Gender-Specific Associations Between Saliva Microbiota and Body Size

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.

Microbiota of Saliva: A Non-invasive Diagnostic Tool

Potential of salivary microbiota as a non-invasive diagnostic tool for various diseases are explained in the present review. Traditional diagnostic methods rely on blood, which has limitations in terms of collection and biomarker specificity. We discuss the concept of normal flora and how disruptions in oral microbiota can be indicative of diseases. Saliva, harboring a diverse microbial community, offers promise as a diagnostic biomarker source for oral and non-oral conditions. We delve into the role of microbial dysbiosis in disease pathogenesis and the prospects of using biological indicators like dysbiosis for diagnosis, prediction, and monitoring. This review also emphasizes the significance of saliva microbiota in advancing early disease detection and timely intervention. We addressed the following research question and objectives: Can the microbiota of saliva serve as a non-invasive diagnostic tool for the early detection and monitoring of both oral and non-oral diseases? To achieve this, we will explore the normal flora of microorganisms in the oral cavity, the impact of microbial dysbiosis, and the potential of using specific pathogenic microorganisms as biomarkers. Additionally, we will investigate the correlation between oral and non-oral diseases by analyzing total saliva or site-specific dental biofilms for signs of symbiosis or dysbiosis. This research seeks to contribute valuable insights into the development of a non-invasive diagnostic approach with broad applications in healthcare.

Smoking induced salivary microbiome dysbiosis and is correlated with lipid biomarkers

BACKGROUND

The oral microbiome plays an essential role in maintaining oral homeostasis and health; smoking significantly affects it, leading to microbial dysbiosis. The study aims to investigate changes in the oral microbiome composition of smokers in the Qatari population and establish a correlation with lipid biomarkers.

METHODS

The oral microbiota was profiled from saliva samples of 200 smokers and 100 non-smokers in the Qatari population, and 16s rRNA V3-V4 region were sequenced using the Illumina MiSeq platform. The operational taxonomic units (OTUs) were clustered using QIIME and the statistical analysis was performed by R.

RESULTS

Non-smokers exhibited a more diverse microbiome, with significant alpha and beta diversity differences between the non-smoker and smoker groups. Smokers had a higher abundance of Firmicutes, Bacteroidota, Actinobacteriota, Patescibacteria, and Proteobacteria at the phylum level and of Streptococcus, Prevotella, Veillonella, TM7x, and Porphyromonas at the genus level. In contrast, non-smokers had more Bacteroidota, Firmicutes, Proteobacteria, Fusobacteriota, and Patescibacteria at the phylum level, and Prevotella, Streptococcus, Veillonella, Porphromonas, and Neisseria at the genus level. Notably, Streptococcus was significantly positively correlated with LDL and negatively correlated with HDL. Additionally, Streptococcus salivarius, within the genus Streptococcus, was substantially more abundant in smokers.

CONCLUSION

This study highlights the significant influence of smoking on the composition of the oral microbiome by enriching anaerobic microbes and depleting aerobic microbes. Moreover, the observed correlation between Streptococcus abundance and the lipid biomarkers suggests a potential link between smokers-induced salivary microbiome dysbiosis and lipid metabolism. Understanding the impact of smoking on altering the oral microbiome composition and its correlation with chemistry tests is essential for developing targeted interventions and strategies to improve oral health and reduce the risk of diseases.

Subgingival biofilm microbiome in individuals with asthma and periodontitis: Metagenomic analysis

OBJECTIVE

This observational study aimed to explore the metagenomics of subgingival biofilms in individuals with varying degrees of asthma, from severe to none, to elucidate the association between the subgingival microbiome and asthma.

MATERIALS AND METHODS

Subgingival biofilm samples were collected from thirty participants at the Asthma Control Program Outpatient Clinic in Bahia (ProAR). These samples were categorized into six groups based on the severity of asthma and the presence or absence of periodontitis. We employed next-generation sequencing (Illumina MiSeq), targeting the 16S rRNA gene, to characterize the microbial communities present. Our analysis included descriptive statistics and sequencing data, evaluated using multivariate statistical methods such as the Shannon index, principal coordinate analysis, and the Bray-Curtis dissimilarity.

RESULTS

Our findings indicate a higher prevalence of periodontally detrimental bacterial genera in individuals with severe asthma and periodontitis. Additionally, individuals with asthma, but without periodontitis, exhibited a tendency toward dysbiosis, particularly in cases of severe asthma.

CONCLUSION

This research provides new insights into the composition of the subgingival microbiome in individuals with varying severities of asthma and periodontitis. The genera identified in this study underscore the need for further investigations to build upon these findings.

Cytokine and microbiota profiles in obesity-related hypertension patients

Background

Systemic arterial hypertension is linked to a heightened risk of cardiovascular diseases on a global scale. In Mexico, nearly half of adults in vulnerable conditions experience hypertension. Imbalance in the oral and intestinal microbiota composition has been observed in patients with hypertension, documented by a decrease of bacteria producing short-chain fatty acids, which play a critical role in blood pressure regulation.

Aim

To examine the cytokines' profile and assess the characteristics of oral and gut microbiota in obesity-related hypertension in Mexican patients.

Methods

A cross-sectional, observational, and analytical study was carried out. Twenty-two patients were categorized by their body mass index (BMI) as overweight and obese, and the diagnosis of primary hypertension. DNA from supragingival dental plaque and feces samples was used to carry out 16S rRNA sequencing. Additionally, 13 cytokines were quantified.

Results

In the oral microbiota, Kluyvera was found to be significantly enriched in obese compared to overweight patients. Instead, the gut microbiota was dominated by Firmicutes. However, the correlation between certain genera and proinflammatory cytokines was noted.

Conclusion

This exploratory study provides insights into the complex relationship between the oral and gut microbiota and their association with systemic inflammation in obesity-related hypertension.

Associations of central obesity and habitual food consumption with saliva microbiota and its enzymatic profiles - a pilot study in Finnish children

Background

Variation in diversity and composition of saliva microbiota has been linked to weight status, but findings have been inconsistent. Focusing on clinically relevant conditions such as central obesity and using advanced sequencing techniques might fill in the gaps of knowledge.

Aims

We investigated saliva microbiota with shallow metagenome sequencing in children with (n = 14) and without (n = 36) central obesity. Additionally, we examined the role of habitual food consumption on microbial enzymatic repertoire.

