Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities

Søren Heidelbach; Sebastian Mølvang Dall; Jeppe Støtt Bøjer; Jacob Nissen; Lucas Nicolaas Ludovic van der Maas; Mantas Sereika; Rasmus Hansen Kirkegaard; Sheila I. Jensen; Sabrina Just Kousgaard; Ole Thorlacius‐Ussing; Katja Hose; Thomas D. Nielsen; Mads Albertsen

doi:10.1101/2024.04.29.591623

BioinformaticsbioRxivApr 29, 2024

Preprint

Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities

Søren Heidelbach iD, Sebastian Mølvang Dall iD, Jeppe Støtt Bøjer, Jacob Nissen iD, Lucas Nicolaas Ludovic van der Maas iD, Mantas Sereika iD, Rasmus Hansen Kirkegaard iD, Sheila I. Jensen iD, Sabrina Just Kousgaard iD, Ole Thorlacius‐Ussing iD, Katja Hose iD, Thomas D. Nielsen iD, Mads Albertsen iD

Abstract

DNA methylation is found across all domains of life but is a rarely used feature in recovery of metagenome-assembled genomes (MAGs). Recently, Oxford Nanopore introduced all context methylation detection models. We leveraged this to develop Nanomotif, which identifies and exploits methylation motifs for enhanced MAG recovery. We demonstrate how Nanomotif enables database-independent contamination removal from high-quality MAGs and host association of plasmids directly from Nanopore sequencing data in complex metagenomes.

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