NCM 2022: Targeted deep metagenomics for the recovery of novel closed microbial genomes from highly complex communities

Metagenomics enables researchers to gain insight into unculturable microorganisms through the recovery of metagenome-assembled genomes (MAGs). An example of an unculturable microorganism includes cable bacteria, which are centimetres-long filamentous bacteria capable of conducting long-distance electron transfer. However, due to reliance on short-read metagenomics, publicly available cable bacteria MAGs are fragmented, while many are incomplete, missing 16S rRNA and other key functional genes. Here, we have performed long-read nanopore sequencing (total 162.4 Gbp) of environmental and enrichment samples to recover 2 closed as wells as 2 high-quality cable bacteria MAGs. The genome drafts were compared against existing cable bacteria MAGs to detect novel genes and genomic elements missing from short-read MAGs. Phylogenetic analysis revealed that two single-contig MAGs recovered in this study belonged to novel species and one of these novel species was found to encode genes for certain physicochemical traits that challenge the current taxonomic framework of cable bacteria.