ArticleMicrobiome2023
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.
Article in Microbiome, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 12 citations in OpenAlex.
- Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.American journal of biological anthropology · 2026Article
- Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus.Scientific reports · 2026Article
- Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.Molecular ecology resources · 2025Article
- Ancient DNA and biomarkers from artefacts: insights into technology and cultural practices in Neolithic Europe.Proceedings. Biological sciences · 2025Article
- SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms.Environmental science & technology · 2025Article
- MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.Bioinformatics (Oxford, England) · 2025Article
- Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment.Briefings in bioinformatics · 2024Review
- Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.Microbial genomics · 2024Review
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Authors and funding
6 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices.
resultsWe analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker.
conclusionsdecOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.
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