IBD subject IBD_2 isolate 4
We isolated Enterococcus strains from non-IBD and IBD patients to confirm whether sagA-positive strains or Enterococcus faecium strains were depleted in IBD stool. For this, we collected Enterococcus strains by plating human stool slurries from non=IBD and IBD patients on Enterococcus-selective bile esculin azide plate and further purified them by streaking on trypticase soy agar with 5% sheep blood (Henry Schein). Genomic DNA was extracted using the KingFisher Flex automated extraction instrument (Thermo Fisher) and the MagMAX DNA Multi-Sample Ultra 2.0 kit reagents (Applied Biosystems). Whole genome sequencing was performed using the NovaSeq 6000 system (Illumina) at the NYU Genome Technology Core.