Diversity and bias in oral microbiome research: A commentary

Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes

The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.

Ectopic colonization by oral bacteria as an emerging theme in health and disease

The number of research papers published on the involvement of the oral microbiota in systemic diseases has grown exponentially over the last 4 years clearly demonstrating the growing interest in this field. Indeed, accumulating evidence highlights the central role of ectopic colonization by oral bacteria in numerous noncommunicable diseases including inflammatory bowel diseases (IBDs), undernutrition, preterm birth, neurological diseases, liver diseases, lung diseases, heart diseases, or colonic cancer. There is thus much interest in understanding the molecular mechanisms that lead to the colonization and maintenance of ectopic oral bacteria. The aim of this review is to summarize and conceptualize the current knowledge about ectopic colonization by oral bacteria, highlight wherever possible the underlying molecular mechanisms and describe its implication in health and disease. The focus lies on the newly discovered molecular mechanisms, showcasing shared pathophysiological mechanisms across different body sites and syndromes and highlighting open questions in the field regarding the pathway from oral microbiota dysbiosis to noncommunicable diseases.

A relational framework for microbiome research with Indigenous communities

Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.

The Oral, Gut Microbiota and Cardiometabolic Health of Indigenous Orang Asli Communities

The Orang Asli (OA) of Malaysia have been relatively understudied where little is known about their oral and gut microbiomes. As human health is closely intertwined with the human microbiome, this study first assessed the cardiometabolic health in four OA communities ranging from urban, rural to semi-nomadic hunter-gatherers. The urban Temuan suffered from poorer cardiometabolic health while rural OA communities were undergoing epidemiological transition. The oral microbiota of the OA were characterised by sequencing the V4 region of the 16S rRNA gene. The OA oral microbiota were unexpectedly homogenous, with comparably low alpha diversity across all four communities. The rural Jehai and Temiar PP oral microbiota were enriched for uncharacterised bacteria, exhibiting potential for discoveries. This finding also highlights the importance of including under-represented populations in large cohort studies. The Temuan oral microbiota were also elevated in opportunistic pathogens such as Corynebacterium, Prevotella, and Mogibacterium, suggesting possible oral dysbiosis in these urban settlers. The semi-nomadic Jehai gut microbiota had the highest alpha diversity, while urban Temuan exhibited the lowest. Rural OA gut microbiota were distinct from urban-like microbiota and were elevated in bacteria genera such as Prevotella 2, Prevotella 9, Lachnospiraceae ND3007, and Solobacterium. Urban Temuan microbiota were enriched in Odoribacter, Blautia, Parabacetroides, Bacteroides and Ruminococcacecae UCG-013. This study brings to light the current health trend of these indigenous people who have minimal access to healthcare and lays the groundwork for future, in-depth studies in these populations.

A Global Perspective of Racial-Ethnic Inequities in Dental Caries: Protocol of Systematic Review

Though current evidence suggests that racial-ethnic inequities in dental caries persist over time and across space, their magnitude is currently unknown from a global perspective. This systematic review aims to quantify the magnitude of racial/ethnic inequities in dental caries and to deconstruct the different taxonomies/concepts/methods used for racial/ethnic categorization across different populations/nations. This review has been registered in PROSPERO; CRD42021282771. An electronic search of all relevant databases will be conducted until December 2021 for both published and unpublished literature. Studies will be eligible if they include data on the prevalence or severity of dental caries assessed by the decayed, missing, filled teeth index (DMFT), according to indicators of race-ethnicity. A narrative synthesis of included studies and a random-effects meta-analysis will be conducted. Forest plots will be constructed to assess the difference in effect size for the occurrence of dental caries. Study quality will be determined via the Newcastle-Ottawa Scale and the GRADE approach will be used for assessing the quality of evidence. This systematic review will enhance knowledge of the magnitude of racial/ethnic inequities in dental caries globally by providing important benchmark data on which to base interventions to mitigate the problem and to visualize the effects of racism on oral health.

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.

Periodontal disease inequities among Indigenous populations: A systematic review and meta-analysis

The prevalence of periodontal disease varies considerably between Indigenous and general populations. The aim of this systematic review was to assess the global prevalence of periodontal disease among Indigenous populations in comparison with non-Indigenous populations. A systematic electronic search of databases and grey literature sources was conducted of all records through to February 2021. Study selection criteria included original data that reported the prevalence of periodontal diseases among an Indigenous population and compared with a non-Indigenous population, without any restriction on age, sex, language or geographical location. Critical appraisal was conducted with the Joanna Briggs Institute (JBI) tool for prevalence studies. A random-effects model using standardised mean difference (SMD) as the effect measure was used to estimate the pooled prevalence of periodontitis. Subgroup analysis of study location and publication source was also performed. Publication bias was assessed using Egger's test, and funnel plots were used for visualisation. A total of 19 articles were included for descriptive and meta-analysis. The overall prevalence of periodontitis was 35% (95% CI: 0.18, 0.52) higher among the Indigenous population than the non-Indigenous population. The pooled prevalence of periodontitis was consistently higher among the Indigenous populations when stratified according to periodontitis definition employed, study location and publication source. Indigenous populations have a higher prevalence of periodontitis than non-Indigenous populations. To decrease oral health inequities, more emphasis should be given to oral health promotion and specific culturally safe interventions working in partnership with Indigenous populations.