mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Metagenomics have enabled the comprehensive and culture-independent study of microbiomes. However, for many applications, only certain taxa are of interest in a microbiome sample, for example, pathogenic bacteria, beneficial microbes, or taxa of low relative abundance. It is highly desirable that a method can effectively enrich bacterial taxa of interest directly from the microbiome. To address this critical need, we developed mEnrich-seq, a method that can enrich taxa of interest from metagenomic DNA before sequencing. We performed in-depth evaluations of mEnrich-seq using both synthetic and real microbiome samples. Sequencing was primarily performed with both MinION flow cell R9.4.1 and Flongle flow cell R9.4.1 (both from ONT), and ONT MinKNOW software (v21) was used for sequencing raw data collection. Human reads were identified and hidden (into Ns) by mapping the nanopore reads to the human reference (GRCh38) using minimap2 (v2.24-r1122).