is one of the first studies to assess salivary microbiome and hypertension as disease models in a large cohort of the Qatari population. Further research is needed to confirm these findings and validate the mechanisms involved.

Relationship between body mass index and oral health indicators: a cross-sectional study

Today's prevalence of obesity is dramatically increasing and a two-way interaction between higher body mass index (BMI) and oral health is described in scientific litterature. Accordingly, the present study was aimed to evaluate the relation of BMI and oral health indicators. In this cross-sectional study, 240 individuals according to their BMI were placed in the following experimental groups; underweight (BMI<18), normal weight (18≤BMI≤24.9), overweight (25≤BMI≤29.9) and obese (30≤BMI). Plaque index (PI), gingival index (GI), bleeding on probing (BOP) and decayed, missed and filled teeth (DMFT) were obtained. Data was analyzed by SPSS 26 using descriptive tests and one-way ANOVA at the level of 0.05. The mean age and sex distribution of participants of experimental groups had no significant difference (p>0.05). GI and BOP were significantly lower in normal weight persons than individuals with high BMI (p<0.05). DMFT, the number of decayed, missed and filled teeth was approximately similar in all experimental groups (p>0.05). Pearson correlation coefficient showed a positive significant relation between GI as well as BOP with BMI (p=0.000). Based on the results achieved by the present study, although periodontal health status of overweight and obese individuals was significantly compromised compared to normal weight persons, the dental health status was not affected by BMI.

Characterization of the oral and gut microbiome in children with obesity aged 3 to 5 years

The ever-increasing global prevalence of obesity has trended towards a younger age. The ecological characteristics and changes of the oral and gut microbial community during childhood are poorly understood.In this study, we analyzed the salivary and fecal microbiota of 30 children with obesity and 30 normal weight children aged 3-5 years via third-generation long-range DNA sequencing,with the aim of understanding the structure of childhood microbiota and identifying specific oral and gut microbial lineages and genera in children that may be associated with obesity.The results revealed significant variation in alpha diversity indices among the four groups (Chao1: P &lt; 0.001; observed species: P &lt; 0.001; Shannon &lt; 0.001). Principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS) revealed significant differences in oral and gut microbial community structure between obesity and controls. The Firmicutes/Bacteroidetes (F/B) abundance ratios of oral and intestinal flora among children with obesity were higher than those of controls. The most abundant phyla and genera found in oral and intestinal flora were Firmicutes, Proteobacteria, Bacteroidetes, Neisseria, Bacteroides, Faecalibacterium, Streptococcus, Prevotella and so on. Linear discriminant analysis effect size (LEfSe) revealed higher proportions of Filifactor (LDA= 3.98; P &lt; 0.05) and Butyrivibrio (LDA = 2.54; P &lt; 0.001) in the oral microbiota of children with obesity, while the fecal microbiota of children with obesity were more enriched with Faecalibacterium (LDA = 5.02; P &lt; 0.001), Tyzzerella (LDA=3.25; P &lt; 0.01), Klebsiella (LDA = 4.31; P &lt; 0.05),which could be considered as dominant bacterial biomarkers for obesity groups.A total of 148 functional bacterial pathways were found to significantly differ in the oral and gut microbiota among controls and obesity using PICRUSt 2. Most predicted functional pathways were clustered in biosynthesis. In conclusion, This work suggests there were significant differences in oral and gut microbiota in controls and obesity groups, microbiota dysbiosis in childhood might have significant effect on the development of obesity.

The Role of the Oral Microbiome in the Development of Diseases

Periodontal disease (PD) is a complex and infectious illness that begins with a disruption of bacterial homeostasis. This disease induces a host inflammatory response, leading to damage of the soft and connective tooth-supporting tissues. Moreover, in advanced cases, it can contribute to tooth loss. The aetiological factors of PDs have been widely researched, but the pathogenesis of PD has still not been totally clarified. There are a number of factors that have an effect on the aetiology and pathogenesis of PD. It is purported that microbiological, genetic susceptibility and lifestyle can determine the development and severity of the disease. The human body’s defence response to the accumulation of plaque and its enzymes is known to be a major factor for PD. The oral cavity is colonised by a characteristic and complex microbiota that grows as diverse biofilms on all mucosal and dental surfaces. The aim of this review was to provide the latest updates in the literature regarding still-existing problems with PD and to highlight the role of the oral microbiome in periodontal health and disease. Better awareness and knowledge of the causes of dysbiosis, environmental risk factors and periodontal therapy can reduce the growing worldwide prevalence of PDs. The promotion of good oral hygiene, limiting smoking, alcohol consumption and exposure to stress and comprehensive treatment to decrease the pathogenicity of oral biofilm can help reduce PD as well as other diseases. Evidence linking disorders of the oral microbiome to various systemic diseases has increased the understanding of the importance of the oral microbiome in regulating many processes in the human body and, thus, its impact on the development of many diseases.

Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus

Several previous studies have shown that oral microbial disorders may be closely related to the occurrence and development of type 2 diabetes mellitus (T2DM). However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We performed metagenomic analyses and nontargeted metabolic analysis of saliva and supragingival plaque samples from patients with T2DM who have not suffered any oral diseases and normal controls. We found that periodontal pathogens such as Porphyromonas gingivalis and Prevotella melaninogenica were significantly enriched, while the abundances of dental caries pathogens such as Streptococcus mutans and Streptococcus sobrinus were not significantly different in patients with T2DM compared to those in normal controls. Metabolomic analyses showed that the salivary levels of cadaverine and L-(+)-leucine of patients with T2DM were significantly higher than those of normal controls, while the supragingival plaque levels of N-acetyldopamine and 3,4-dimethylbenzoic acid in patients with T2DM were significantly higher than those in the normal controls. Additionally, we identified the types of oral microorganisms related to the changes in the levels of circulating metabolites, and the oral microorganisms were involved in the dysregulation of harmful metabolites such as cadaverine and n, n-dimethylarginine. Overall, our study first described the changes in the composition of oral microorganisms and their metabolites in patients with T2DM who have not suffered any oral diseases, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in T2DM. IMPORTANCE The incidence of oral diseases in type 2 diabetic patients might increase, and the severity might also be more serious. At present, the relationship between oral microorganisms and type 2 diabetes mellitus (T2DM) has become a hot topic in systemic health research. However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We found that even if the oral condition of T2DM is healthy, their oral microbes and metabolites have changed, thus increasing the risk of periodontal disease. Our study first described the changes in the composition of oral microorganisms and their metabolites in T2DM who have not suffered any oral diseases and revealed the correlation between oral microorganisms and their metabolites, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in patients with T2DM.

