Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples.

ABSTRACT: Whole genome sequencing (WGS) offers advantages over DNA chip-based genotyping, typically using blood-derived DNA. However, saliva and buccal samples-popular in direct-to-consumer tests-suffer reduced accuracy because of oral bacterial contamination. Decontamination strategies using decoy bacterial genomes yielded limited improvements, likely because they cover only a subset of oral bacteria with available isolate genomes. To overcome this, we developed a decontamination pipeline leveraging metagenome-assembled genomes (MAGs). Concordance analysis of variant calling between blood and matched oral samples confirmed the superiority of MAG-augmented decontamination over conventional methods relying mainly on isolate genomes. Although the underlying mechanism remains unclear, it particularly i

SUBMITTER: An Z 

PROVIDER: S-EPMC12616088 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature