Fecal microbial taxonomic signatures are differentially associated with distinct stages of irC. (A and B) Longitudinal taxonomic profiling of irC patients’ microbiomes at pre-irC, irC-initial, irC-late, and post-irC in terms of (A) relative abundance of operational taxonomic units at the phylum-level by metagenomic profiling and (B) absolute abundance. (C) Top bacterial genus associated with pre-irC versus irC-initial identified by MaAsLin2 using metagenomically sequenced microbiomes of irC patients at pre-irC (orange, n = 13) and irC-initial (purple, n = 9 where n = 4 from LC and n = 5 from CVC). Random effect adjusted for non-independence of repeated measures. The horizontal bar length indicates log₁₀(q-value), in which q-value was calculated by BH adjustment of P value. Genus presented q < 0.25. MaAsLin2 parameters included centered log ratio normalization and linear model analysis. (D–G) Temporal dynamic changes in the relative abundance of (D) Faecalibacterium prausnitzii, (E) unclassified Oscillibacter species, (F) Veillonella genus, (G) Proteobacteria phylum in irC patients at pre-irC, irC-initial, irC-late, and post-irC. irC-initial samples were pooled from both irC cohorts (LC and CVC). Based on metagenomic profiles. Each symbol represents data from an individual patient; the boxplot displays a central line presenting the median, accompanied by a box that encloses the interquartile range (IQR) and extends whiskers up to the farthest data point within 1.5 times the IQR.