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

Camila Duitama González, Riccardo Vicedomini, Teo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi

Keywords: ancient metagenomics, microbial source tracking, k-mer matrix, paleogenomics

TL;DR: We have build a tool to check how contaminated an ancient oral metagenomic sample is.

Abstract:

The 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 MaskedName for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. MaskedName estimates the contributions of several source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art machine learning methods for source tracking, FEAST and mSourceTracker. We anticipate that MaskedName will be a valuable tool for MST of ancient metagenomic studies.
Note: This submission is under revision in a journal at the moment
Supplementary File: https://drive.google.com/file/d/1aDjWdg9Jx0f2vZqzzTC9JHcQB3Lw4IYZ/view?usp=sharing