111 Microbiome association analysis Microbiome analyses were performed using the vegan package in R).29 The concordance between antibody profiles and fecal microbial composition was determined by comparing the CLR-transformed relative abundances of bacterial taxa between carriers and non-carriers of each antibody-bound peptide using logistic regression analysis, while adjusting for the effects of age and sex. To assess the contributing effect of microbial taxa on the variation in antibody responses, permutational multivariate ANOVA (PERMANOVA) was used while adopting 1,000 permutations (Adonis function). PCoA was performed to characterize the fecal microbial composition and relate this to microbial dysbiosis, which was quantified using a dysbiosis score based on median BrayCurtis dissimilarities to a reference sample set of metagenomes.30 Associations between dysbiosis and the presence of antibody-bound peptides were assessed using logistic regression analysis adjusted for age and sex. The antibody epitope repertoire in IBD
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