Methods

Data comprised 50 children (50% male) with a mean age of 14.2 (SD 0.3) years, selected from the Finnish Health in Teens (Fin-HIT) cohort. Dietary scores for consumption frequency of sweet treats (STI), dairy products (DCI) and plants (PCI) were derived based on a self-administered food frequency questionnaire. Central obesity was defined based on waist-height ratio using the cut-off 0.5. Saliva samples were subjected to whole-metagenome shotgun sequencing, and taxonomic and functional profiling was achieved with METAnnotatorX2 bioinformatics platform.

Results

Groups had an average 20 (95% CI 14-27) cm difference in waist circumference. We identified the lack of Pseudomonas guguagenesis and Prevotella scopos, oulorum and oris as putative biomarkers associated with central obesity and observed a total of 16 enzymatic reactions differing between the groups. DCI was associated with the highest number of enzyme profiles (122), followed by STI (60) and DCI (25) (Pearson correlation p < 0.05). Intriguingly, STI showed a high positive/negative correlation ratio (5.09), while DCI and PCI showed low ratios (0.54 and 0.33, respectively). Thus, the main driver of enzymatic reactions was STI, and the related pathways involved nitrate metabolism induced by Haemophilus parainfluenzae and Veilonella dispar among others.

Conclusion

Clinically relevant differences in central obesity were only modestly reflected in the composition of saliva microbiota. Habitual consumption of sweet treats was a strong determinant of enzymatic reactions of saliva microbiota in children with and without central obesity. The clinical relevance of these findings warrants further studies.

The Oral Microbiome Profile of Water Polo Players Aged 16-20

OBJECTIVES

Chlorine has a strong antibacterial property and is the disinfectant most frequently used in swimming pools. Therefore, the microbiota community in the oral cavity of those who practice water sports is assumed to be special due to their regular immersion in water. Adverse changes in the composition of oral cavity microbiota may have serious health consequences. We aimed to compare the oral microbiome between water polo players and non-athletes. We hypothesized that the oral cavity microbiota community differed between water polo players and non-athletes.

MATERIALS AND METHODS

Altogether, 124 water polo players (62 males and 62 females, aged between 9 and 20 years) and 16 non-athlete youths (control group, eight males and eight females, aged between 16 and 20 years, mean age + SD = 17.1 + 1.4 years) who participated in body structure examinations voluntarily agreed to participate in the study. In a randomly selected subsample of water polo players (n: 29, aged between 16 and 20 years, mean age + SD = 17.3 + 1.0 years), saliva samples were also collected. Saliva samples were collected from all non-athlete youths (n: 16, aged between 16 and 20 years). The oral microbiome was determined from a saliva sample, and DNA was isolated using the QIAmp DNA Blood Mini Kit. The 16S rRNA gene amplicon sequencing method was used to analyze the microbiome community. PCR primers were trimmed from the sequence reads with Cutadapt. R library DADA2 was used to process reads in the abundance analysis.

RESULTS

In general, Streptococcus, Veilonella, and Prevotella genera constituted more than 50% of the oral microbiome community in the two participant groups combined (n = 45). The oral microbial profile had significant sexual dimorphism and differed between water polo players and the non-athletes. Compared to females, males had a higher (p < 0.05) relative abundance of the Atopobium (medium effect size) and Pravotella_7 (very large effect size) genera and a lower (p < 0.05) relative abundance of the Fusobacterium (large effect size), Gemella (large effect size), and Streptococcus (large effect size) genera. Compared to non-athletes, water polo players had higher (p < 0.05, medium effect size) relative abundance of the genus Veillonella and lower (p < 0.05, large effect size) relative abundance of the genus Gemella.

CONCLUSIONS

The results suggest that regular water training can unfavorably alter the composition of the oral microbial community.

Bypass gastroplasty impacts oral health, salivary inflammatory biomarkers, and microbiota: a controlled study

OBJECTIVES

Knowledge about the impact of gastroplasty on oral health and salivary biomarkers is limited. The aim was to prospectively evaluate oral health status, salivary inflammatory markers, and microbiota in patients undergoing gastroplasty compared with a control group undergoing a dietary program.

MATERIALS AND METHODS

Forty participants with obesity class II/III were included (20 individuals in each sex-matched group; 23-44 years). Dental status, salivary flow, buffering capacity, inflammatory cytokines, and uric acid were assessed. Salivary microbiological analysis (16S-rRNA sequencing) assessed the abundance of genus, species, and alpha diversity. Cluster analysis and mixed-model ANOVA were applied.

RESULTS

Oral health status, waist-to-hip ratio, and salivary alpha diversity were associated at baseline. A subtle improvement in food consumption markers was observed, although caries activity increased in both groups, and the gastroplasty group showed worse periodontal status after three months. IFNγ and IL10 levels decreased in the gastroplasty group at 3 months, while a decrease was observed in the control group at 6 months; IL6 decreased in both groups (p < 0.001). Salivary flow and buffering capacity did not change. Significant changes in Prevotella nigrescens and Porphyromonas endodontalis abundance were observed in both groups, while alpha diversity (Sobs, Chao1, Ace, Shannon, and Simpson) increased in the gastroplasty group.

CONCLUSIONS

Both interventions changed in different degrees the salivary inflammatory biomarkers and microbiota, but did not improve the periodontal status after 6 months.

CLINICAL RELEVANCE

Although the observed discrete improvement in dietary habits, caries activity increased with no clinical improvement in the periodontal status, emphasizing the need of oral health monitoring during obesity treatment.

A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans

Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core to specific body fluids and are greatly influenced by geographical location and ethnicity. Bacteria in body fluids could also be due to bacterial infection; hence, it would be worthwhile taking into consideration bacterial species associated with diseases. The present review reports bacterial species characteristic of diseased and healthy body fluids across geographical locations, and bacteria described in forensic studies, with the aim of collating a set of bacteria to serve as the core species-specific markers for forensic body fluid identification. The most widely reported saliva-specific bacterial species are Streptococcus salivarius, Prevotella melaninogenica, Neisseria flavescens, with Fusobacterium nucleatum associated with increased diseased state. Lactobacillus crispatus and Lactobacillus iners are frequently dominant in the vaginal microbiome of healthy women. Atopobium vaginae, Prevotella bivia, and Gardnerella vaginalis are more prevalent in women with bacterial vaginosis. Semen and urine-specific bacteria at species level have not been reported, and menstrual blood bacteria are indistinguishable from vaginal fluid. Targeting more than one bacterial species is recommended for accurate body fluid identification. Although metagenomic sequencing provides information of a broad microbial profile, the specific bacterial species could be used to design biosensors for rapid body fluid identification. Validation of microbial typing methods and its application in identifying body fluids in a mixed sample would allow regular use of microbial profiling in a forensic workflow.

