Heritage-specific oral microbiota in Indigenous Australian dental calculus

Abstract

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 = 18) and without PD (n = 20) were characterized using 16S rRNA 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 x 1 0 −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 inclusion of Indigenous peoples in microbiota research, highlighting the microbiota as a novel field of enquiry to improve Indigenous health. Lay Summary The community of microorganisms in the mouth (oral microbiota) has recently been linked to several chronic diseases that disproportionately impact Indigenous Australians. In this study, oral microbiota differ significantly between Indigenous Australians and non-Indigenous counterparts, suggesting the microbiota could be a novel factor with potential to improve Indigenous health outcomes.

Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities

“…Another constraint for the 16S enrichment method is the a priori design of probes, which limits the ability to identify microbes that have yet been characterized. Future studies should consider developing new probe designs that include novel oral taxa that have been characterized in recent studies ( Klapper et al, 2023 ; Velsko et al, 2023 ; Handsley-Davis et al, 2022 ). Adding these taxa into the probe design may improve characterizing the microbial diversity for poorly preserved samples where most of the DNA originates from contaminant sources.…”

Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases

“…Initial colonization begins with pioneer species, and once tooth eruption begins, a more complex microbial community is established on the hard surfaces (Deo and Deshmukh 2019). While a core microbiome consisting of Streptococcus, Lactobacillus, Actinomyces, Neisseria, and Veillonella bacteria is common across individuals, significant variation can arise depending on an individual's unique environment, lifestyle, physiology, and heritage (Deo and Deshmukh 2019;Verma, Garg, and Dubey 2018;Gomez et al 2017;Weyrich 2021;Handsley-Davis et al 2022). The oral microbiome performs several critical functions underlying systemic health.…”

“…While a core microbiome consisting of Streptococcus , Lactobacillus , Actinomyces , Neisseria, and Veillonella bacteria is common across individuals, significant variation can arise depending on an individual’s unique environment, lifestyle, physiology, and heritage ( Deo and Deshmukh 2019 ; Verma, Garg, and Dubey 2018 ; Gomez et al . 2017 ; Weyrich 2021 ; Handsley-Davis et al . 2022 ).…”

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes

“…Example evidence for potential environment-human transfer of microbial CPP comes from Endomicrobia species found in oral microbiota of indigenous peoples from central Australia (Handsley-Davis et al, 2022). Endomicrobia species provide energetic advantage for cellulose digestion in the guts of termites and wood-eating insects-and transfer to humans has occurred likely through use of termites and termite mounds in traditional food and medicine (Handsley-Davis et al, 2022). Speculatively, our results suggest that if broad supplementation of human microbiota CPP capacity is required (spanning a range of health-supporting biomolecules), this may require exposure to multiple types of environments.…”