The sequenced Nanopore reads were assembled using metaFlye v2.9.1, polished with Racon v1.5.0 (3x rounds) and Medaka v1.6.1 (2x rounds), followed by polishing with Illumina reads using Racon v1.5.0. Automated coting binning was performed using the ensemble method with Metabat2 v2.15, MaxBin2 v2.2.7, Vamb v3.0.7, and Metabinner v1.4.3, while Das Tool v1.1.3 was used to generate the final refined metagenomic bins. To improve genome recovery, coverage values from multiple Illumina read datasets were used as input for the binners.
High quality (HQ) metagenome assembled genomes (MAGs), including full-length rRNA genes were determined based on mmlong2 v0.0.1. In some cases, 16S or 23S rRNA genes were not picked up by barrnap v0.9, and so Infernal v1.1.2 (arguments: cmscan --cut_ga --rfam --nohmmonly --fmt 2) was used. Dereplicated bins were checked for completeness and contamination using CheckM2 v0.1.3 and CheckM1 v1.1.2 (Parks et al., 2015) –lineage_wf resulting in 214 HQ MAGs.
Taxonomic classification at the phylogenetic level in relation to the genome taxonomy database and maximum likelihood placement was conducted using GTDB-Tk v1.4.1 (Refseq release 207).