Bacterial 16S rRNA gene and shotgun metagenomic sequencing data from adult humans infected by SARS-CoV-2

Stool samples collected from N=60 NYU Langone Health and N=36 Yale New Haven Hospital adult patients with laboratory-confirmed SARS-CoV-2 infection; bacterial DNA extraction with Qiagen PowerSoil Pro kit on the QiaCube HT; samples prepared for 16S rRNA gene sequencing by using KAPA HiFi polymerase to amplify the V4 region of the 16S rRNA gene and sequenced on Illumina MiSeq using paired-end 2x250 reads and MiSeq Reagent Kitv2; samples prepared for shotgun metagenomic sequencing with a procedure adapted from the Nextera Library Prep kit (Illumina), and sequenced on an Illumina NovaSeq using paired-end 2x150 reads (Illumina) aiming for 100M read depth