Shotgun Metagenomics of human feces: PWH fecal microbiome
Total genomic DNA was extracted from fecal samples using the DNeasy 96 PowerSoil Pro QIAcube HT kit on a QIAcube platform following standard manufacturer protocols. Shotgun metagenomic sequencing was conducted by the University of Minnesota Genomics Core, where DNA libraries were prepared using the Illumina NexteraXT DNA library preparation kit (Cat. #FC-131-1096). The NexteraXT protocol involves enzymatic fragmentation and simultaneous addition of adapter sequences through a transposase-mediated tagmentation reaction, followed by limited-cycle PCR amplification to add unique dual indexes and sequencing adapters. A total of 40 dual-indexed libraries were prepared to enable sample multiplexing and reduce index-hopping artifacts. Sequencing was performed on an Illumina NovaSeq SP platform using paired-end chemistry to generate 150 bp reads from both ends of each DNA fragmentby the University of Minnesota Genomics Core (UMGC). Briefly, the libraries were prepared using the Illumina NexteraXT DNA library preparation kit (Cat. #FC-131-1096) according to the manufacturer's guidelines. Sequencing was performed on
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2680-Month3_S16