sequences of bacteria
Quality control of raw reads was performed with Fastp (v0.20.0) and clean reads were assembled into contigs using MEGAHIT (v1.1.2). For metagenomic binning, quality control was conducted using FastQC and then clean reads were co-assembled with MEGAHIT (v1.2.8). MAGs were obtained using MetaBAT 2, MaxBin 2.0 and CONCOCT. The completeness and contamination of MAGs were estimated using CheckM. Taxonomy was assigned to each MAG by Kraken2 and the abundance of each MAG was obtained using CoverM.