Genome enrichment of rare and unknown species from complicated microbiome by nanopore selective sequencing
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In metagenomic sequencing, the low-abundance microorganisms (sometimes referred to as rare biosphere) are often missed or simply neglected due to low sequencing coverage. However, pieces of evidence show the low-abundance microbiota may play essential roles in community functionality. Benefiting from the selective sequencing enabled by nanopore sequencing, we rejected DNA of microorganisms with high abundance and enriched rare taxa when metagenomic sequencing of the community of thermophilic anaerobic digester (TAD). By structurally altering the sequencing community in this way, we obtained more low abundance and high-quality metagenome-assembled genomes (HQ MAGs).