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

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

Influential factors of saliva microbiota composition

The oral microbiota is emerging as an influential factor of host physiology and disease state. Factors influencing oral microbiota composition have not been well characterised. In particular, there is a lack of population-based studies. We undertook a large hypothesis-free study of the saliva microbiota, considering potential influential factors of host health (frailty; diet; periodontal disease), demographics (age; sex; BMI) and sample processing (storage time), in a sample (n = 679) of the TwinsUK cohort of adult twins. Alpha and beta diversity of the saliva microbiota was associated most strongly with frailty (alpha diversity: β = -0.16, Q = 0.003, Observed; β = -0.16, Q = 0.002, Shannon; β = -0.16, Q = 0.003, Simpson; Beta diversity: Q = 0.002, Bray Curtis dissimilarity) and age (alpha diversity: β = 0.15, Q = 0.006, Shannon; β = 0.12, Q = 0.003, Simpson; beta diversity: Q = 0.002, Bray Curtis dissimilarity; Q = 0.032, Weighted UniFrac) in multivariate models including age, frailty, sex, BMI, frailty and diet, and adjustment for multiple testing. Those with a more advanced age were more likely to be dissimilar in the saliva microbiota composition than younger participants (P = 5.125e-06, ANOVA). In subsample analyses, including consideration of periodontal disease (total n = 138, periodontal disease n = 66), the association with frailty remained for alpha diversity (Q = 0.002, Observed ASVs; Q = 0.04 Shannon Index), but not beta diversity, whilst age was not demonstrated to associate with alpha or beta diversity in this subsample, potentially due to insufficient statistical power. Length of time that samples were stored prior to sequencing was associated with beta diversity (Q = 0.002, Bray Curtis dissimilarity). Six bacterial taxa were associated with age after adjustment for frailty and diet. Of the factors studied, frailty and age emerged as the most influential with regards to saliva microbiota composition. Whilst age and frailty are correlates, the associations were independent of each other, giving precedence to both biological and chronological ageing as processes of potential importance when considering saliva microbiota composition.

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.

The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations

Human saliva contains diverse bacterial communities, reflecting health status, dietary patterns and contributing to variability in the sensory perception of food. Many descriptions of the diversity of the salivary microbiome have focused on the changes induced by certain diseased states, but the commonalities and differences within healthy saliva have not been fully described. Here, we define and explore the core membership of the human salivary microbial community by collecting and re-analysing raw 16S rRNA amplicon sequencing data from 47 studies with 2206 saliva samples. We found 68 core bacterial taxa that were consistently detected. Differences induced by various host intrinsic and behaviour factors, including gender, age, geographic location, tobacco usage and alcohol consumption were evident. The core of the salivary microbiome was verified by collecting and analysing saliva in an independent study. These results suggest that the methods used can effectively define a core microbial community in human saliva. The core salivary microbiome demonstrated both stability and variability among populations. Geographic location was identified as the host factor that is most associated with the structure of salivary microbiota. The independent analysis confirmed the prevalence of the 68 core OTUs we defined from the global data and provides information about how bacterial taxa in saliva varies across human populations.

Taxifolin increased semen quality of Duroc boars by improving gut microbes and blood metabolites

Taxifolin (TAX), as a natural flavonoid, has been widely focused on due to its strong anti-oxidation, anti-inflammation, anti-virus, and even anti-tumor activity. However, the effect of TAX on semen quality was unknown. The purpose of this study was to analyze the beneficial influences of adding feed additive TAX to boar semen in terms of its quality and potential mechanisms. We discovered that TAX increased sperm motility significantly in Duroc boars by the elevation of the protein levels such as ZAG, PKA, CatSper, and p-ERK for sperm quality. TAX increased the blood concentration of testosterone derivatives, antioxidants such as melatonin and betaine, unsaturated fatty acids such as DHA, and beneficial amino acids such as proline. Conversely, TAX decreased 10 different kinds of bile acids in the plasma. Moreover, TAX increased “beneficial” microbes such as Intestinimonas, Coprococcus, Butyrivibrio, and Clostridium_XlVa at the Genus level. However, TAX reduced the “harmful” intestinal bacteria such as Prevotella, Howardella, Mogibacterium, and Enterococcus. There was a very close correlation between fecal microbes, plasma metabolites, and semen parameters by the spearman correlation analysis. Therefore, the data suggest that TAX increases the semen quality of Duroc boars by benefiting the gut microbes and blood metabolites. It is supposed that TAX could be used as a kind of feed additive to increase the semen quality of boars to enhance production performance.

Nutrient composition influences the gut microbiota in chronic thoracic spinal cord-injured rats

Chronic spinal cord injury (SCI) results in an increased predisposition to various metabolic problems that can be exacerbated by consuming a diet rich in calories and saturated fat. In addition, gastrointestinal symptoms have been reported after SCI, including intestinal dysbiosis of the gut microbiome. The effects of both diet and SCI on the gut microbiome of adult male Long Evans rats euthanized 16 wk after injury were investigated. The rats were either thoracic spinal contused or received sham procedures. After 12 wk of either a low-fat or high-fat diet, cecal contents were analyzed, revealing significant microbial changes to every taxonomic level below the kingdom level. Shannon α diversity analyses demonstrated a significant difference in diversity between the groups based on the surgical condition of the rats. SCI produced a unique signature of changes in commensal bacteria that were significantly different than Sham. Specific changes in commensal bacteria as a result of diet manipulation had high fidelity with reports in the literature, such as Clostridia, Thiohalorhabdales, and Pseudomonadales. In addition, novel changes in commensal bacteria were identified that are unique dietary influences on SCI. Linear regression analysis on body fat and lean mass showed that a consequence of chronic SCI produces uncoupled associations between some commensal bacteria and body composition. In conclusion, despite tightly controlling the protein content and varying the carbohydrate and fat contents, Sham and SCI rats respond uniquely to diet. These data provide potential direction for therapeutic modulation of the microbiome to improve health and wellness following SCI.

