Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study

Integrating microbiome, transcriptome and metabolome data to investigate gastric disease pathogenesis: a concise review

Microbiome, the study of microbial communities in specific environments, has developed significantly since the Human Microbiome Project began. Microbiomes have been associated with changes within environmental niches and the development of various diseases. The development of high-throughput technology such as next-generation sequencing has also allowed us to perform transcriptome studies, which provide accurate functional profiling data. Metabolome studies, which analyse the metabolites found in the environment, are the most direct environmental condition indicator. Although each dataset provides valuable information on its own, the integration of multiple datasets provides a deeper understanding of the relationship between the host, agent and environment. Therefore, network analysis using multiple datasets might give a clearer understanding of disease pathogenesis.

Healthy Oral Lifestyle Behaviours Are Associated with Favourable Composition and Function of the Oral Microbiota

Modifiable lifestyle interventions may influence dental disease by shifting the composition of the oral microbiota. This study aimed to test whether lifestyle traits are associated with oral microbiota composition and function. Swedish volunteers, aged 16 to 79 years, completed a lifestyle traits questionnaire including lifestyle characteristics and oral health behaviours. Bacterial 16S rDNA amplicons were sequenced and classified into genera and species, using salivary DNA. Microbiota functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and the KO Database of Molecular Functions by ortholog annotation. Tests for association used partial least squares and linear regression analysis with correction for multiple testing. The main analysis included 401 participants and 229 common bacterial species (found in ≥10% of the participants). The overall microbiota composition was strongly associated with questions "do you think caries is a disease?" and "do you use floss or a toothpick?". Enriched relative abundance of Actinomyces, Campylobacter, Dialister, Fusobacterium, Peptidophaga and Scardovia genera (all p < 0.05 after adjustment for multiple testing), and functional profiles showing enrichment of carbohydrate related functions, were found in participants who answered "no" to these questions. Socio-demographic traits and other oral hygiene behaviours were also associated. Healthier oral microbiota composition and predicted functions are found in those with favourable oral health behaviours. Modifiable risk factors could be prioritized for possible interventions.

At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics

Microbial forensics represents a promising tool to strengthen traditional forensic investigative methods and fill related knowledge gaps. Large-scale microbiome studies indicate that microbial fingerprinting can assist forensics in areas such as trace evidence, source tracking, geolocation, and circumstances of death. Nevertheless, the majority of forensic microbiome studies focus on soil and internal organ samples, whereas the microbiome of skin, mouth, and especially vaginal samples that are routinely collected in sexual assault and femicide cases remain underexplored. This review discusses the current and emerging insights into vaginal, skin, and salivary microbiome-modulating factors during life (e.g., lifestyle and health status) and after death (e.g., environmental influences and post-mortem interval) based on next-generation sequencing. We specifically highlight the key aspects of female reproductive tract, skin, and mouth microbiome samples relevant in forensics. To fill the current knowledge gaps, future research should focus on the degree to which the post-mortem succession rate and profiles of vaginal, skin, and saliva microbiota are sensitive to abiotic and biotic factors, presence or absence of oxygen and other gases, and the nutrient richness of the environment. Application of this microbiome-related knowledge could provide valuable complementary data to strengthen forensic cases, for example, to shed light on the circumstances surrounding death with (post-mortem) microbial fingerprinting. Overall, this review synthesizes the present knowledge and aims to provide a framework to adequately comprehend the hurdles and potential application of vaginal, skin, and salivary post-mortem microbiomes in forensic investigations.