Pre-Diagnostic Saliva Microbiota of School-Aged Children Who Developed Type 1 Diabetes or Inflammatory Bowel Diseases

Altered commensal microbiota composition has been associated with pediatric type 1 diabetes mellitus (T1D) and inflammatory bowel diseases (IBD), but the causal relationship is still unclear. To search for potential pre-diagnostic biomarkers for pediatric T1D or IBD, we compared microbiota in saliva samples in a nested case-control design comprising children developing T1D (n_children = 52) or IBD (n_children = 21) and controls with a similar age, sex, and residential area (n_children = 79). The pre-diagnostic saliva microbiota alpha- and beta-diversity of children who would develop T1D (n_samples = 27) or IBD (n_samples = 14) minimally varied from that of controls. The relative abundances of Abiotrophia were higher, while those of Veillonella, Actinomyces, Megasphaera, Butyrivibrio, and Candidatus ancillula were lower in children who would develop T1D. Within 2 years before diagnosis, the metabolic PWY-5677 pathway (converting succinate into butyrate) was lower in pre-T1D samples than in controls (q = 0.034). No significant pre-IBD differences were found. In conclusion, saliva microbiota diversity or composition were not successful predictors for pediatric T1D nor IBD. Intriguingly, the succinate fermentation pathway was predicted to be lowered before the onset of T1D. Thus, investigating functional pathways might provide a better approach in searching for biomarkers for autoimmune disease in the future.

Microbiome Dysbiosis: A Pathological Mechanism at the Intersection of Obesity and Glaucoma

The rate at which obesity is becoming an epidemic in many countries is alarming. Obese individuals have a high risk of developing elevated intraocular pressure and glaucoma. Additionally, glaucoma is a disease of epidemic proportions. It is characterized by neurodegeneration and neuroinflammation with optic neuropathy and the death of retinal ganglion cells (RGC). On the other hand, there is growing interest in microbiome dysbiosis, particularly in the gut, which has been widely acknowledged to play a prominent role in the etiology of metabolic illnesses such as obesity. Recently, studies have begun to highlight the fact that microbiome dysbiosis could play a critical role in the onset and progression of several neurodegenerative diseases, as well as in the development and progression of several ocular disorders. In obese individuals, gut microbiome dysbiosis can induce endotoxemia and systemic inflammation by causing intestinal barrier malfunction. As a result, bacteria and their metabolites could be delivered via the bloodstream or mesenteric lymphatic vessels to ocular regions at the level of the retina and optic nerve, causing tissue degeneration and neuroinflammation. Nowadays, there is preliminary evidence for the existence of brain and intraocular microbiomes. The altered microbiome of the gut could perturb the resident brain-ocular microbiome ecosystem which, in turn, could exacerbate the local inflammation. All these processes, finally, could lead to the death of RGC and neurodegeneration. The purpose of this literature review is to explore the recent evidence on the role of gut microbiome dysbiosis and related inflammation as common mechanisms underlying obesity and glaucoma.

Impact of Gut Dysbiosis on the Risk of Non-Small-Cell Lung Cancer

Background: The imbalance of gut microbiota, dysbiosis, is associated with various malignant diseases. This study aimed to identify the characteristics of gut microbiota in age-matched treatment-naïve non-small-cell lung cancer (NSCLC) patients and healthy individuals to investigate possible gut-microbe-related pathways involved in the development of NSCLC. Methods: We enrolled 34 age-matched NSCLC patients and 268 healthy individuals. Hypervariable V3−V4 amplicons of 16S rRNA in freshly collected fecal samples were sequenced. Diversity, microbial composition, functional pathways, smoking history, and gut-microbe-related comorbidities were analyzed to assess the factors associated with the risk of NSCLC. Results: Microbial alpha diversity was decreased in the patients with NSCLC, and beta diversity was significantly different between the patients and controls (p < 0.001). After adjustments for sex, smoking history, hypertension, diabetes mellitus, chronic obstructive pulmonary disease, and 11 abundant microbes with significant differences between the patients and controls, the enrichment of Anaerotruncus spp. and Bacteroides caccae was associated with an increased risk of NSCLC (p = 0.003 and 0.007, respectively). The areas under receiver operating characteristic curves were 71.4% and 66.9% for Anaerotruncus spp. and Bacteroides caccae, respectively (both p < 0.001). Furthermore, the abundance of Bacteroides caccae was positively correlated with steroid hormone biosynthesis (p < 0.001), N-glycan biosynthesis (p = 0.023), glycosaminoglycan degradation (p < 0.001), lipoic acid metabolism (p = 0.039), peroxisome (p < 0.001), and apoptosis (p < 0.001), but inversely related to glycerolipid metabolism (p < 0.001). Anaerotruncus spp. was positively associated with decreased biosynthesis of ansamycin only (p = 0.001). No overlapping signaling pathways were modulated by Bacteroides caccae or Anaerotruncus spp. Conclusions: Our results revealed that fecal Anaerotruncus spp. and Bacteroides caccae were abundant and may be associated with the risk of NSCLC regardless of sex, smoking history, and gut-microbe-related comorbidities. Further investigations on the mechanism underlying the potential association between gut dysbiosis and the development of NSCLC are warranted.

