Multi-centre extraction and sequencing of IBD mucosal microbiome
Templates were prepared following the Illumina protocol for 16S rRNA gene amplicons for the MiSeq platform with modifications described elsewhere [23]. Briefly, the 16S rRNA gene V4 region was amplified using primers 515fXT (GTGBCAGCMGCCGCGGTAA) and 806rXT (GGACTACHVGGGTWTCTAAT). Quality control, quantification, normalization, pooling and sequencing of the library was performed according to manufacturer instructions, and approximately 11 pM of the pools and 37.5% PhiX spike-in control DNA were used for sequencing using the V3 chemistry (600 cycles; 2  300 bp). A single Illumina MiSeq run was performed on 65 multiplexed samples including a no-template control (NTC) and mock community of known composition (HM-782D; BEI Resources, Manassas, VA).