163 The differences in microbial abundances between different fecal samples were evaluated by quantifying the beta-diversity of the gut microbiota, which was performed by calculating BrayCurtis dissimilarity distances. The beta-diversity was significantly different between IBD samples and samples from HC in the first two principal coordinates (P<0.001), as can be observed from the principal coordinate analysis (PCoA) plots shown in Figure 2. Permutational multivariate analysis of variance using distance matrices (PERMANOVA, using the ADONIS function) demonstrated that sample origin (IBD vs. HC) was able to explain 20.5% of the variation in the beta-diversity of the gut microbiota (P=0.01). In contrast, beta-diversity was not significantly changed after the MACS procedure in the first two principal coordinates (both PCoA1 and PCoA2: P>0.05), which was confirmed after ADONIS analysis which revealed that only 2.2% of the variation (P=0.02) could be explained by sample handling (IgG-coating procedure vs. no coating). No significant associations between shifts (before and after IgG-coating) in the first four PCoAs versus clinical characteristics were observed (Supplementary Figure S1). Antimicrobial IgG immune responses in IBD
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