Short-term head-down bed rest microgravity simulation alters salivary microbiome in young healthy men

Microgravity influences are prevalent during orbital flight and can adversely affect astronaut physiology. Notably, it may affect the physicochemical properties of saliva and the salivary microbial community. Therefore, this study simulates microgravity in space using a ground-based -6° head-down bed rest (HDBR) test to observe the effects of microgravity on oral salivary secretion function and the salivary microbiome. Sixteen healthy young male volunteers were recruited for the 15-day -6° HDBR test. Non-stimulated whole saliva was collected on day 1 (pre-HDBR), on days 5, 10, and 15 of HDBR, and day 6 of recovery. Salivary pH and salivary flow rate were measured, and the V3-V4 region of the 16S rRNA gene was sequenced and analyzed in 80 saliva samples. The results showed that there were no significant differences in salivary pH, salivary flow rate, and alpha diversity between any two time points. However, beta diversity analysis revealed significant differences between pre-HDBR and the other four time points. After HDBR, the relative abundances of Actinomyces, Parvimonas, Peptostreptococcus, Porphyromonas, Oribacterium, and Capnocytophaga increased significantly, whereas the relative abundances of Neisseria and Haemophilus decreased significantly. However, the relative abundances of Oribacterium and Capnocytophaga did not recover to the pre-HDBR level on day 6 of recovery. Network analysis revealed that the number of relationships between genera decreased, and the positive and negative correlations between genera changed in a complex manner after HDBR and did not reach their original levels on day 6 of recovery. PICRUSt analysis demonstrated that some gene functions of the salivary microbiome also changed after HDBR and remained significantly different from those before HDBR on day 6 of recovery. Collectively, 15 days of -6° HDBR had minimal effect on salivary secretion function but resulted in significant changes in the salivary microbiome, mainly manifested as an increase in oral disease-related bacteria and a decrease in oral health-related commensal bacteria. Further research is required to confirm these oral microbial changes and explore the underlying pathological mechanisms to determine the long-term effects on astronauts embarking on long-duration voyages to outer space.

Is oral microbiota associated with overweight and obesity in children and adolescents? A systematic review

This article aims to verify the relationship between the composition and diversity of oral microbiota with overweight and obese children and adolescents. This systematic review was registered in PROSPERO, followed PRISMA 2020, and included an electronic search until March 2022, in PubMed/MEDLINE, Web of Science, Scopus, and The Cochrane Library databases. Studies were eligible if they compared the oral microbiota according to nutrition status among children and adolescents. Independent peers using JBI Critical Appraisal Checklists assessed the quality of studies. Eleven studies were eligible to be included in this review, with a total of 1,695 children and adolescents, 224 were obese, 190 were overweight, 1,154 were eutrophics and 127 were underweight. The most frequent phyla in overweight and obese children and adolescents, in comparison to their counterparts were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria. It was identified that nine of the eleven articles selected showed an association between oral microbiota and overweight and obesity in children and adolescents. We observed that there is an important association between oral bacterial composition diversity and overweight and obesity. This finding indicates the relevance of the evaluation and surveillance in oral health to control cases of overweight and obesity in children and adolescents.

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.

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.

The Composition and Functional Capacities of Saliva Microbiota Differ Between Children With Low and High Sweet Treat Consumption

Excess sugar consumption—common in youth—is associated with poor health. Evidence on the relationship between sugar consumption and the oral microbiome, however, remains scarce and inconclusive. We explored whether the diversity, composition, and functional capacities of saliva microbiota differ based on the consumption of select sugary foods and drinks (“sweet treats”). Using 16S rRNA gene sequencing, we characterized saliva microbiota from 11 to 13-year-old children who participated in the Finnish Health in Teens (Fin-HIT) cohort study. The sample comprised children in the lowest (n = 227) and highest (n = 226) tertiles of sweet treat consumption. We compared differences in the alpha diversity (Shannon, inverse Simpson, and Chao1 indices), beta diversity (principal coordinates analysis based on Bray–Curtis dissimilarity), and abundance (differentially abundant operational taxonomic units (OTUs) at the genus level) between these low and high consumption groups. We performed PICRUSt2 to predict the metabolic pathways of microbial communities. No differences emerged in the alpha diversity between low and high sweet treat consumption, whereas the beta diversity differed between groups (p = 0.001). The abundance of several genera such as Streptococcus, Prevotella, Veillonella, and Selenomonas was higher in the high consumption group compared with the low consumption group following false discovery rate correction (p < 0.05). Children with high sweet treat consumption exhibited higher proportions of nitrate reduction IV and gondoate biosynthesis pathways compared with the low consumption group (p < 0.05). To conclude, sweet treat consumption shapes saliva microbiota. Children who consume a high level of sweet treats exhibited different compositions and metabolic pathways compared with children who consume low levels of sweet treats. Our findings reveal novel insights into the relationship between sugary diets and oral microbiota.

Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa

Obesity is an increasing global health concern and is associated with a broad range of morbidities. The gut microbiota are increasingly recognized as important contributors to obesity and cardiometabolic health. This study aimed to characterize oral and gut microbial communities, and evaluate host: microbiota interactions between clinical obesity classifications. We performed 16S rRNA sequencing on fecal and salivary samples, global metabolomics profiling on plasma and stool samples, and dietary profiling in 135 healthy individuals. We grouped individuals by obesity status, based on body mass index (BMI), including lean (BMI 18-124.9), overweight (BMI 25-29.9), or obese (BMI ≥30). We analyzed differences in microbiome composition, community inter-relationships, and predicted microbial function by obesity status. We found that salivary bacterial communities of lean and obese individuals were compositionally and phylogenetically distinct. An increase in obesity status was positively associated with strong correlations between bacterial taxa, particularly with bacterial groups implicated in metabolic disorders including Fretibacterium, and Tannerella. Consumption of sweeteners, especially xylitol, significantly influenced compositional and phylogenetic diversities of salivary and fecal bacterial communities. In addition, obesity groups exhibited differences in predicted bacterial metabolic activity, which was correlated with host's metabolite concentrations. Overall, obesity was associated with distinct changes in bacterial community dynamics, particularly in saliva. Consideration of microbiome community structure and inclusion of salivary samples may improve our ability to understand pathways linking microbiota to obesity and cardiometabolic disease.