The Effect of Short-Term Consumption of Lactic Acid Bacteria on the Gut Microbiota in Obese People

Obesity is a problem of modern health care that causes the occurrence of many concomitant diseases: arterial hypertension, diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. New strategies for the treatment and prevention of obesity are being developed that are based on using probiotics for modulation of the gut microbiota. Our study aimed to evaluate the bacterial composition of the gut of obese patients before and after two weeks of lactic acid bacteria (Lactobacillus acidophilus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and Lactobacillus delbrueckii) intake. The results obtained showed an increase in the number of members of the phylum Actinobacteriota in the group taking nutritional supplements, while the number of phylum Bacteroidota decreased in comparison with the control group. There has also been an increase in potentially beneficial groups: Bifidobacterium, Blautia, Eubacterium, Anaerostipes, Lactococcus, Lachnospiraceae ND3007, Streptococcus, Escherichia-Shigella, and Lachnoclostridium. Along with this, a decrease in the genera was demonstrated: Faecalibacterium, Pseudobutyrivibrio, Subdoligranulum, Faecalibacterium, Clostridium sensu stricto 1 and 2, Catenibacterium, Megasphaera, Phascolarctobacterium, and the Oscillospiraceae NK4A214 group, which contribute to the development of various metabolic disorders. Modulation of the gut microbiota by lactic acid bacteria may be one of the ways to treat obesity.

Metagenomic analysis reveals associations between salivary microbiota and body composition in early childhood

Several studies have shown that body mass index is strongly associated with differences in gut microbiota, but the relationship between body weight and oral microbiota is less clear especially in young children. We aimed to evaluate if there is an association between child growth and the saliva microbiome. We hypothesized that associations between growth and the saliva microbiome would be moderate, similarly to the association between growth and the gut microbiome. For 236 toddlers participating in the New Hampshire Birth Cohort Study, we characterized the association between multiple longitudinal anthropometric measures of body height, body weight and body mass. Body Mass Index (BMI) z-scores were calculated, and dual-energy x-ray absorptiometry (DXA) was used to estimate body composition. Shotgun metagenomic sequencing of saliva samples was performed to taxonomically and functionally profile the oral microbiome. We found that within-sample diversity was inversely related to body mass measurements while community composition was not associated. Although the magnitude of associations were small, some taxa were consistently associated with growth and modified by sex. Certain taxa were associated with decreased weight or growth (including Actinomyces odontolyticus and Prevotella melaninogenica) or increased growth (such as Streptococcus mitis and Corynebacterium matruchotii) across anthropometric measures. Further exploration of the functional significance of this relationship will enhance our understanding of the intersection between weight gain, microbiota, and energy metabolism and the potential role of these relationships on the onset of obesity-associated diseases in later life.

Salivary microbiome differences in prepubertal children with and without adrenal androgen excess

BACKGROUND

Premature adrenarche is a condition of childhood adrenal androgen excess (AAE) in the absence of gonadotropin-dependent puberty, and has been linked to insulin resistance and progression to metabolic syndrome. Microbial dysbiosis is associated with progression of inflammatory states and chronic diseases. Here, we aimed to examine the salivary microbiomes of children with AAE and assess the relationship with adrenal androgens and metabolic parameters.

METHODS

In a prospective cross-sectional study of children with AAE and healthy controls, adrenal and metabolic parameters were characterized and salivary microbiome was profiled using V3-V4 16S rDNA gene amplicon sequencing.

RESULTS

There was increased α-diversity in AAE (5 M, 15 F) compared to controls (3 M, 8 F), with positive correlation of 11OHA4, 11KA4, testosterone, androstenedione, DHEA, and DHEAS. Subanalyses showed increased α-diversity in both overweight/obese AAE and normal weight AAE compared to normal weight controls. Genus Peptostreptococcus, Veillonella, and Streptococcus salivarius were increased in normal weight AAE. Genus Prevotella, Abiotrophia, and Neisseria were increased in overweight/obese AAE.

CONCLUSION

These pilot data demonstrate differences in salivary microbiome profiles of children with and without AAE. Further studies are needed to assess the causal relationships between adrenal androgens, metabolic dysfunction, and salivary microbiome composition.

IMPACT

This study is the first to report the salivary microbiome of prepubertal children with adrenal androgen excess (AAE). α-Diversity is increased in the salivary microbiome of children with AAE independent of weight status, and in this study cohort several serum androgens are positively associated with α-diversity. Several taxa that have been associated with periodontal disease and inflammation are found to be significantly increased in AAE.

Taxonomic and functional alterations in the salivary microbiota of children with and without severe early childhood caries (S-ECC) at the age of 3

Background

Primary dental caries is the most prevalent oral disease among preschool children, which can cause severe damage to teeth and even affect the mental well-being of children. Various studies have demonstrated that the oral microbiome plays a pivotal role in the onset and development of dental caries. However, it remains uncertain about the key microbial markers associated with caries, owing to the limited evidence.

Methods

Fifteen S-ECC children and fifteen healthy controls were selected from three-year-old children in this study. Their clinical data and oral saliva samples were collected. Shotgun sequencing was conducted to investigate the microbial differences and the relevant functions between the two groups.

Results

We observed no apparent difference in oral microbial community diversity between the two groups. Still, at the genus/species levels, several characteristic genera/species such as Propionibacterium, Propionibacterium acidifaciens, Prevotella denticola, Streptococcus mutans and Actinomyces sp. oral taxon 448/414 increased significantly in S-ECC children, compared with the oral health group. Furthermore, we found that functional pathways involving glycolysis and acid production, such as starch and sucrose metabolism, fructose and mannose metabolism, glycolysis/gluconeogenesis, were prominently up-regulated in the high-caries group.

Conclusions

Our study showed that dental caries in children were associated with the alterations in the oral microbiota at the composition and functional levels, which may potentially inspire the exploration of microbial diagnosis or therapeutic treatments.

