USTC cohort: 16S rRNA-microbiota sequencing of CD patients and healthy donors
Faecal  samples were taken from human at the indicated time points and stored at 80 C until 16S rRNA analysis. DNA was extracted from faecal pellets with a QIAamp stool DNA mini kit, following the vendors instructions (QIAGEN). 16S rRNA amplicons were generated using the primer 515F/806R recommended by the Earth Microbiome Project2. The primer sequences included the 515F forward barcode primer: AATGATACGGCGACCACCGAGATCTACACGCTXXXXXXXXXXXXTATGGTAATTG TGTGYCAGCMGCCGCGGTAA and 806R reverse primer: CAAGCAGAAGACGGCATACGAGATAGTCAGCCAGCCGGACTACNVGGGTWTCTAAT. PCR products were quantified, pooled and cleaned using the PCR Cleanup kit (QIAGEN) and subsequently sequenced using 250bp paired-end sequencing (Illumina MiSeq V3 kit).