Estimating the Time Since Deposition of Saliva Stains With a Targeted Bacterial DNA Approach: A Proof-of-Principle Study

Information on the time when a stain was deposited at a crime scene can be valuable in forensic investigations. It can link a DNA-identified stain donor with a crime or provide a post-mortem interval estimation in cases with cadavers. The available methods for estimating stain deposition time have limitations of different types and magnitudes. In this proof-of-principle study we investigated for the first time the use of microbial DNA for this purpose in human saliva stains. First, we identified the most abundant and frequent bacterial species in saliva using publicly available 16S rRNA gene next generation sequencing (NGS) data from 1,848 samples. Next, we assessed time-dependent changes in 15 identified species using de-novo 16S rRNA gene NGS in the saliva stains of two individuals exposed to indoor conditions for up to 1 year. We selected four bacterial species, i.e., Fusobacterium periodonticum, Haemophilus parainfluenzae, Veillonella dispar, and Veillonella parvula showing significant time-dependent changes and developed a 4-plex qPCR assay for their targeted analysis. Then, we analyzed the saliva stains of 15 individuals exposed to indoor conditions for up to 1 month. Bacterial counts generally increased with time and explained 54.9% of the variation (p = <2.2E–16). Time since deposition explained ≥86.5% and ≥88.9% of the variation in each individual and species, respectively (p = <2.2E–16). Finally, based on sample duplicates we built and tested multiple linear regression models for predicting the stain deposition time at an individual level, resulting in an average mean absolute error (MAE) of 5 days (ranging 3.3–7.8 days). Overall, the deposition time of 181 (81.5%) stains was correctly predicted within 1 week. Prediction models were also assessed in stains exposed to similar conditions up to 1 month 7 months later, resulting in an average MAE of 8.8 days (ranging 3.9–16.9 days). Our proof-of-principle study suggests the potential of the DNA profiling of human commensal bacteria as a method of estimating saliva stains time since deposition in the forensic scenario, which may be expanded to other forensically relevant tissues. The study considers practical applications of this novel approach, but various forensic developmental validation and implementation criteria will need to be met in more dedicated studies in the future.

Subgingival microflora in adolescent females with polycystic ovary syndrome and its association with oral hygiene, gingivitis, and selected metabolic and hormonal parameters

OBJECTIVES

Research studies suggest that polycystic ovary syndrome (PCOS) may influence the composition of the oral microflora in women. This study aimed to investigate factors affecting the number of selected periopathogens in a young cohort of females with PCOS and to assess the association between oral hygiene, subgingival microbiome, gingival health, and metabolic and hormonal parameters.

MATERIALS AND METHODS

Thirty-two subjects with PCOS and twenty-three healthy controls aged 15-19 years were examined periodontally by a calibrated dentist. A real-time PCR method was used for the identification of 9 subgingival microorganisms. Subjects with PCOS underwent blood tests for determination of FSH, LH, total testosterone, DHEA-S, estradiol, SHBG, fasting glucose, fasting insulin, and lipid profile.

RESULTS

Gingival index (GI), the proportion of bleeding sites (BOP%), probing depth (PD), and plaque index (PLI) did not differ significantly between cases and healthy age-mates. The control group had significantly higher levels of Peptostreptococcus micros and substantially greater percentage of subjects infected by Treponema denticola. Capnocytophaga gingivalis count was positively correlated with the level of estradiol, while the concentration of HDL-C was negatively correlated with the number of Aggregatibacter actinomycetemcomitans and orange complex bacteria.

CONCLUSIONS

PCOS in young patients was not associated with higher pathogenicity of subgingival biofilms.

CLINICAL RELEVANCE

Further studies are needed to explain the relationship between hormonal and metabolic abnormalities, subgingival microflora, and periodontal health in patients with PCOS.

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.

Baseline Oral Microbiome and All-cancer Incidence in a Cohort of Nonsmoking Mexican American Women

