Oral Microbiome Dynamics in Historical and Modern Contexts

The oral microbiome, a complex community of bacteria, archaea, fungi and viruses, has undergone profound shifts in diversity and function over human history. From hunter‐gatherer diets to the agricultural introduction of fermentable carbohydrates, the Industrial Revolution’s dietary excesses and the modern Antibiotic Era, each societal transition has left distinctive imprints on oral ecosystems. Calcified dental plaque, or dental calculus, serves as a molecular archive, enabling reconstruction of ancient microbial communities through DNA, protein and metabolite analyses. Contemporary sequencing of saliva and plaque biofilms complements these findings, revealing a resilient core microbiota that persists despite dietary, environmental and pharmacological perturbations. Comparative studies across geographical regions and among non‐human primates highlight host genetics, lifestyle and ecology as key determinants of community structure. Insights into the emergence of cariogenic species, the rise of antimicrobial resistance genes and the interplay between host immune factors and pathogens inform strategies to prevent caries, periodontitis and resist the spread of resistance in modern populations.

Research from Nature Portfolio

Recent studies employing palaeoproteomic analyses of ancient dental calculus have elucidated the protein profiles of both host and bacterial origin in individuals from the Okhotsk period, revealing the persistence of key pathogenic factors and innate immune components across centuries. Complementarily, quantitative metaproteomics of medieval (ca. 1100–1450 CE) dental calculus has distinguished molecular signatures correlating with oral health predisposition and disease susceptibility, uncovering health‐related groupings not apparent from traditional skeletal analyses. These proteomic approaches underscore the value of calcified plaque as a substrate for reconstructing the molecular history of oral microbial communities and host–microbe interactions.

Oral Microbiome Dynamics in Historical and Modern Contexts publication trend

The graph below shows the total number of articles in oral microbiome dynamics in historical and modern contexts across all publications each year (not limited to Nature Index journals).

Technical terms

Oral microbiome: The community of microorganisms inhabiting the mouth, including bacteria, archaea, fungi and viruses.

Dental calculus: Mineralised dental plaque that forms on teeth and preserves biomolecules over archaeological timescales.

Metagenomics: The study of genetic material recovered directly from environmental samples, enabling identification of microbial species and functions.

Metaproteomics: The large‐scale characterisation of all proteins present within a complex microbial community.

Palaeoproteomics: The analysis of ancient proteins preserved in archaeological materials to infer past biological interactions.

Biofilm: A structured microbial community embedded in a self‐produced matrix, adherent to surfaces such as teeth.

Antimicrobial resistance genes: Genetic elements that confer tolerance to antibiotic compounds and can be exchanged among microbes.

Cariogenic bacteria: Microbial species that produce acids from carbohydrate fermentation, leading to tooth enamel demineralisation.

Periodontitis: A chronic inflammatory disease affecting the supporting structures of teeth, driven by dysbiotic biofilm communities.

References

1. Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes. Microbial Genomics (2024).
2. A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review. Microorganisms (2024).
3. Resilience of the oral microbiome. Periodontology 2000 (2021).
4. Quantitative metaproteomics of medieval dental calculus reveals individual oral health status. Nature Communications (2018).
5. The saliva microbiome of Pan and Homo. BMC Microbiology (2013).
6. Oral microbiome diversity in chimpanzees from Gombe National Park. Scientific Reports (2019).