We first identified the microbial features associated with disease phenotype and IBD-associated risk variant rs1893217 within the PTPN2 gene locus and rs2476601 within the PTPN22 gene using MaAsLin pipeline that takes into account the possible effect of clinical metadata as confounding factors in microbiota analysis and runs statistical analysis accordingly. Here, PTPN22 is linked to irritable bowel syndrome.