The Caries and Caries-Free Archaeome

The difficulty of establishing a relationship between archaea and oral diseases such as dental caries stems from the challenges of detecting, identifying, and isolating these microorganisms. This study aimed to detect archaea in publicly available datasets comprising caries and caries-free saliva and dental plaque by using a tailored bioinformatic pipeline for shotgun sequencing analysis. A systematic search was performed to identify studies using shotgun metagenomics or metatranscriptomics on samples obtained from individuals with dental caries. Two reviewers selected studies based on eligibility criteria. Sequencing and metadata from each study were retrieved from the SRA Bioproject. A count table was generated for each database by mapping reads against an archaea genome database, specifically tailored for this study, using stringent filtering parameters of greater than 97% similarity and 90% query coverage. Archaeal prevalence was determined using an arbitrary cutoff point (>500 reads). An effect size meta-analysis was performed to determine the overall prevalence. Phyloseq and DESeq2 packages were used to determine alpha and beta diversities, differential abundance in different taxonomic levels, and differential expression comparing caries and caries-free samples. Spearman correlation was performed with the bacteriome. The search yielded 154 titles, from which a collection of 7 datasets from 8 studies was obtained. Of 397 samples, <i>N</i> = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%-40%) and identifying <i>Euryarchaeota</i>, <i>Thermoplasmatota</i>, and <i>Nitrosphaeria</i>. Methanogens were present in both the caries and caries-free groups (<i>Methanobrevibacter</i> spp., <i>Methanosarcina</i>, and <i>Methanosphaera</i>) and positively correlated with <i>Stenotrophomonas</i>, <i>Streptococcus</i>, <i>Actinomyces</i>, <i>Abiotrophia</i>, <i>Gemella</i>, and <i>Corynebacterium</i>. Several methanogenesis genes, including methyl-coenzyme M reductase, which catalyzes the final step of methane production in methanogens, were underexpressed in caries-active samples compared with caries-free samples. Saliva and dental plaque emerged as sites of low-abundance archaea, with methanogenesis genes underexpressed in caries-active samples.