The Oral-Microbiome-Brain Axis and Neuropsychiatric Disorders: An Anthropological Perspective

In the 21st century, neuropsychiatric disorders (NPDs) are on the rise, yet the causal mechanisms behind this global epidemic remain poorly understood. A key to these unknowns may lie within the vast communities of bacteria, fungi, and viruses in the body (microbiota), which are intimately linked with health and disease. NPDs were recently shown to be connected to gut microbiota, which can communicate with and influence the brain through the Gut-Brain-Axis (GBA). Parallel studies examining oral microbiota and their connections to the brain also suggest that microbes in the mouth can similarly influence NPD outcomes. However, the mechanisms and pathways that illuminate how oral microbiota and brain communicate in NPDs remain unknown. Here, we review identified mechanisms and pathways that oral microbiota use to engage the brain, and we lay the theoretical foundation for an oral-microbiota-brain axis (OMBA). Specifically, we examine established neuroinflammatory and immune system activation responses that underpin interactions between the oral microbiota and the central nervous system (CNS), detailing four specific mechanisms: (1) microbial and metabolite escape, (2) neuroinflammation, (3) CNS signaling, and (4) response to neurohormones. We then scrutinize why including the OMBA, in addition to the GBA, is critically needed to elucidate specific causal relationships between microbial dysbiosis and observed NPD development and progression. Furthermore, we argue for comprehensive, interdisciplinary approaches that integrate lab-based microbiome research and population-level studies that examine the OMBA to improve NPDs. We specifically identify key anthropological perspectives that integrate sociocultural, epidemiological, genetic, and environmental factors that shape the oral microbiome and its interactions with NPDs. Together, future studies of the OMBA in conjunction with interdisciplinary approaches can be used to identify NPD risks and improve outcomes, as well as develop novel intervention and treatment strategies.

Differential analysis of the bacterial community in colostrum samples from women with gestational diabetes mellitus and obesity

Gestational Diabetes Mellitus (GDM) and obesity affect the functioning of multiple maternal systems and influence colonization of the newborn gastrointestinal through the breastmilk microbiota (BMM). It is currently unclear how GDM and obesity affect the human BMM composition. Here, we applied 16S-rRNA high-throughput sequencing to human colostrum milk to characterize BMM taxonomic changes in a cohort of 43 individuals classified in six subgroups according to mothers patho-physiological conditions (healthy control (n = 18), GDM (n = 13), or obesity (n = 12)) and newborn gender. Using various diversity indicators, including Shannon/Faith phylogenetic index and UniFrac/robust Aitchison distances, we evidenced that BMM composition was influenced by the infant gender in the obesity subgroup. In addition, the GDM group presented higher microbial diversity compared to the control group. Staphylococcus, Corynebacterium 1, Anaerococcus and Prevotella were overrepresented in colostrum from women with either obesity or GDM, compared to control samples. Finally, Rhodobacteraceae was distinct for GDM and 5 families (Bdellovibrionaceae, Halomonadaceae, Shewanellaceae, Saccharimonadales and Vibrionaceae) were distinct for obesity subgroups with an absolute effect size greater than 1 and a q-value ≤ 0.05. This study represents the first effort to describe the impact of maternal GDM and obesity on BMM.

Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis

Periodontitis is a globally prevalent disease that imposes a functional and aesthetic burden on patients. The oral microbiome influences human health. The aim of this study was at assessing gender variation in the subgingival bacterial microbiome of elderly patients with initial periodontitis and to determine the causes of this variation. Twelve males and twenty females (range 50-68 years old) with initial periodontitis provided subgingival plaque samples. 16S rRNA gene sequencing, QIIME-based data processing, and statistical analyses were carried out using several different analytical approaches to detect differences in the oral microbiome between the two groups. Males had higher Chao1 index, observed species, and phylogenetic diversity whole tree values than females. Analysis of β-diversity indicated that the samples were reasonably divided by the gender. The linear discriminant analysis effect size showed that the most representative biomarkers were the genus Haemophilus in males, whereas the dominant bacteria in females were Campylobacter. Kyoto Encyclopedia of Genes and Genomes analysis showed that predicting changes in the female oral microbiota may be related to the immune system and immune system diseases are the main factor in males. These data suggest that gender may be a differentiating factor in the microbial composition of subgingival plaques in elderly patients with initial periodontitis. These results could deepen our understanding of the role of gender in the oral microbiota present during initial periodontitis.

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.

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.

Observational Study Regarding the Relationship between Nutritional Status, Dental Caries, Mutans Streptococci, and Lactobacillus Bacterial Colonies

The prevalence of dental caries and obesity is high as both raise significant health problems. The objective of this study was to evaluate the relationship between dental caries, the number of salivary colonies forming units of Mutans Streptococci (MS) and Lactobacillus (LB), and the nutritional status in a group of children from Transylvania. This observational study used a sample of 154 school children, aged 9 to 12 years. The prevalence of caries was measured using the decayed, missing, and filled teeth index for deciduous teeth (dmft index) and for permanent teeth (DMFT index). Height and weight were assessed for each subject, and their body mass index (BMI) percentile was calculated. Salivary levels of Mutans Streptococci (MS) and Lactobacillus (LB) were determined using the CRT Bacteria Test from Ivoclar Vivadent. In our study, we found a positive association between the BMI percentile, MS count, LB count, tooth brushing frequency, and the incidence of dental caries in children aged 9 to 12 years old. Future preventive programs should include nutrition control in order to prevent both the apparition of dental caries and obesity in children.

High abundance of sugar metabolisers in saliva of children with caries

Dental caries is a biofilm-mediated, dynamic disease with early onset. A balanced salivary microbiota is a foundation of oral health, while dysbiosis causes tooth decay. We compared the saliva microbiota profiles in children with and without caries. The study consisted of 617 children aged 9–12 years from the Finnish Health in Teens (Fin-HIT) study with available register data on oral health. Caries status was summarised based on Decayed, Missing, and Filled Teeth (DMFT) index in permanent dentition. The children were then classified into the following two groups: DMFT value ≥ 1 was considered as cavitated caries lesions (hereafter called ‘caries’) (n = 208) and DMFT = 0 as ‘cavity free’ (n = 409). Bacterial 16S rRNA gene (V3–V4 regions) was amplified using PCR and sequenced by Illumina HiSeq. The mean age (SD) of the children was 11.7 (0.4) years and 56% were girls. The children had relatively good dental health with mean DMFT of 0.86 (1.97). Since sex was the key determinant of microbiota composition (p = 0.014), we focused on sex-stratified analysis. Alpha diversity indexes did not differ between caries and cavity free groups in either sexes (Shannon: p = 0.40 and 0.58; Inverse Simpson: p = 0.51 and 0.60, in boys and girls, respectively); neither did the composition differ between the groups (p = 0.070 for boys and p = 0.230 for girls). At the genus level, Paludibacter and Labrenzia had higher abundances in the caries group compared to cavity free group in both sexes (p < 0.001). Taken together, there were minor differences in saliva microbiota between children with and without caries. Potential biomarkers of caries were the sugar metabolisers Paludibacter and Labrenzia. These bacteria presumably enhance salivary acidification, which contributes to progression of dental caries. The clinical relevance of our findings warrants further studies.

