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

ABSTRACT:

Background

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 decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices.

Results

We 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-o

SUBMITTER: Duitama Gonzalez C 

PROVIDER: S-EPMC10626679 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature