Whole genome sequencing Metagenome analysis
The WGS Metagenome data was processed using Metagenomic analysis tool kit, Version 2 (MOCAT2),38(http://vm-lux.embl.de/~kultima/MOCAT/). The raw reads were filtered by removing low quality reads, followed by mapping of high quality filtered reads to theRefMG.v1 database ( http://www.bork.embl.de/software/mOTU/) and themOTU.v1 database (http://www.bork.embl.de/software/mOTU/download.html)39 . These databases were used to generate taxonomic profiles using single copy marker gene method or metagenomic operational taxonomic units-mOTU, from phylum to species for all samples. Data transformation was performed using Cumulative-sum scaling (CSS), a widely used method for normalizing microbial community composition data40 .The data was further transformed to log2 to account for the non-normal distribution of taxonomic counts. Statistical analyses were executed using the Calypso software V8.7241 (cgenome.net/calypso/).