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota

BACKGROUND

While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors.

RESULTS

Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features.

CONCLUSIONS

Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.

The salivary microbiota of Thai adults with metabolic disorders and association with diet

OBJECTIVE

This study aimed to investigate abundance of specific bacterial taxa in the saliva of 105 Thai adults with different BMI (lean, overweight, and obese) and T2DM subjects using qPCR targeting the 16S rRNA gene of various bacteria taxa.

DESIGN

We employed qPCR targeting 16S rRNA genes to explore the bacterial profiles and abundances in the saliva of Thai adult subjects with different BMI and T2DM. Multivariate statistical analyses (multiple factor analysis (MFA) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) were performed to assess the associations of salivary bacteria with diet, blood profile, gender, age, and use of antibiotics.

RESULTS

We found that abundance profiles of the examined salivary bacteria were similar across the four groups. When diet, blood profile, and gender, age, and use of antibiotics were considered, significant differences were noted between subgroups. A positive correlation was also found between consumption of carbonate soft drinks and Bacteroidetes, Gamma-proteobacteria, Veillonella, Fusobacterium and Fusobacterium nucleatum.

CONCLUSIONS

This is the first study demonstrating the relative abundance of salivary bacteria in adult Thai subjects with different levels of BMI and T2DM. Regardless of the similar pattern of bacterial profiles across groups, sPLS-DA analysis highlighted the influence of host variables (gender, age, and use of antibiotics) on the abundance of salivary microbiota. Our findings pave the way for further hypothesis testing to gain insight into the association between host factors and salivary microbiome.

Dysbiosis in the Salivary Microbiome Associated with IgA Nephropathy-‍A‍ ‍Japanese Cohort Study

IgA nephropathy is one of the leading causes of chronic kidney disease in Japan. Since the origin and mechanisms by which IgA nephropathy develops currently remain unclear, a confirmed disease diagnosis is currently only possible by highly invasive renal biopsy. With the background of the salivary microbiome as a rich source of biomarkers for systemic diseases, we herein primarily aimed to investigate the salivary microbiome as a tool for the non-invasive diagnosis of IgA nephropathy. In a comparison of salivary microbiome profiles using 16S rRNA amplicon sequencing, significant differences were observed in microbial diversity and richness between IgA nephropathy patients and healthy controls. Furthermore, recent studies reported that patients with IgA nephropathy are more likely to develop inflammatory bowel diseases and that chronic inflammation of the tonsils triggered the recurrence of IgA nephropathy. Therefore, we compared the salivary microbiome of IgA nephropathy patients with chronic tonsillitis and ulcerative colitis patients. By combining the genera selected by the random forest algorithm, we were able to distinguish IgA nephropathy from healthy controls with an area under the curve (AUC) of 0.90, from the ulcerative colitis group with AUC of 0.88, and from the chronic tonsillitis group with AUC of 0.70. Additionally, the genus Neisseria was common among the selected genera that facilitated the separation of the IgA nephropathy group from healthy controls and the chronic tonsillitis group. The present results indicate the potential of the salivary microbiome as a biomarker for the non-invasive diagnosis of IgA nephropathy.

Microbiome: A Supportive or a Leading Actor in Lung Cancer?

Lung cancer is still the leading cause of cancer death worldwide. Despite the major diagnostic and therapeutic innovations, the effect on mortality has been modest and the overall survival is still poor. Better understanding of the pathology of these tumors is necessary in order to develop personalized therapeutic strategies in lung cancer patients. Human microbiome has been associated with normal physiology and function, and increasing evidence points towards a key role of the microbiome in promoting the progression of lung disease. Studies have shown that although poorly understood, lung has a distinctive microbiome that may an important role in lung cancer development and progression, and interactions between microbial populations have the potential to influence disease, suggesting that microbiome can be an emerging target in cancer therapeutics. We will review mechanisms how the lung microbiota influences carcinogenesis, focusing on the bacterial dysbiosis and inflammation. Moreover, we will discuss the link between the microbiome and cancer and the consequences induced by the immune system, as the host microbiota plays an essential role in activating and modulating the immune response. We summarize current research advances in the lung microbiome and demonstrate the potential to exploit microbiome as a mechanism to prevent carcinogenesis and modulate therapeutic strategy, suggesting microbiome as a valuable approach in lung cancer patients.

Improved High-Throughput Sequencing of the Human Oral Microbiome: From Illumina to PacBio

Background

A comprehensive understanding of the commensal microflora and its relation to health is essential for preventing and combating diseases. The aim of this study was to examine the structure of the oral microbiome by using different sequencing technologies. Material and Methods. Five preschool children with no symptoms of oral and systemic diseases were recruited. Samples of saliva were collected. A 468 bp insert size library was constructed on the MiSeq platform and then subjected to 300 bp paired-end sequencing. Libraries with longer insert sizes, including a full-length 16S rDNA gene, were sequenced on the PacBio RS II platform.

Results

A total of 122.6 Mb of raw data, including 244,967 high-quality sequences, were generated by the MiSeq platform, while 134.6 Mb of raw data, including 70,030 high-quality reads, were generated by the PacBio RS II platform. Clustering of the unique sequences into OTUs at 3% dissimilarity resulted in an average of 225 OTUs on the MiSeq platform; however, the number of OTUs generated on the PacBio RS II platform was 449, far greater than the number of OTUs generated on the MiSeq platform. A total of 437 species belonging to 10 phyla and 60 genera were detected by the PacBio RS II platform, while 163 species belonging to 12 phyla and 72 genera were detected by the MiSeq platform.

Conclusions

The oral microflora of healthy Chinese children were analyzed. Compared with traditional 16S rRNA sequencing technology, the PacBio system, despite providing a lower amount of clean data, surpassed the resolution of the MiSeq platform by improving the read length and annotating the nucleotide sequences at the species or strain level. This trial is registered with NCT02341352.

The evolutionary history of the human oral microbiota and its implications for modern health

Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.

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.

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.

