decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods

Area of Science:

• Genomics
• Bioinformatics
• Archaeology

Background:

• Ancient metagenomic studies are challenged by contaminant DNA, complicating microbial source tracking (MST).
• Current MST methods perform poorly on ancient metagenomic datasets.
• A novel k-mer-based method, decOM, was developed for classifying ancient and modern metagenomic samples.

Discussion:

• decOM demonstrates high accuracy in estimating environmental source contributions in ancient oral metagenomes.
• The method was validated using 360 diverse metagenomic samples (ancient oral, modern oral, soil, skin) via cross-validation.
• decOM surpasses the performance of established MST tools like FEAST and mSourceTracker.

Key Insights:

• decOM provides accurate microbial source tracking for ancient oral metagenomic data.
• The developed method effectively distinguishes between environmental and modern contaminants.
• This tool enhances the reliability of analyzing ancient microbial communities.

Outlook:

• The generic nature of decOM allows adaptation for various ancient and modern metagenomic datasets.
• decOM is expected to become an essential tool for future ancient metagenomic research.
• Further applications in microbiome research and paleogenomics are anticipated.