Genomic analysis of Enterococcus isolates from non-IBD and IBD patients
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. This analysis provide the insight into the correlation between sagA-positive strains including E. faecium and IBD.