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota

BACKGROUND

From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood₂₀₁₀ cohort.

RESULTS

Both bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa.

CONCLUSIONS

Current study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child. Video Abstract.

Breastfeeding may have a long-term effect on oral microbiota: results from the Fin-HIT cohort

BACKGROUND

Breastfeeding contributes to gastrointestinal microbiota colonization in early life, but its long-term impact is inconclusive. We aimed to evaluate whether the type of feeding during the first six months of life was associated with oral microbiota in adolescence.

METHODS

This is a cross-sectional sub-study using baseline information of 423 adolescents from the Finnish Health in Teens (Fin-HIT) cohort. Type of feeding was recalled by parents and dichotomized as (i) No infant formula; (ii) Infant formula (breastmilk + formula or only formula). Saliva microbiota was analysed using 16S rRNA (V3-V4) sequencing. Alpha diversity and beta diversity were compared between feeding type groups using ANCOVA and PERMANOVA, respectively. Differential bacteria abundance was tested using appropriate general linear models.

RESULTS

Mean age and body mass index were 11.7 years and 18.0 kg/m2, respectively. The No formula group contained 41% of the participants. Firmicutes (51.0%), Bacteroidetes (19.1%), and Proteobacteria (16.3%) were the most abundant phyla among all participants. Alpha and beta diversity indices did not differ between the two feeding groups. Three Operational Taxonomic Units (OTUs) belonging to Eubacteria and Veillonella genera (phylum Firmicutes) were more abundant in the No formula than in the Infant formula group (log2fold changes/ p - values - 0.920/ < 0.001, - 0.328/ 0.001, - 0.577/ 0.004).

CONCLUSION

Differences exist in abundances of some OTUs in adolescence according to feeding type during the first six months of life, but our findings do not support diversity and overall oral microbiota composition in adolescents being affected by early feeding type.

Meal Regularity Plays a Role in Shaping the Saliva Microbiota

BACKGROUND

Diet may influence health directly or indirectly via the human microbiota, emphasizing the need to unravel these complex relationships for future health benefits. Associations between eating habits and gut microbiota have been shown, but less is known about the association between eating habits and saliva microbiota.

OBJECTIVE

The aim of this study was to investigate if eating habits and meal patterns are associated with the saliva microbiota.

METHODS

In total, 842 adolescents, aged 11-14 years, from the Finnish Health in Teens (Fin-HIT) study cohort were included in this study. Eating habits and breakfast and dinner patterns were derived from a web-based questionnaire answered in school. Three major eating habit groups were identified: fruit and vegetable avoiders (FV avoiders), healthy and unhealthy. Microbiota profiles were produced from 16S rRNA gene (V3-V4) sequencing of DNA from the saliva samples. Statistical models were adjusted for gender, age, parental language, body mass index (BMI) categories, and sequencing depth.

RESULTS

Regular breakfast eaters had a higher alpha diversity (Shannon index with mean (standard error of means) 2.27 (0.03) vs. 2.22 (0.03), p = 0.06, inverse Simpson's index with 6.27 (0.17) vs. 5.80 (0.02), p = 0.01), and slight differences in bacterial composition (PERMANOVA: p = 0.001) compared with irregular breakfast eaters. A similar trend in alpha diversity was observed between regular and irregular dinner eaters (Shannon index with 2.27 (0.03) vs. 2.22 (0.03), p = 0.054, inverse Simpson's index with 6.23 (0.17) vs. 6.04 (0.22), p = 0.28), while no difference was found in composition (PERMANOVA: p = 0.08). No differences were identified between eating habit groups and saliva microbiota diversity (Shannon index p = 0.77, inverse Simpson's index p = 0.94) or composition (PERMANOVA: p = 0.13). FV avoiders, irregular breakfast eaters and irregular dinner eaters had high abundances of Prevotella.

CONCLUSION

Regularity of eating, especially breakfast eating, was associated with more diverse saliva microbiota and different composition compared with irregular eaters. However, the dissimilarities in composition were small between regular and irregular breakfast eaters. Our results suggest that Prevotella abundances in saliva were common in FV avoiders and meal skippers. However, the clinical implications of these findings need to be evaluated in future studies.

Profiling the Salivary microbiome of the Qatari population

BACKGROUND

The role of the human microbiome in human health and disease has been studied in various body sites. However, compared to the gut microbiome, where most of the research focus is, the salivary microbiome still bears a vast amount of information that needs to be revealed. This study aims to characterize the salivary microbiome composition in the Qatari population, and to explore specific microbial signatures that can be associated with various lifestyles and different oral conditions.

MATERIALS AND METHODS

We characterized the salivary microbiome of 997 Qatari adults using high-throughput sequencing of the V1-V3 region of the 16S rRNA gene.

RESULTS

In this study, we have characterized the salivary microbiome of 997 Qatari participants. Our data show that Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria are the common phyla isolated from the saliva samples, with Bacteroidetes being the most predominant phylum. Bacteroidetes was also more predominant in males versus females in the study cohort, although differences in the microbial diversity were not statistically significant. We also show that, a lower diversity of the salivary microbiome is observed in the elderly participants, with Prevotella and Treponema being the most significant genera. In participants with oral conditions such as mouth ulcers, bleeding or painful gum, our data show that Prevotella and Capnocytophaga are the most dominant genera as compared to the controls. Similar patterns were observed in participants with various smoking habits as compared to the non-smoking participants. Our data show that Streptococcus and Neisseria are more dominant among denture users, as compared to the non-denture users. Our data also show that, abnormal oral conditions are associated with a reduced microbial diversity and microbial richness. Moreover, in this study we show that frequent coffee drinkers have higher microbial diversity compared to the non-drinkers, indicating that coffee may cause changes to the salivary microbiome. Furthermore, tea drinkers show higher microbial richness as compared to the non-tea drinkers.

CONCLUSION

This is the first study to assess the salivary microbiome in an Arab population, and one of the largest population-based studies aiming to the characterize the salivary microbiome composition and its association with age, oral health, denture use, smoking and coffee-tea consumption.

