Dame-Teixeira, N., Lynch, J., Yu, X. et al. (2 more authors) (2025) The Caries and Caries-Free Archaeome. Journal of Dental Research. ISSN 0022-0345
Abstract
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, N = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%–40%) and identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria. Methanogens were present in both the caries and caries-free groups (Methanobrevibacter spp., Methanosarcina, and Methanosphaera) and positively correlated with Stenotrophomonas, Streptococcus, Actinomyces, Abiotrophia, Gemella, and Corynebacterium. 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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | This is an author produced version of an article published in the Journal of Dental Research, made available under the terms of the Creative Commons Attribution License (CC-BY), which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited. |
Keywords: | Archaea domain, oral archaeome, methanogens, oral microbiome, dental caries, bioinformatic analysis |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Medicine and Health (Leeds) > School of Dentistry (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 25 Feb 2025 14:01 |
Last Modified: | 01 May 2025 11:30 |
Status: | Published online |
Publisher: | SAGE |
Identification Number: | 10.1177/0022034525132934 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:223718 |