: Table S1). Demultiplexed raw sequences were either downloaded from EBI or available locally as previously generated . Metadata were obtained either directly from the sequence repository/manuscript , or from collaborators . This resulted in a total of 5151 samples and 2179 subjects available prior to processing and quality control.We manually curated subject- and sample-specific metadata across studies to ensure consistency. Variables collected and curated include:Type of controls .
° HMP2: ileum classification kept unchanged; cecum, ascending/right-sided colon, transverse colon, descending/left-sided colon, and sigmoid colon were aggregated as colon.° Pouchitis: terminal ileum, pouch, pre-pouch ileum aggregated as ileum; sigmoid colon aggregated to colon.° RISK: terminal ileum was aggregated to ileum; rectum kept unchanged.° Location for CDs , available for BIDMC-FMT, CS-PRISM, Herfarth, Jansson-Lamendella, LSS-PRISM, and Pouchitis.
Age at diagnosis . Directly available for CS-PRISM, HMP2, LSS-PRISM, and Pouchitis, inferred as baseline age for PROTECT and RISK as these were new-onset cohorts. Gender . Available for BIDMC-FMT, CS-PRISM, Herfarth, HMP2, Jansson-Lamendella, LSS-PRISM, MucosalIBD, Pouchitis, PROTECT,
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