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

TL;DR

Using metagenome-assembled genomes improves DNA sequencing accuracy in saliva samples by better removing bacterial contamination.

Contribution

A new decontamination pipeline using metagenome-assembled genomes improves variant calling in oral DNA sequencing.

Findings

MAG-augmented decontamination outperforms conventional methods in variant calling accuracy.

Decontamination improves detection of variants in GC-rich genomic regions.

Some bacterial regions mimic human DNA, potentially causing genotyping errors.

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 improves variant calls in GC-rich regions, recovering many likely pathogenic variants. Additionally, we demonstrate that certain bacterial genomic regions mimic human regions with clinically relevant variants, potentially confounding genotyping. These results highlight the need for MAG-based bacterial read decontamination to achieve accurate personal genotyping from non-invasive, self-collected oral samples.

•Decontamination of oral DNA samples via oral bacterial genomes improves genotyping•Metagenome-assembled genomes enhanced bacterial read decontamination and genotyping•Decontamination improves the detection of variants in challenging genomic regions•Multiple oral bacteria harbor sequences that misalign to clinically relevant genomic regions

Decontamination of oral DNA samples via oral bacterial genomes improves genotyping

Metagenome-assembled genomes enhanced bacterial read decontamination and genotyping

Decontamination improves the detection of variants in challenging genomic regions

Multiple oral bacteria harbor sequences that misalign to clinically relevant genomic regions

Computational bioinformatics; Genomic analysis; Genomics

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