Given the increasing evidence that the oral microbiome is involved in obesity, diabetes, and cancer risk, we investigated baseline oral microbiota profiles in relation to all-cancer incidence among nonsmoking women enrolled in a Texas cohort of first- and second-generation immigrants of Mexican origin. We characterized the 16Sv4 rDNA microbiome in oral mouthwash samples collected at baseline from a representative subset of 305 nonsmoking women, ages 20-75 years. We evaluated within- (alpha) and between-sample (beta) diversity by incident cancer status and applied linear discriminant analysis (LDA) effect size analysis to assess differentially abundant taxa. Diversity and candidate taxa in relation to all-cancer incidence were evaluated in multivariable-adjusted Cox regression models. Over 8.8 median years of follow-up, 31 incident cancer cases were identified and verified. Advanced age, greater acculturation, and cardiometabolic risk factors were associated with all-cancer incidence. Higher alpha diversity (age-adjusted P _difference < 0.01) and distinct biological communities (P _difference = 0.002) were observed by incident cancer status. Each unit increase in the Shannon diversity index yielded >8-fold increase in all-cancer and obesity-related cancer risk [multivariable-adjusted HR (95% confidence interval), 8.11 (3.14-20.94) and 10.72 (3.30-34.84), respectively] with similar findings for the inverse Simpson index. Streptococcus was enriched among women who did not develop cancer, while Fusobacterium, Prevotella, Mogibacterium, Campylobacter, Lachnoanaerobaculum, Dialister, and Atopobium were higher among women who developed cancer (LDA score ≥ 3; q-value < 0.01). This initial study of oral microbiota and overall cancer risk in nonsmoking Mexican American women suggests the readily accessible oral microbiota as a promising biomarker. PREVENTION RELEVANCE: Mexican American women suffer a disproportionate burden of chronic health conditions that increase cancer risk. Few investigations of the microbiome, a key determinant of host health, have been conducted among this group. Oral microbiota profiles may provide early and accessible cancer biomarker data on invasive bacteria or community disruptions.

The water chemistry and microbiome of household wells in Medawachchiya, Sri Lanka, an area with high prevalence of chronic kidney disease of unknown origin (CKDu)

Chronic kidney disease (CKD) of unknown etiology (CKDu) mostly affects agricultural communities in Central America, South Asia, Africa, but likely also in North America and Australia. One such area with increased CKDu prevalence is the Medawachchiya District Secretariat Division of the Anuradhapura District in the North Central Province of Sri Lanka. Recent research has focused on the presence of various microbial pathogens in drinking water as potential causal or contributing factors to CKDu, yet no study to date has performed a more comprehensive microbial and water chemistry assessment of household wells used for domestic water supply in areas of high CKDu prevalence. In this study, we describe the chemical composition and total microbial content in 30 domestic household wells in the Medawachchiya District Secretariat Division. While the chemical composition in the tested wells mostly lies within standard drinking water limits, except for high levels of fluoride (F), magnesium (Mg), sodium (Na), chloride (Cl) and calcium (Ca) in some samples, we find a frequent presence of cyanotoxin-producing Microcystis, confirming earlier studies in Sri Lanka. Since the total microbial content of drinking water also directly influences the composition of the human gut microbiome, it can be considered an important determinant of health. Several bacterial phyla were previously reported in the gut microbiome of patients with CKD. Using these bacteria phyla to define operational taxonomic units, we found that these bacteria also occur in the microbiome of the sampled well water. Based on available environmental data, our study demonstrates associations between the abundances of these bacteria with geographical distribution, well water temperature and likely fertilizer use in the local surface water catchment area of the individual household wells. Our results reinforce the recommendation that household wells with stagnant or infrequently used water should be purged prior to use for drinking water, bathing and irrigation. The latter is suggested because of the reported potential accumulation of bacterial toxins by agricultural crops. The observation that bacteria previously found in chronic kidney disease patients are also present in household wells requires a more detailed systematic study of both the human gut and drinking water microbiomes in CKDu patients, in relation to disease prevalence and progression.

