Sequencing and Identification of bacterial DNA
The pool of stool DNA was sequenced in one sequencing run. Sequences
were obtained using an Illumina MiSeq paired-end 250-bp protocol for 500
cycles. The PCR was performed in one batch with appropriate negative
controls following which paired-end sequencing (2×250bp) was performed
on the Illumina MiSeq platform (Illumina, San Diego, CA, US) and
processed using the Quantitative Insights Into Microbial Ecology 2
(QIIME2) pipeline17. Samples were rarefied prior to
alpha and beta diversity analysis. Taxonomy assignment was done against
the Silva-132-99% OTUs database and differences in relative abundance
of taxa between cohorts were analyzed using linear discriminant analysis
(LDA) effect size (LEfSe). Taxa with LDA > 2 at a p value
< 0.05 were considered significant.