Gut microbiota and vitamin status in persons with obesity: A key interplay

There are numerous factors involved in obesity progression and maintenance including systemic low-grade inflammation, adipose tissue dysfunction, or gut microbiota dysbiosis. Recently, a growing interest has arisen for vitamins' role in obesity and related disorders, both at the host and gut bacterial level. Indeed, vitamins are provided mostly by food, but some, from the B and K groups in particular, can be synthesized by the gut bacterial ecosystem and absorbed in the colon. Knowing that vitamin deficiency can alter many important cellular functions and lead to serious health issues, it is important to carefully monitor the vitamin status of patients with obesity and potentially already existing comorbidities as well as to examine the dysbiotic gut microbiota and thus potentially altered bacterial metabolism of vitamins. In this review, we examined both murine and human studies, to assess the prevalence of sub-optimal levels of several vitamins in obesity and metabolic alterations. This review also examines the relationship between vitamins and the gut microbiota in terms of vitamin production and the modulation of the gut bacterial ecosystem in conditions of vitamin shortage or supplementation. Furthermore, some strategies to improve vitamin status of patients with severe obesity are proposed within this review.

Alternations in the gut microbiota and metabolome with newly diagnosed unstable angina

Gut microbiota plays an important role in coronary heart disease, but its compositional and functional changes in unstable angina (UA) remain unexplored. We performed metagenomic sequencing of 133 newly diagnosed UA patients and 133 sex- and age-matched controls, and profiled the fecal and plasma metabolomes in thirty case-control pairs. The alpha diversity of gut microbiota was increased in UA patients: the adjusted odds ratios (ORs) per standard deviation increase in Shannon and Simpson indices were 1.30 (95% confidence interval, 1.01-1.70) and 1.36 (1.05-1.81), respectively. Two common species (depleted Klebsiella pneumoniae and enriched Streptococcus parasanguinis; P ≤ 0.002) and three rare species (depleted Weissella confusa, enriched Granulicatella adiacens and Erysipelotrichaceae bacterium 6_1_45; P ≤ 0.005) were associated with UA. The UA-associated gut microbiota was depleted in the pathway of L-phenylalanine degradation (P = 0.001), primarily contributed by Klebsiella pneumoniae. Consistently, we found increased circulating phenylalanine in UA patients (OR = 2.76 [1.17-8.16]). Moreover, S. parasanguinis was negatively correlated with fecal citrulline (Spearman's r_s = -0.470, P = 0.009), a metabolite depleted in UA patients (OR = 0.26 [0.08-0.63]). These findings are informative to help understand the metabolic connection between gut microbiota and UA.

Salivary Microbiota Is Significantly Less Diverse in Patients with Chronic Spontaneous Urticaria Compared to Healthy Controls: Preliminary Results

Background: Because of the important role in regulating the immune system, increasing evidence suggests a possible implication of gut microbiota in Chronic spontaneous urticaria (CSU). Although the oral cavity is the first site of contact between microbiota and the immune system, the association between salivary microbiota and CSU has not yet been reported. Objective: This case-control study aimed to compare differences in salivary microbiota between CSU patients and healthy controls (HC). Twenty-three participants—13 patients with CSU and 10 HC were enrolled; salivary microbiota was determined by molecular approach targeting 16S ribosomal RNA. Terminal restriction fragment length polymorphism (T-RFLP) analysis was performed. Results: Alpha diversity of salivary microbiota in CSU patients was significantly reduced compared to HC, resulting in alteration of the community composition. Species richness determined via the Shannon index was significantly reduced in the CSU group. Conclusion: Dysbiosis of salivary microbiota may contribute to a dysregulated immune system in the development of CSU. To our knowledge, this was the first study that reported an alteration in salivary microbiota composition in CSU patients.

The association between body mass index and the oral Firmicutes and Bacteroidetes profiles of healthy individuals

INTRODUCTION

Microbiome status is considered an important factor that contributes to obesity. Investigations have shown that the oral microbiome comprises a vast array of bacterial species that can influence human health.

OBJECTIVE

To determine the association between the presence of the bacterial phyla Firmicutes and Bacteroidetes and the body mass index (BMI) status of normal, overweight and obese subjects in Duhok, Iraq. Additionally, to investigate the composition of oral Firmicutes and Bacteroidetes profiles for individuals with different BMI statuses.

METHODS

A total of 155 saliva samples were collected from participants in Duhok, Iraq. Bacterial genomic DNA was then extracted from the collected saliva. The presence of Firmicutes and Bacteroidetes phyla was detected via polymerase chain reaction.

RESULTS

Firmicutes and Bacteroidetes were detected in 63.2 and 37.4% of the population, respectively. Differences in the carriage rates of oral Firmicutes in overweight (78%) and obese individuals (83%) were statistically significant when compared to normal weight individuals (36%) (P<0.0001). The percentage rates of Bacteroidetes in obese individuals (26.4%) was statistically significant when compared to normal weight individuals (50.8%) (P=0.0078). The Firmicutes/ Bacteroidetes ratios (obese=3.1, overweight= 2.5 and normal weight=0.7) were higher with increasing BMI.

CONCLUSION

This study provides evidence of the Firmicutes/Bacteroidetes ratio growing with increasing BMI. High rates of Firmicutes could serve a role in the development of obesity. Further studies are required to clarify the exact relationship between oral bacteria and obesity, which could lead to a promising therapeutic method for improving the physical health of humans.

Evaluations and comparisons of microbial diversities in four types of body fluids based on two 16S rRNA gene sequencing methods

BACKGROUND

Body fluids are one of the common biological traces at crime scenes. Understanding the types of these biological traces could provide key clues for the investigations of the forensic cases. In recent years, partial hypervariable regions of 16S rRNA gene sequencing and full-length 16S rRNA gene sequencing have attracted the interests of researchers and we intend to explore which method can be better applied to forensic researches.

METHODS

In this study, the 16S rRNA gene V3-V4 (short-read) sequencing based on next-generation sequencing and the full-length 16S rRNA gene sequencing based on single molecule real-time sequencing were used to classify microbes in saliva, peripheral blood, vaginal secretion and menstrual blood samples.

RESULTS

Alpha diversity metrics in short-read sequencing were larger than those of full-length sequencing. Phylum-level bacteria in four kinds of body fluids obtained from the two platforms were similar, while their abundances were different. The results of principal coordinates analysis and analysis of molecular variance indicated the microbial compositions of vaginal secretion and menstrual blood samples were similar, and the microbial compositions among saliva, peripheral blood, vaginal secretion or menstrual blood samples were significantly different. The linear discriminant analysis effect size showed the differential bacteria screened among the four kinds of body fluids were variant in two sequencing results.

