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/).