147 Antigen phage library and Illumina sequencing primers Antigen phage library primers Forward GATGCGCCGTGGGAATTCT Reverse GTCGGGTGGCAAGCTTTCA Illumina amplicon sequencing primers PCR1 tcgtcggcagcgtcagatgtgtataagagacagGTTACTCGAGTGCGGCCGCAAGC gtctcgtgggctcggagatgtgtataagagacagATGCTCGGGGATCCGAATTC PCR2 Illumina Nextera combinatorial dual index primers PCR3 (of PCR2 pools) AATGATACGGCGACCACCGA CAAGCAGAAGACGGCATACGA R1 primer ttactcgagtgcggccgcaagctttca R2 primer tgtgtataagagacagatgctcggggatccgaattct Supplementary Methods Antigen phage library and Illumina sequencing primers Origin and composition of the antigen phage microbiota (“Agilent”) library The composition of the antigen phage microbiota library and the antigen sequences it contains can be roughly divided into seven different parts, which are summarized below. Full details on the library composition can be found elsewhere.1 (Part I) Bacterial genes (~50%) Roughly half of the full antigen microbiota phage library is dedicated to antigens from bacterial genes, whichwere derived frommetagenomics shotgun sequencing data of an Israeli populationbased cohort, as previously described.1,2 Mapping of bacterial genes and calculation of their relative abundances was performed using the Integrated Gene Catalog database,2 and bacterial genes of this background cohort consisted of approximately 4 million different mapped genes. Antigens from these genes were selected based on abundance and annotation, as described previously.1 (Part II) Bacterial strains (~10%) Several commonly abundant bacterial strains were added to the library using MetaPhlAn2, a bioinformatics tool, to characterize the taxonomic composition of microbial communities derived from metagenomics shotgun sequencing data.3 The ten most-abundant bacterial strains were selected using MetaPhlAn2, from which protein antigen sequences were downloaded from the NCBI. The antibody epitope repertoire in IBD
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