CONCLUSION

Both sequencing methods could be used to detect bacterial diversities in four different types of body fluids and provide potential tools for microbes to identify the four kinds of body fluids in forensic investigation, in which full-length sequencing could provide more accurate taxonomy.

MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys

As our understanding of the microbiome has expanded, so has the recognition of its critical role in human health and disease, thereby emphasizing the importance of testing whether microbes are associated with environmental factors or clinical outcomes. However, many of the fundamental challenges that concern microbiome surveys arise from statistical and experimental design issues, such as the sparse and overdispersed nature of microbiome count data and the complex correlation structure among samples. For example, in the human microbiome project (HMP) dataset, the repeated observations across time points (level 1) are nested within body sites (level 2), which are further nested within subjects (level 3). Therefore, there is a great need for the development of specialized and sophisticated statistical tests. In this paper, we propose multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys. We develop a variational approximation method for maximum likelihood estimation and inference. It uses optimization, rather than sampling, to approximate the log-likelihood and compute parameter estimates, provides a robust estimate of the covariance of parameter estimates and constructs a Wald-type test statistic for association testing. We evaluate and demonstrate the performance of our method using extensive simulation studies and an application to the HMP dataset. We have developed an R package MZINBVA to implement the proposed method, which is available from the GitHub repository https://github.com/liudoubletian/MZINBVA.

Minimal Associations between Short-Term Dietary Intake and Salivary Microbiome Composition

Background: Increasing evidence points to the esophageal microbiome as an important co-factor in esophageal neoplasia. Esophageal microbiome composition is strongly influenced by the oral microbiome. Salivary microbiome assessment has emerged as a potential non-invasive tool to identify patients at risk for esophageal cancer, but key host and environmental factors that may affect the salivary microbiome have not been well-defined. This study aimed to evaluate the impact of short-term dietary intake on salivary microbiome composition. Methods: Saliva samples were collected from 69 subjects prior to upper endoscopy who completed the Automated Self-Administered 24-Hour (ASA24) Dietary Assessment. Salivary microbiome composition was determined using 16S rRNA amplicon sequencing. Results: There was no significant correlation between alpha diversity and primary measures of short-term dietary intake (total daily calories, fat, fiber, fruit/vegetables, red meat intake, and fasting time). There was no evidence of clustering on beta diversity analyses. Very few taxonomic alterations were found for short-term dietary intake; an increased relative abundance of Neisseria oralis and Lautropia sp. was associated with high fruit and vegetable intake, and an increased relative abundance of a taxon in the family Gemellaceae was associated with increased red meat intake. Conclusions: Short-term dietary intake was associated with only minimal salivary microbiome alterations and does not appear to have a major impact on the potential use of the salivary microbiome as a biomarker for esophageal neoplasia.

Forensic Analysis of Human Microbiome in Skin and Body Fluids Based on Geographic Location

High-throughput DNA sequencing technologies have facilitated the in silico forensic analysis of human microbiome. Specific microbial species or communities obtained from the crime scene provide evidence of human contacts and their body fluids. The microbial community is influenced by geographic, ethnic, lifestyle, and environmental factors such as urbanization. An understanding of the effects of these external stressors on the human microbiome and determination of stable and changing elements are important in selecting appropriate targets for investigation. In this study, the Forensic Microbiome Database (FMD) (http://www.fmd.jcvi.org) containing the microbiome data of various locations in the human body in 35 countries was used. We focused on skin, saliva, vaginal fluid, and stool and found that the microbiome distribution differed according to the body part as well as the geographic location. In the case of skin samples, Staphylococcus species were higher than Corynebacterium species among Asians compared with Americans. Holdemanella and Fusobacterium were specific in the saliva of Koreans and Japanese populations. Lactobacillus was found in the vaginal fluids of individuals in all countries, whereas Serratia and Enterobacter were endemic to Bolivia and Congo, respectively. This study is the first attempt to collate and describe the observed variation in microbiomes from the forensic microbiome database. As additional microbiome databases are reported by studies worldwide, the diversity of the applications may exceed and expand beyond the initial identification of the host.

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

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

Placentas delivered by pre-pregnant obese women have reduced abundance and diversity in the microbiome

Maternal pre‐pregnancy obesity may have an impact on both maternal and fetal health. We examined the microbiome recovered from placentas in a multi‐ethnic maternal pre‐pregnant obesity cohort, through an optimized microbiome protocol to enrich low bacterial biomass samples. We found that the microbiomes recovered from the placentas of obese pre‐pregnant mothers are less abundant and less diverse when compared to those from mothers of normal pre‐pregnancy weight. Microbiome richness also decreases from the maternal side to the fetal side, demonstrating heterogeneity by geolocation within the placenta. In summary, our study shows that the microbiomes recovered from the placentas are associated with pre‐pregnancy obesity.

Importance

Maternal pre‐pregnancy obesity may have an impact on both maternal and fetal health. The placenta is an important organ at the interface of the mother and fetus, and supplies nutrients to the fetus. We report that the microbiomes enriched from the placentas of obese pre‐pregnant mothers are less abundant and less diverse when compared to those from mothers of normal pre‐pregnancy weight. More over, the microbiomes also vary by geolocation within the placenta.

Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index-A Pilot Study

The potential role of the salivary microbiome in human diseases has increasingly been explored. The salivary microbiome has been characterized in several global populations, except the Arabian Gulf region. Hence, in this pilot study, we profiled the salivary microbiome of Kuwaiti adolescents with varied body mass indexes (BMI). The analyses of core microbiome composition showed Firmicutes, Bacteroidota, Proteobacteria, Patescibacteria, Fusobacteriota, Actinobacteriota, and Campylobacterota as the common phylum found in the Kuwaiti adolescent population. We also illustrated a diverse microbial community among the sampled individuals grouped according to their BMI. Notably, the overweight group was found with a higher number of distinct taxa than other groups. As such, the core microbiome composition was found to be significantly different (p-value < 0.001) across different BMI groups. Overall, this pilot investigation outlined the microbial diversity and suggested that changes in salivary microbiome composition in people with obese or overweight BMI might reflect their susceptibility to oral diseases.