Shifts in the bacterial community of saliva give insights on the relationship between obesity and oral microbiota in adolescents

The current study aimed at the determination of the impact of obesity on the salivary microbiome in adolescents. Sixty subjects ranging 14-17 years old were enrolled (obese: n = 30-50% females, and normal weight: n = 30-50% females). Stimulated saliva was collected for denaturing gradient gel electrophoresis (DGGE) band patterns and massive 16S rRNA gene sequencing using the Ion Torrent platform. Overall, data analysis revealed that male subjects harbored a higher diverse salivary microbiome, defined by a significant higher richness (32.48 versus 26.74) and diversity (3.36 versus 3.20), higher Simpson values (0.96 versus 0.95) and distinct bacterial community structure considering either sex or condition (p < 0.05). Bacterial community fingerprinting analysis in human saliva showed a positive correlation with increased body mass index (BMI) in adolescents. Veillonella, Haemophilus and Prevotella occurrence was found to be affected by BMI, whereas Neisseria and Rothia occurrence was significantly impacted by sex in obese subjects. Our findings suggest that male and female adolescents may harbor a naturally distinct salivary microbiota and that obesity may specifically have an impact on their oral bacterial community. The potential dysbiotic oral microbiome in obese adolescents raises new insights on the etiology and prevention of future conditions in these populations.

Salivary Microbiological and Gingival Health Status Evaluation of Adolescents With Overweight and Obesity: A Cluster Analysis

Given the high prevalence of obesity in children and adolescents, the investigation of early markers is of clinical importance to better manage this condition. Thus, the aim was to evaluate the cross-sectional relationship between salivary microbiota, gingival health status, and excess weight in adolescents. A total of 248 students (14-17 y; 119 girls) were included, free of caries lesions and periodontal pockets. Physical examination included measures of height, weight, and body fat percentage (%BF). Oral examination was performed to gather information on dental (DMFT index) and gingival health status. Unstimulated saliva was submitted to qPCR reactions to quantify Streptococcus mutans, Porphyromonas gingivalis, Bifidobacteria, and Streptococcus pneumoniae percentages and the NFKappaB expression. Two-way ANOVA was applied considering group (normal-weight/overweight/obesity) and sex factors, in addition to cluster analysis. Group effect was significant for %S. mutans (partial eta² = 0.20; p < 0.001) and %Bifidobacteria (partial eta² = 0.19; p < 0.001), with overweight and obesity groups showing the highest levels compared to normal-weight ones, with no significant sex effect. There was no difference in the frequency of gingivitis, P. gingivalis, and S. pneumoniae percentages or NFKappaB expression between groups. Cluster analysis generated three clusters according to body fat accumulation: "Higher %BF," "Moderate %BF," and "Lower %BF." "Higher %BF" cluster was characterized by higher body fat percentage and higher salivary %Bifidobacteria, while cluster "Lower %BF" was characterized by lower body fat percentage and lower frequency of gingivitis ("Moderate %BF" cluster was the contrast). According to nutritional status, a difference in salivary S. mutans and Bifidobacteria percentages was found, with overweight or obesity adolescents showing the highest percentages than normal-weight ones. Besides, a positive relationship between body fat accumulation and Bifidobacteria count was observed, indicating a possible interaction between oral bacteria communities and weight gain.

Bacterial salivary microbiome associates with asthma among african american children and young adults

Several studies have shown that the airways of asthma patients contain higher diversity of bacteria and are enriched in pathogenic species. However, sampling the airways in children is challenging. Here we aimed to identify differences in the salivary bacterial composition between African Americans children with and without asthma. Saliva samples from 57 asthma cases and 57 healthy controls were analyzed by means of 16S ribosomal RNA amplicon profiling. Measurements of bacterial diversity and genus relative abundance were compared between cases and controls using the nonparametric Wilcoxon test and multivariate regression models. A total of five phyla and a mean of 56 genera were identified. Among them, 15 genera had a relative abundance greater than 1%, being Prevotella, Haemophilus, Streptococcus, and Veillonella the most abundant genera. Differences between cases and controls were found in terms of diversity, as well as in relative abundance for Streptococcus genus (13.0% in cases vs 18.3% in controls; P = .003) and Veillonella genus (11.1% in cases vs 8.0% in controls; P = .002). These differences remained significant after correction for multiple comparisons and when potential confounders were taken into account in logistic regression models. In conclusion, we identified changes in the salivary microbiota associated with asthma among African Americans.

The microbiome and cancer for clinicians

The human microbiome is an emerging target in cancer development and therapeutics. It may be directly oncogenic, through promotion of mucosal inflammation or systemic dysregulation, or may alter anti-cancer immunity/therapy. Microorganisms within, adjacent to and distant from tumors may affect cancer progression, and interactions and differences between these populations can influence the course of disease. Here we review the microbiome as it pertains to cancer for clinicians. The microbiota of cancers including colorectal, pancreas, breast and prostate are discussed. We examine "omics" technologies, microbiota associated with tumor tissue and tumor-site fluids such as feces and urine, as well as indirect effects of the gut microbiome. We describe roles of the microbiome in immunotherapy, and how it can be modulated to improve cancer therapeutics. While research is still at an early stage, there is potential to exploit the microbiome, as modulation may increase efficacy of treatments, reduce toxicities and prevent carcinogenesis.

Metaproteomics analysis of microbial diversity of human saliva and tongue dorsum in young healthy individuals

Background: The human oral microbiome influences initiation or progression of diseases like caries or periodontitis. Metaproteomics approaches enable the simultaneous investigation of microbial and host proteins and their interactions to improve understanding of oral diseases.

Objective: In this study, we provide a detailed metaproteomics perspective of the composition of salivary and tongue microbial communities of young healthy subjects.

Design: Stimulated saliva and tongue samples were collected from 24 healthy volunteers, subjected to shotgun nLC-MS/MS and analyzed by the Trans-Proteomic Pipeline and the Prophane tool.

Results: 3,969 bacterial and 1,857 human proteins could be identified from saliva and tongue, respectively. In total, 1,971 bacterial metaproteins and 1,154 human proteins were shared in both sample types. Twice the amount of bacterial metaproteins were uniquely identified for the tongue dorsum compared to saliva. Overall, 107 bacterial genera of seven phyla formed the microbiome. Comparative analysis identified significant functional differences between the microbial biofilm on the tongue and the microbiome of saliva.

Conclusion: Even if the microbial communities of saliva and tongue dorsum showed a strong similarity based on identified protein functions and deduced bacterial composition, certain specific characteristics were observed. Both microbiomes exhibit a great diversity with seven genera being most abundant.