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The Caries and Caries-Free Archaeome.

N Dame-Teixeira1, J Lynch2, X Yu2

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|April 21, 2025
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Archaea are present in oral samples, but their role in dental caries is unclear. This study found archaea in 20% of samples, with specific genes underexpressed in caries-active individuals, suggesting a complex relationship.

Keywords:
Archaea domainbioinformatic analysisdental cariesmethanogensoral archaeomeoral microbiome

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Oral Health Research

Background:

  • Establishing a link between archaea and oral diseases like dental caries is challenging due to detection and isolation difficulties.
  • Archaea are microorganisms with diverse metabolic capabilities, and their presence in the oral cavity warrants investigation for potential roles in health and disease.

Purpose of the Study:

  • To detect and characterize archaea in saliva and dental plaque samples from individuals with and without dental caries using bioinformatic analysis of public shotgun sequencing datasets.
  • To investigate the prevalence and potential correlation of archaea with dental caries and the oral bacteriome.

Main Methods:

  • Systematic literature search for shotgun metagenomics/metatranscriptomics studies on dental caries.
  • Bioinformatic pipeline utilizing stringent parameters for read mapping against a tailored archaea genome database.
  • Meta-analysis for prevalence, diversity analysis (alpha and beta), differential abundance, and differential gene expression (using Phyloseq and DESeq2), and correlation with bacteriome (Spearman).

Main Results:

  • Out of 397 samples analyzed, 63 (20%) were positive for archaea, identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria.
  • Methanogens (e.g., Methanobrevibacter spp.) were found in both caries and caries-free groups and correlated positively with specific bacterial genera.
  • Key methanogenesis genes, including methyl-coenzyme M reductase, were underexpressed in caries-active samples compared to caries-free samples.

Conclusions:

  • Saliva and dental plaque harbor low-abundance archaea, with potential implications for oral health.
  • The underexpression of methanogenesis genes in caries-active samples suggests a potential role for archaeal metabolism in the context of dental caries, warranting further investigation.