Same Household adress as Patient (Control Group)
DNA was extracted from all 156 stool samples using the QIAamp PowerFecal DNA kit (Qiagen, Netherlands) following the manufacturers instructions. The V5-V6 region (based on Escherichia coli) of the 16S ribosomal RNA (rRNA) was targeted for amplification by PCR using the forward primer: S-D-Bact-0785-a-S-18, GGMTTAGATACCCBDGTA and reverse primer: S-*-Univ-1100-a-A-15, GGGTYKCGCTCGTTR81. The CS1 (ACACTGACGACATGGTTCTACA) and CS2 (TACGGTAGCAGAGACTTGGTCT ) tags were used to add a barcode and Illumina adapters. Amplification was performed using Q5 High Fidelity DNA polymerase (New England BioLabs) with PCR cycles as follows: initial denaturation step of 98C, for 30 secs, before 23 cycles of 98C, for 10 secs, 58C, for 15 secs and 72C, for 30 secs, with the final extension at 72C, for 2 min. The MiSeq250 platform was used for 2 x 250 bp paired-end sequencing of the resulting PCR products.