Four-stage workflow for integrating gut microbiome assessments and MCIs into immunotherapy. Stage 1: diagnosing the disease and identifying patients requiring intervention. Stage 2: various assays (mass spectrometry, ELISA, flow cytometry, metagenomics analyses) are conducted on blood and stool samples to evaluate gut microbial composition, systemic immune markers, and metabolite concentrations. Stage 3: integrative computational approaches are applied to the multi-omics assays, exemplified here by the TOPOSCORE network (Derosa et al., 2024), to identify microbial–immune interactions and dysbiotic markers predictive of treatment outcomes. Stage 4: key therapeutic strategies—including dietary modifications, FMT, and supplementation with probiotics, prebiotics, or synbiotics—aimed at restoring microbial balance and enhancing ICB efficacy. Stage 5: a timeline comparing results from before (time point 0 [T0]) and after (time point 1 [T1]) the chosen MCI, enabling a clearer delineation of its mechanism of action. Figure was created using BioRender.