Biocultural Drivers of Salivary Microbiota in Australian Aboriginal and Torres Strait Islander Children

Characterising healthy Australian oral microbiomes for 'super donor' selection

OBJECTIVES

Among healthy people, we understand very little about the sociodemographic, lifestyle, and dental hygiene behaviours that shape their oral microbiota. This study investigates how sociodemographic, lifestyle and dental hygiene behaviours shape oral microbiota diversity and composition in an Australian population to better inform healthy oral microbiota donors for Oral Microbiota Transplantation (OMT).

METHODS

The study comprised 93 healthy adults who underwent comprehensive oral examinations and questionnaires to assess their health status. Participants were excluded if they had any active systemic or oral disease. All completed a questionnaire containing information on socio-economic, lifestyle, behavioural, and oral health factors. Supragingival plaque was collected, and 16S ribosomal RNA (rRNA) amplicon sequencing was used to analyse microbial composition. Associations between the core microbiome, alpha- (within-sample), beta-diversity (between-sample) and an individual's co-variates were tested for statistical significance. A redundancy analysis (RDA), multivariate adonis, differential abundance and correlation analysis were performed to characterise which factors drive the variation in the healthy oral microbiome.

RESULTS

Streptococcus and Corynebacterium were the most prevalent and abundant genera among healthy Australians. The alpha and beta diversity were higher among unemployed non-Australian-born students who consumed low carbohydrates, fat, and sugar and had not visited the dentist for over 12 months. Additionally, beta diversity was significantly higher among daily flossers who abstained from fluoride treatment and had high salivary pH, although no single factor explained >4 % of the total variation (R2= 0.042). Alloprevotella, Lachnosporacea, and Parvimonas were significantly abundant among non-Australians who did not visit the dentist within a year. The RDA analysis revealed associations between microbiome composition and factors such as high carbohydrate, sugar, and fat consumption, low fibre intake, and regular dental checks among Australian-born individuals.

CONCLUSION

These findings indicate that alpha and beta diversity of the oral microbiome varied significantly with sociodemographic, lifestyle, and dietary factors, including non-Australian birthplaces, unemployment, diet, and infrequent dental visits.

CLINICAL SIGNIFICANCE

These findings underscore the importance of considering diverse sociodemographic, lifestyle, and dietary factors in oral health management. Before microbiome transplantations, clinicians should account for individual characteristics that may be beneficial for shaping and maintaining optimal oral microbiome diversity and health.

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 remain 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 USA 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 sources.

CONCLUSION

Our findings demonstrate that by studying populations within Nepal, we can isolate an important role of 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. Video Abstract.

Supragingival Plaque Microbiomes in a Diverse South Florida Population

Trillions of microbes comprise the human oral cavity, collectively acting as another bodily organ. Although research is several decades into the field, there is no consensus on how oral microbiomes differ in underrepresented groups such as Hispanic, Black, and Asian populations living in the United States. Here, using 16S ribosomal RNA sequencing, we examine the bacterial ecology of supragingival plaque from four quadrants of the mouth along with a tongue swab from 26 healthy volunteers from South Florida (131 total sequences after filtering). As an area known to be a unique amalgamation of diverse cultures from across the globe, South Florida allows us to address the question of how supragingival plaque microbes differ across ethnic groups, thus potentially impacting treatment regiments related to oral issues. We assess overall phylogenetic abundance, alpha and beta diversity, and linear discriminate analysis of participants based on sex, ethnicity, sampling location in the mouth, and gingival health. Within this cohort, we find the presence of common phyla such as Firmicutes and common genera such as Streptococcus. Additionally, we find significant differences across sampling locations, sex, and gingival health. This research stresses the need for the continued incorporation of diverse populations within human oral microbiome studies.

Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries

Early childhood caries (ECC) is influenced by microbial and host factors, including social, behavioral, and oral health. In this cross-sectional study, we analyze interkingdom dynamics in the dental plaque microbiome and its association with host variables. We use 16S rRNA and ITS1 amplicon sequencing on samples collected from preschool children and analyze questionnaire data to examine the social determinants of oral health. The results indicate a significant enrichment of Streptococcus mutans and Candida dubliniensis in ECC samples, in contrast to Neisseria oralis in caries-free children. Our interkingdom correlation analysis reveals that Candida dubliniensis is strongly correlated with both Neisseria bacilliformis and Prevotella veroralis in ECC. Additionally, ECC shows significant associations with host variables, including oral health status, age, place of residence, and mode of childbirth. This study provides empirical evidence associating the oral microbiome with socioeconomic and behavioral factors in relation to ECC, offering insights for developing targeted prevention strategies.

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study

AIM

The oral microenvironment contributes to microbial composition and immune equilibrium. It is considered to be influenced by dietary habits. Phenylketonuria (PKU) patients, who follow a lifelong low-protein diet, exhibit higher prevalence of oral diseases such as periodontitis, offering a suitable model to explore the interplay between diet, oral microbiota and oral health.

MATERIALS AND METHODS

We conducted 16S rDNA sequencing on saliva and subgingival plaque from 109 PKU patients (ages 6-68 years) and 114 age-matched controls and correlated oral microbial composition and dental health.

RESULTS

PKU patients exhibited worse dental health, reduced oral microbial diversity and a difference in the abundance of specific taxa, especially Actinobacteriota species, compared to controls. PKU patients with poor periodontal health exhibited higher alpha diversity than the orally healthy ones, marked by high abundance of the genus Tannerella. Notably, the observed taxonomic differences in PKU patients with normal indices of decayed/missing/filled teeth, plaque control record, gingival bleeding index and periodontal screening and recording index generally differed from microbial signatures of periodontitis.