Isolation and Identification of Potentially Pathogenic Microorganisms Associated with Dental Caries in Human Teeth Biofilms

Dental caries is attributed to the predominance of cariogenic microorganisms. Cariogenic microorganisms are pathological factors leading to acidification of the oral microenvironment, which is related to the initiation and progression of caries. The accepted cariogenic microorganism is Streptococcus mutans (S. mutans). However, studies have found that caries could occur in the absence of S. mutans. This study aimed to assess the presence of potentially cariogenic microorganisms in human teeth biofilm. The microorganisms were isolated from human mouth and freshly extracted human maxillary incisors extracted for reasons of caries. The isolates were sorted based on their acidogenic and aciduric properties, and the S. mutans was used as the reference strain. Four potentially cariogenic strains were selected. The selected strains were identified as Streptococcus salivarius (S. salivarius), Streptococcus anginosus (S. anginosus), Leuconostoc mesenteroides (L. mesenteroides), and Lactobacillus sakei (L. sakei) through morphological analysis followed by 16S rRNA gene sequence analysis. The cariogenicity of isolates was analyzed. We show, for the first time, an association between L. sakei (present in fermented food) and dental caries. The data provide useful information on the role of lactic acid bacteria from fermented foods and oral commensal streptococci in dental caries.

The Oral Microbiome of Healthy Japanese People at the Age of 90

For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. Pyrosequencing was performed using MiSeq. Operational taxonomic units (OTUs) were assigned on the basis of a 97% identity search in the EzTaxon-e database. Using the threshold of 100% detection on the species level, 13 species were detected: Streptococcus sinensis, Streptococcus pneumoniae, Streptococcus salivarius, KV831974_s, Streptococcus parasanguinis, Veillonella dispar, Granulicatella adiacens, Streptococcus_uc, Streptococcus peroris, KE952139_s, Veillonella parvula, Atopobium parvulum, and AFQU_vs. These species represent potential candidates for the core make-up of the human microbiome.

Oral Candida albicans colonization in healthy individuals: prevalence, genotypic diversity, stability along time and transmissibility

In this study, 181 healthy individuals, including 29 couples, were analysed regarding oral yeast colonization using a culture-based approach. Results showed that 39% of the individuals were yeast carriers, 89% being colonized with Candida albicans, 5% with C. guilliermondi, 3% with C. lusitaniae and 3% with C. parapsilosis. Sixty-two percent of the couples had at least one member colonized. Colonization and CFU counts were higher in the couples´ group. Eighty percent of the volunteers were colonized with C. albicans strains with only one CAI genotype, while two but similar CAI genotypes inhabited the oral cavity of the remaining 20% individuals. The same CAI genotypes were found in 66.6% of the couples when both were colonized. Our results indicate that the intimacy among couples increases the probability of heavy cross-colonization, which is potentiated when one member of the couple is a smoker.

The Genomics and Metagenomics of Asthma Severity (GEMAS) Study: Rationale and Design

Asthma exacerbations are a major contributor to the global disease burden, but no significant predictive biomarkers are known. The Genomics and Metagenomics of Asthma Severity (GEMAS) study aims to assess the role of genomics and the microbiome in severe asthma exacerbations. Here, we present the design of GEMAS and the characteristics of patients recruited from March 2018 to March 2020. Different biological samples and demographic and clinical variables were collected from asthma patients recruited by allergy and pulmonary medicine units in several hospitals from Spain. Cases and controls were defined by the presence/absence of severe asthma exacerbations in the past year (oral corticosteroid use, emergency room visits, and/or asthma-related hospitalizations). A total of 137 cases and 120 controls were recruited. After stratifying by recruitment location (i.e., Canary Islands and Basque Country), cases and controls did not differ for most demographic and clinical variables (p > 0.05). However, cases showed a higher proportion of characteristics inherent to asthma exacerbations (impaired lung function, severe disease, uncontrolled asthma, gastroesophageal reflux, and use of asthma medications) compared to controls (p < 0.05). Similar results were found after stratification by recruitment unit. Thereby, asthma patients enrolled in GEMAS are balanced for potential confounders and have clinical characteristics that support the phenotype definition. GEMAS will improve the knowledge of potential biomarkers of asthma exacerbations.

