The Caries and Caries-Free Archaeome

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.