Shotgun metagenomics: human stool
DNA Extraction from stool samples was carried out in two stages: First stage involved lysing of the samples in Lysis Matrix E tubes on the Precelleys Tissue Homogenizer followed by transferring the supernatant into a deep well 96-well plate. Second stage consisted of DNA isolation from the supernatant, obtained from the previous stage, using Qiagen MagAttract PowerMicrobiome DNA/RNA EP Kit on Eppendorf automated liquid handling system. Dual-index amplification and sequencing approach was taken to assess the composition of microbial communities from the given samples using shotgun metagenomic sequencing on the Illumina NextSeq 2000 platform. This method uses the Illumina DNA Prep kit with Nextera CD DNA indexes to construct sequencing libraries.