Oral Microbiota of Children Is Conserved across Han, Tibetan and Hui Groups and Is Correlated with Diet and Gut Microbiota

The oral microbiota can be affected by several factors; however, little is known about the relationship between diet, ethnicity and commensal oral microbiota among school children living in close geographic proximity. In addition, the relationship between the oral and gut microbiota remains unclear. We collected saliva from 60 school children from the Tibetan, Han and Hui ethnicities for a 16S rRNA gene sequencing analysis and comparison with previously collected fecal samples. The study revealed that Bacteroidetes and Proteobacteria were the dominant phyla in the oral microbiota. The Shannon diversity was lowest in the Tibetan group. A PCA showed a substantial overlap in the distribution of the taxa, indicating a high degree of conservation among the oral microbiota across ethnic groups while the enrichment of a few specific taxa was observed across different ethnic groups. The consumption of seafood, poultry, sweets and vegetables was significantly correlated with multiple oral microbiotas. Furthermore, 123 oral genera were significantly associated with 191 gut genera. A principal coordinate analysis revealed that the oral microbiota clustered separately from the gut microbiota. This work extends the findings of previous studies comparing microbiota from human populations and provides a basis for the exploration of the interactions governing the tri-partite relationship between diet, oral microbiota and gut microbiota.

Obesity Drives an Oral Microbiota Signature of Female Patients with Periodontitis: A Pilot Study

The aim of this study was to analyze the link between oral microbiota and obesity in humans. We conducted a pilot study including 19 subjects with periodontitis divided into two groups: normo-weighted subjects (NWS) with a body mass index (BMI) between 20 and 25 (n = 9) and obese subjects (OS) with a BMI > 30 (n = 10). Obesity was associated with a poor oral health status characterized by an increased number of missing teeth and a higher score of periodontal-support loss associated with dysbiotic oral microbiota (39.45 ± 3.74 vs. 26.41 ± 11.21, p = 0.03 for the Chao 1 index). Oral microbiota taxonomic analysis showed that the abundance of the Capnocytophaga genus was higher (2.47% ± 3.02 vs. 0.27% ± 0.29, p = 0.04) in OS compared to NWS. Obese females (OF) were characterized by an increase in the Streptococcus genus (34.12% ± 14.29 vs. 10.55% ± 10.42, p = 0.05) compared to obese males (OM), where the Neisseria genus was increased (5.75% ± 5.03 vs. 58.05% ± 30.64, p = 0.008). These first data suggest that sex/gender is determinant in the link between oral dysbiotic microbiota and obesity in patients with periodontitis. Our results could lead to recommendations concerning therapeutic strategies for obese patients with periodontitis following the sex/gender.

Association Between Serum Thyroid-Stimulating Hormone Levels and Salivary Microbiome Shifts

High serum thyroid-stimulating hormone (TSH) levels are linked to many metabolic disorders, but the effects of TSH levels on the oral microbiota are still largely unknown. This study aimed to explore the association between the salivary microbiome in adults and serum TSH levels. Saliva and fasting blood samples were obtained from a health census conducted in Southeast China. All participants were divided according to serum TSH levels. The microbial genetic profiles and changes were acquired by 16S rDNA sequencing and bioinformatics analysis. Relevant anthropometric and biochemical measurements such as insulin resistance, blood lipids, and body composition were evaluated with laboratory tests and physical examinations. The salivary microbiome in individuals with higher TSH level showed significantly higher taxa diversity. Principal coordinates analysis and partial least squares discriminant analysis showed distinct clustering in the Abnormal and Normal Groups (Adonis, P=0.0320). Granulicatella was identified as a discriminative genus for comparison of the two groups. Fasting serum insulin, Homeostatic Model Assessment for Insulin Resistance, and hemoglobin A1 were elevated in the Abnormal Group (P<0.05), showing the presence of insulin resistance in individuals with abnormal higher serum TSH levels. Distance-based redundancy analysis revealed the association of this distinctive difference with salivary microbiome. In conclusion, shifts in microbial profile were observed in the saliva of individuals with different serum TSH levels, and insulin resistance may play an important role in the biochemical and microbial alteration.

Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation

BACKGROUND

The microbiota presents a compartmentalized distribution across different gut segments. Hence, the exogenous microbiota from a particular gut segment might only invade its homologous gut location during microbiota transplantation. Feces as the excreted residue contain most of the large-intestinal microbes but lack small-intestinal microbes. We speculated that whole-intestinal microbiota transplantation (WIMT), comprising jejunal, ileal, cecal, and colonic microbiota, would be more effective for reshaping the entire intestinal microbiota than conventional fecal microbiota transplantation fecal microbiota transplantation (FMT).

RESULTS

We modeled the compartmentalized colonization of the gut microbiota via transplanting the microbiota from jejunum, ileum, cecum, and colon, respectively, into the germ-free mice. Transplanting jejunal or ileal microbiota induced more exogenous microbes' colonization in the small intestine (SI) of germ-free mice rather than the large intestine (LI), primarily containing Proteobacteria, Lactobacillaceae, and Cyanobacteria. Conversely, more saccharolytic anaerobes from exogenous cecal or colonic microbiota, such as Bacteroidetes, Prevotellaceae, Lachnospiraceae, and Ruminococcaceae, established in the LI of germ-free mice that received corresponding intestinal segmented microbiota transplantation. Consistent compartmentalized colonization patterns of microbial functions in the intestine of germ-free mice were also observed. Genes related to nucleotide metabolism, genetic information processing, and replication and repair were primarily enriched in small-intestinal communities, whereas genes associated with the metabolism of essential nutrients such as carbohydrates, amino acids, cofactors, and vitamins were mainly enriched in large-intestinal communities of germ-free mice. Subsequently, we compared the difference in reshaping the community structure of germ-free mice between FMT and WIMT. FMT mainly transferred LI-derived microorganisms and gene functions into the recipient intestine with sparse SI-derived microbes successfully transplanted. However, WIMT introduced more SI-derived microbes and associated microbial functions to the recipient intestine than FMT. Besides, WIMT also improved intestinal morphological development as well as reduced systematic inflammation responses of recipients compared with FMT.

CONCLUSIONS

Segmented exogenous microbiota transplantation proved the spatial heterogeneity of bacterial colonization along the gastrointestinal tract, i.e., the microbiota from one specific location selectively colonizes its homologous gut region. Given the lack of exogenous small-intestinal microbes during FMT, WIMT may be a promising alternative for conventional FMT to reconstitute the microbiota across the entire intestinal tract. Video Abstract.

