Target-enriched long-read sequencing (TELS) contextualizes function in metagenomes

Metagenomic data can be used to profile high-importance functions across microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes. These limitations preclude colocalization analysis, i.e., the ability to characterize the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of the ARGs and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELS). Custom probes covering >5,500 known ARGs were used to capture and amplify metagenomic DNA from feces and a mock community with known microbial composition. Reads at >40,000 bp were produced, and ARG sequences increased by >10,000-fold and MGE sequences by >100,000-fold due to in situ genomic linkage.