Nanopore-based high-quality metagenome-assembled genomes reveal the microbial genomic dark matter in the human gut

We used a hybrid, ultra-deep metagenomic sequencing strategy to explore efficiency in deep metagenomic analysis. Based on a large amount of sequencing data, we straightforward assembled a large amount of highly creditable and circular genomes and greatly expanded available high-quality MIMAG. Moreover, we demonstrated that the usability of these high-quality in uncovering the genomic dark matter for gut microbiota; and explored the proportion and diversity in the genome of the problematic region (i.e., 16S rRNA gene, insert sequence, prophage et al.) in short-read assembly.