STyph
Bacterial cultures were prepared in rich media (basal for Bacteroides spp. and LB for E. coli and S. Typhimurium). Genomic DNA (gDNA) extraction was performed using the Wizard Genomic DNA Purification Kit (Promega) according to protocol. The extracted gDNA was sheared using Covaris DNA Shearing, and the library was prepared using Kapa Biosystem DNA Hyper Prep NGS Library (Dana Faber Core MBCFL Genomics). Sequencing was performed on the Illumina MiSeq instrument, with the 150 bp paired End (PE150) reagents.