Salivary microbiome composition changes after bariatric surgery

Recent studies show that the salivary microbiome in subjects with obesity differ from those without obesity, but the mechanism of interaction between the salivary microbiome composition and body weight is unclear. Herein we investigate this relation by analyzing saliva samples from 35 adult patients with obesity undergoing bariatric surgery. Our aim was to describe salivary microbiome changes during body weight loss on an individual-specific level, and to elucidate the effect of bariatric surgery on the salivary microbiome which has not been studied before. Analysis of samples collected before and 1 day after surgery, as well as 3 and 12 months after surgery, showed that the salivary microbiome changed in all study participants, but these changes were heterogeneous. In the majority of participants proportions of Gemella species, Granulicatella elegans, Porphyromonas pasteri, Prevotella nanceiensis and Streptococcus oralis decreased, while Veillonella species, Megasphaera micronuciformis and Prevotella saliva increased. Nevertheless, we found participants deviating from this general trend which suggests that a variety of individual-specific factors influence the salivary microbiome composition more effectively than the body weight dynamics alone. The observed microbiome alternations could be related to dietary changes. Therefore, further studies should focus on association with altered taste preferences and potential oral health consequences.

Impact of Diabetes on the Gut and Salivary IgA Microbiomes

Mucosal surfaces like those present in the lung, gut, and mouth interface with distinct external environments. These mucosal gateways are not only portals of entry for potential pathogens but also homes to microbial communities that impact host health. Secretory immunoglobulin A (SIgA) is the single most abundant acquired immune component secreted onto mucosal surfaces and, via the process of immune exclusion, shapes the architecture of these microbiomes. Not all microorganisms at mucosal surfaces are targeted by SIgA; therefore, a better understanding of the SIgA-coated fraction may identify the microbial constituents that stimulate host immune responses in the context of health and disease. Chronic diseases like type 2 diabetes are associated with altered microbial communities (dysbiosis) that in turn affect immune-mediated homeostasis. 16S rRNA gene sequencing of SIgA-coated/uncoated bacteria (IgA-Biome) was conducted on stool and saliva samples of normoglycemic participants and individuals with prediabetes or diabetes (n = 8/group). These analyses demonstrated shifts in relative abundance in the IgA-Biome profiles between normoglycemic, prediabetic, or diabetic samples distinct from that of the overall microbiome. Differences in IgA-Biome alpha diversity were apparent for both stool and saliva, while overarching bacterial community differences (beta diversity) were also observed in saliva. These data suggest that IgA-Biome analyses can be used to identify novel microbial signatures associated with diabetes and support the need for further studies exploring these communities. Ultimately, an understanding of the IgA-Biome may promote the development of novel strategies to restructure the microbiome as a means of preventing or treating diseases associated with dysbiosis at mucosal surfaces.

Comparative analysis of oral microbiome from Zang and Han populations living at different altitudes

OBJECTIVES

The aim of this study was to obtain greater insight into the environmental and genetic factors affecting the oral microbiome.

DESIGN

To this end, we investigated the oral microbiome composition in Han and Zang populations living at different altitudes. The saliva microbiome in 115 individuals from Zang and Han populations living at different altitudes was analyzed using the 16 s rRNA gene sequencing method on the Illumina MiSeq platform. The dominant species in the oral microbiome were verified by quantitative real-time polymerase chain reaction (qPCR) analysis.

RESULTS

The Han population, living at an altitude of 500 m, had higher microbiome diversity than the Zang population living at altitudes of 3000-4000 m. People living at 3000 m had a higher relative abundance of Leptothrix genus, but people living at 500 m had a higher relative abundance of Capnocytophaga genus according to Lefse difference analysis (P < 0.05). Compared to the Zang population, the Han population had higher relative abundances of Porphyromonas and Treponema genus organisms, especially Porphyromonas (P < 0.001). qPCR analysis confirmed that people living at high altitudes had the highest relative abundance of Porphyromonas gingivalis (P < 0.01).

CONCLUSIONS

This study showed that both genetics and the environment had significant influences on the oral microbiome composition. The study proposed a meaningful research direction to explore the relationship between different ethnic and altitude groups and oral diseases, such as periodontal diseases.

Alterations of Oral Microbiota in Chinese Patients With Esophageal Cancer

Emerging evidence supports that oral microbiota are associated with health and diseases of the esophagus. How oral microbiota change in Chinese patients with esophageal cancer (EC) is unknown, neither is their biomarker role. For an objective to understand alterations of oral microbiota in Chinese EC patients, we conducted a case-control study including saliva samples from 39 EC patients and 51 healthy volunteers. 16S rDNA genes of V3-V4 variable regions were sequenced to identify taxon. Relationship between oral flora and disease was analyzed according to alpha diversity and beta diversity. Resultantly, the Shannon index (p = 0.2) and the Simpson diversity index (p = 0.071) were not significant between the two groups. Yet we still found several species different in abundance between the two groups. For the EC group, the most significantly increased taxa were Firmicutes, Negativicutes, Selenomonadales, Prevotellaceae, Prevotella, and Veillonellaceae, while the most significantly decreased taxa were Proteobacteria, Betaproteobacteria, Neisseriales, Neisseriaceae, and Neisseria. In conclusion, there are significant alterations in abundance of some oral microbiomes between the EC patients and the healthy controls in the studied Chinese participants, which may be meaningful for predicting the development of EC, and the potential roles of these species in EC development deserve further studies.

Assessing the Variation within the Oral Microbiome of Healthy Adults

The human oral cavity is inhabited by a diverse community of microbes, known as the human oral microbiome. These microbes play a role in maintaining both oral and systemic health and, as such, have been proposed to be useful biomarkers of disease. However, to identify these biomarkers, we first need to determine the composition and variation of the healthy oral microbiome. In this report, we investigate the oral microbiome of 1,049 healthy individuals to determine which genera and amplicon sequence variants are commonly found between individual oral microbiomes. We then further investigate how lifestyle, anthropometric, and dietary choices impact overall microbiome composition. Interestingly, the results from this investigation showed that while many features were significantly associated with oral microbiome composition, no single biological factor explained a variation larger than 2%. These results indicate that future work on biomarker detection may be encouraged by the lack of strong confounding factors.

