Shotgun-sequenced raw reads were processed using SeqPrep (
https://github.com/jstjohn/SeqPrep) under default settings to merge overlapping paired-end reads and trim adaptors. Metagenomic assembly and binning were performed using the Aviary pipeline: pre-processed reads (post-SeqPrep) were first assembled with metaSPAdes, then Minimap2 and Samtools were used to map sequences back to the assemblies and CoverM was used to generate coverage reports. Multiple tools were used in the binning step of Aviary pipeline, including CONCOCT, VAMB, MetaBAT, MetaBAT2, MaxBin2, Rosella and DASTool.