Cross-study consistency analysis of differential abundance. The percentage of significant species is plotted against the number of studies where each species was identified as significant, conducted on five IBD cohorts. Results for the average SOTA model are shown in white. The expected results are presented in black (see the “ Methods ” section). Additionally, a parallel analysis on shuffled labels is provided for the ANCOM-BC2 model (green). The models’ performance exceeds that of the expected random model. However, certain tools, such as ANCOM-BC2, exhibit artificially consistent results, as indicated in the inner plot of ( C ). For a comprehensive analysis of all 13 tools, refer to Supplementary Material Fig. S 4