CONCLUSIONS

PKU patients' reduced microbial diversity may be due to their diet's metabolic challenges disrupting microbial and immune balance, thus increasing oral inflammation. Higher alpha diversity in PKU patients with oral inflammation is likely related to expanded microbial niches.

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.

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries

BACKGROUND

Oral microbiome sequencing has revealed key links between microbiome dysfunction and dental caries. However, these efforts have largely focused on Western populations, with few studies on the Middle Eastern communities. The current study aimed to identify the composition and abundance of the oral microbiota in saliva samples of children with different caries levels using machine learning approaches.

METHODS

Oral microbiota composition and abundance were identified in 250 Saudi participants with high dental caries and 150 with low dental caries using 16 S rRNA sequencing on a NextSeq 2000 SP flow cell (Illumina, CA) using 250 bp paired-end reads, and attempted to build a classifier using random forest models to assist in the early detection of caries.

RESULTS

The ADONIS test results indicate that there was no significant association between sex and Bray-Curtis dissimilarity (p ~ 0.93), but there was a significant association with dental caries status (p ~ 0.001). Using an alpha level of 0.05, five differentially abundant operational taxonomic units (OTUs) were identified between males and females as the main effect along with four differentially abundant OTUs between high and low dental caries. The mean metrics for the optimal hyperparameter combination using the model with only differentially abundant OTUs were: Accuracy (0.701); Matthew's correlation coefficient (0.0509); AUC (0.517) and F1 score (0.821) while the mean metrics for random forest model using all OTUs were:0.675; 0.054; 0.611 and 0.796 respectively.

CONCLUSION

The assessment of oral microbiota samples in a representative Saudi Arabian population for high and low metrics of dental caries yields signatures of abundances and diversity.

Heritage-specific oral microbiota in Indigenous Australian dental calculus

Background and objectives

Aboriginal Australians and Torres Strait Islanders (hereafter respectfully referred to as Indigenous Australians) experience a high burden of chronic non-communicable diseases (NCDs). Increased NCD risk is linked to oral diseases mediated by the oral microbiota, a microbial community influenced by both vertical transmission and lifestyle factors. As an initial step towards understanding the oral microbiota as a factor in Indigenous health, we present the first investigation of oral microbiota in Indigenous Australian adults.

Methodology

Dental calculus samples from Indigenous Australians with periodontal disease (PD; n = 13) and non-Indigenous individuals both with (n = 19) and without PD (n = 20) were characterized using 16S ribosomal RNA gene amplicon sequencing. Alpha and beta diversity, differentially abundant microbial taxa and taxa unique to different participant groups were analysed using QIIME2.

Results

Samples from Indigenous Australians were more phylogenetically diverse (Kruskal–Wallis H = 19.86, P = 8.3 × 10−6), differed significantly in composition from non-Indigenous samples (PERMANOVA pseudo-F = 10.42, P = 0.001) and contained a relatively high proportion of unique taxa not previously reported in the human oral microbiota (e.g. Endomicrobia). These patterns were robust to stratification by PD status. Oral microbiota diversity and composition also differed between Indigenous individuals living in different geographic regions.

Conclusions and implications

Indigenous Australians may harbour unique oral microbiota shaped by their long relationships with Country (ancestral homelands). Our findings have implications for understanding the origins of oral and systemic NCDs and for the inclusion of Indigenous peoples in microbiota research, highlighting the microbiota as a novel field of enquiry to improve Indigenous health.

Predicting dental caries increment using salivary biomarkers in a remote Indigenous Australian child population

BACKGROUND

The burden of childhood dental caries amongst Indigenous Australians is higher than in other Australians. Because of differences in lifestyle and the evolutionary history of the oral microbiota, associated risk indicators may differ. Here, we evaluate associations between caries increment, salivary biomarkers and baseline caries among children aged 5-17 years residing in a remote rural Indigenous community.

METHODS

This study was part of a trial assessing cost-effectiveness of an intervention to prevent dental caries among children. Baseline epidemiology and application of topical caries-preventive measures was conducted in 2015, followed-up in 2016 and 2017. Children who did not consent or failed to attend the prevention visits but did attend for follow-up epidemiology constituted a natural comparison group for evaluating the intervention. Saliva flow, pH, buffering and bacterial loads were measured at all visits. Caries was scored by the International Caries Detection and Assessment system. Outcome was caries increment. Explanatory variables were sex, being in experimental or comparison group, baseline caries, saliva flowrate and buffering, pH, and salivary loads of mutans streptococci (MS), Lactobacilli (LB), and yeast. Chi Square tests compared caries incidence in relation to explanatory variables and Generalised Linear Models explored associations between explanatory and outcome variables.

RESULTS

Of 408 participants at baseline, only 208 presented at 2-year follow-up. Of caries-free children at baseline, significantly fewer had incipient (p = 0.01) and advanced (p = 0.04) caries after two years. Children in the experimental group experienced fewer tooth surfaces with advanced caries (p = 0.02) than comparison children. Having caries at baseline (p = 0.02) and low salivary flow-rates (p < 0.001) saw a significant increase in advanced caries after two years. Children with high salivary loads of MS (p = 0.03) and LB (p = 0.004) experienced more advanced carious surfaces. Multivariable analysis revealed 58% reduction (p = 0.001) in advanced caries among children with high salivary flow rates. Caries increment was 61% (p = 0.03) more for incipient and 121% (p = 0.007) more for advanced caries among children who harboured higher loads of MS.

CONCLUSION

As with other ethnicities, children with low salivary flow and those with high MS had higher incipient and advanced caries increments after two years. Such risk assessments facilitate targeted preventive interventions for such communities.

TRIAL REGISTRATION

Australian New Zealand Clinical Trials Registry (ANZCTR), No: ACTRN12615000693527: 3 July 2015.