Oral Microbiome in Four Female Centenarians

The oral microbiome of healthy older adults has valuable information about a healthy microbiome. In this study, we collected and analyzed the oral microbiome of denture plaque and tongue coating samples from four female centenarians. After DNA extraction and purification, pyrosequencing of the V3–V4 hypervariable regions of the 16S rRNA was carried out. The bacterial taxonomy for each lead was assigned based on a search of the EzBioCloud 16S database. We obtained a total of 199,723 valid, quality-controlled reads for denture plaque and 210,750 reads for tongue coating. The reads were assigned 407 operational taxonomic units with a 97% identity cutoff. Twenty-nine species were detected in both denture plaque and tongue coatings from all subjects. Firmicutes was the most abundant phylum; the Streptococcus salivarius group was the most abundant species in both the denture plaque and tongue coatings; and the Fusobacterium nucleatum group was detected in all subjects. In the bacterial profile, species formed clusters composed of bacteria with a wide range of prevalence and abundance, not dependent on phyla; each cluster may have specific species that could be candidates for a core microbiome. Firmicutes and Veillonella were abundant phyla on both plaque and tongue coatings of centenarians.

Patients With Reflux Esophagitis Possess a Possible Different Oral Microbiota Compared With Healthy Controls

Background and Aim

Reflux Esophagitis (RE) is caused by a variety of factors including anatomical and functional alterations involved in the pathogenesis. Oral microbiota is influenced by many factors such as heredity, nutrition, environments and host conditions, but little is known about relationship between oral microbiota and RE. The aim of this study was to explore whether the oral microbiota is changed in patients with RE.

Methods

To clarify this correlation, fresh saliva samples from all subjects were collected and then oral microorganism diversity was analysed in 55 patients with RE and 51 controls via hypervariable tag sequencing and analyzing the V3–V4 region of the 16S rDNA gene.

Results

There was no difference found in oral microbial diversity between RE patients and healthy controls by Shannon diversity index (p=0.60) and Simpson diversity index (p= 0.38). The abundance of Proteobacteria was lower, but Bacteroidetes was higher in patients with RE at the phylum level. At the genus level the abundances of Prevotella, Veillonella, Megasphaera, Peptostreptococcus, Atopobium, Oribacterium, Eubacterium, and Lachnoanaerobaculum were increased, while Neisseria, Streptococcus, Rothia, Granulicatella, Gemella, Aggregatibacter, Treponema, Campylobacter, Filifactor, Corynebacterium, and Lactivibrio were decreased in RE patients than the controls.

Conclusions

Our study suggested oral microbial dysbiosis in patients with RE, and identified bacterial species with potential biomarker significance. Further studies are required to understand role of oral microbial dysbiosis in the pathogenesis of RE.

Salivary metabolites to detect patients with cancer: a systematic review

Novel adjunctive screening aids are needed to reduce the morbidity and mortality related to cancer, and every effort should be made for early diagnosis. This systematic review aimed to evaluate salivary metabolites and their diagnostic value in patients with cancer.The systematic review was performed in two phases and included studies that focused on the diagnostic value of salivary metabolites in humans with solid malignant neoplasms. Five electronic databases were searched, and the risk of bias in individual studies was evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies criteria (QUADAS-2). All procedures were performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.Of the 1151 studies retrieved, 25 were included; 13 studies used targeted and 12 untargeted metabolomics approaches. Most studies included patients with breast and oral cancer. Except for one, all studies had case-control designs, and none fulfilled all quality assessments. Overall, 140 salivary metabolites were described. The most frequently reported metabolites were alanine, valine, and leucine. Among the 11 studies that reported diagnostic test accuracy (DTA) values, proline, threonine, and histidine in combination and monoacylglycerol alone demonstrated the highest DTA for breast cancer. Combined choline, betaine, pipecolinic acid, and L-carnitine showed better discriminatory performance for early oral cancer.This systematic review highlights the current evidence on salivary metabolites that may be used as a future strategy to diagnose cancer. Further studies including larger sample sizes with confirmation of the results by untargeted analysis are warranted.