More than 1,000 different species of microbes have been found to live within the human oral cavity, where they play important roles in maintaining both oral and systemic health. Several studies have identified the core members of this microbial community; however, the factors that determine oral microbiome composition are not well understood. In this study, we exam the salivary oral microbiome of 1,049 Atlantic Canadians using 16S rRNA gene sequencing to determine which dietary, lifestyle, and anthropometric features play a role in shaping microbial community composition. Features that were identified as being significantly associated with overall composition then were additionally examined for genera, amplicon sequence variants, and predicted pathway abundances that were associated with these features. Several associations were replicated in an additional secondary validation data set. Overall, we found that several anthropometric measurements, including waist-hip ratio (WHR), height, and fat-free mass, as well as age and sex, were associated with overall oral microbiome structure in both our exploratory and validation data sets. We were unable to validate any dietary impacts on overall taxonomic oral microbiome composition but did find evidence to suggest potential contributions from factors such as the number of vegetable and refined grain servings an individual consumes. Interestingly, each one of these factors on its own was associated with only minor shifts in the overall taxonomic composition of the oral microbiome, suggesting that future biomarker identification for several diseases associated with the oral microbiome can be undertaken without the worry of confounding factors obscuring biological signals.

IMPORTANCE The human oral cavity is inhabited by a diverse community of microbes, known as the human oral microbiome. These microbes play a role in maintaining both oral and systemic health and, as such, have been proposed to be useful biomarkers of disease. However, to identify these biomarkers, we first need to determine the composition and variation of the healthy oral microbiome. In this report, we investigate the oral microbiome of 1,049 healthy individuals to determine which genera and amplicon sequence variants are commonly found between individual oral microbiomes. We then further investigate how lifestyle, anthropometric, and dietary choices impact overall microbiome composition. Interestingly, the results from this investigation showed that while many features were significantly associated with oral microbiome composition, no single biological factor explained a variation larger than 2%. These results indicate that future work on biomarker detection may be encouraged by the lack of strong confounding factors.

Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition

BACKGROUND

The human microbiota contributes to health and well-being. Antimicrobials (AM) have an immediate effect on microbial diversity and composition in the gut, but next to nothing is known about their long-term contribution to saliva microbiota. Our objectives were to investigate the long-term impact of AM use on saliva microbiota diversity and composition in preadolescents. We compared the lifetime effects by gender and AMs. We used data from 808 randomly selected children in the Finnish Health In Teens (Fin-HIT) cohort with register-based data on AM purchases from the Social Insurance Institution of Finland. Saliva microbiota was assessed with 16S rRNA (V3-V4) sequencing. The sequences were aligned to the SILVA ribosomal RNA database and classified and counted using the mothur pipeline. Associations between AM use and alpha-diversity (Shannon index) were identified with linear regression, while associations between beta-diversity (Bray-Curtis dissimilarity) and low, medium or high AM use were identified with PERMANOVA.

RESULTS

Of the children, 53.6% were girls and their mean age was 11.7 (0.4) years. On average, the children had 7.4 (ranging from 0 to 41) AM prescriptions during their lifespan. The four most commonly used AMs were amoxicillin (n = 2622, 43.7%), azithromycin (n = 1495, 24.9%), amoxicillin-clavulanate (n = 1123, 18.7%) and phenoxymethylpenicillin (n = 408, 6.8%). A linear inverse association was observed between the use of azithromycin and Shannon index (b - 0.015, p value = 0.002) in all children, the effect was driven by girls (b - 0.032, p value = 0.001), while not present in boys. Dissimilarities were marked between high, medium and low users of all AMs combined, in azithromycin users specifically, and in boys with amoxicillin use. Amoxicillin and amoxicillin-clavulanate use was associated with the largest decrease in abundance of Rikenellaceae. AM use in general and phenoxymethylpenicillin specifically were associated with a decrease of Paludibacter and pathways related to amino acid degradations differed in proportion between high and low AM users.

CONCLUSIONS

A systematic approach utilising reliable registry data on lifetime use of AMs demonstrated long-term effects on saliva microbiota diversity and composition. These effects are gender- and AM-dependent. We found that frequent lifelong use of AMs shifts bacterial profiles years later, which might have unforeseen health impacts in the future. Our findings emphasise a concern for high azithromycin use, which substantially decreases bacterial diversity and affects composition as well. Further studies are needed to determine the clinical implications of our findings. Video Abstract.

The Role of Oral Microbiota in Intra-Oral Halitosis

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

Screening for prevalence and abundance of Capnocytophaga spp by analyzing NGS data: A scoping review

BACKGROUND

Capnocytophaga spp. are commensal bacteria of the oral cavity and constitute a genus of the core microbiome.

OBJECTIVE

This genus is responsible for many local and systemic conditions in both the immunocompetent and immunocompromised patients, but its beneficial or deleterious role in the microbiota has been little explored.

DESIGN

Online databases were used to identify papers published from 1999 to 2019 based on next-generation sequencing (NGS) data to study comparative trials. Work using other identification methods, case reports, reviews, and non-comparative clinical trials was excluded.

RESULTS AND CONCLUSION

We selected 42 papers from among 668 publications. They showed a link between the abundance of Capnocytophaga spp. in the oral microbiota and various local pathologies (higher for gingivitis and halitosis; lower in active smokers, etc.) or systemic diseases (higher for cancer and carcinomas, IgA nephropathy, etc.). After discussing the limits inherent to the NGS techniques, we present several technical and biological hypotheses to explain the diversity of results observed between studies, as well as the links between the higher or lower abundance of Capnocytophaga spp and the appearance of local or systemic conditions and diseases.

Vitamin B and vitamin D as modulators of gut microbiota in overweight individuals

Growing evidence indicates that vitamin B (VB) and vitamin D (VD) are associated with the development of obesity. The effects of supplemental dietary VB and VD on the gut microbiota of obese individuals are still largely unknown. In the present study, 997 normoweight (NW) and 773 overweight (OW) samples were screened from the American Gut Project. The microbial α-diversity was not affected by VB, VD or VB combined with VD (VBD) supplementation in the normoweight population or the overweigh population. VD significantly modulated 20 gut microbial metabolic pathways in NW. Moreover, VBD supplementation significantly affected 3 phyla and 3 families and 22 pathways in the OW gut microbiota. In summary, our results highlight that VD and VBD might be necessary for reshaping the gut microbiota in NW and OW, respectively.