Extended Data Fig. 2: Study heterogeneity shows a strong influence on alpha and beta diversity.
a, Alpha diversity as measured with the Shannon index was computed for all gut microbial species (n = 849), reference mOTUs (n = 246), and meta-mOTUs (n = 603) separately. P values were computed using a two-sided Wilcoxon test, while the overall P value (on top) was calculated using a two-sided blocked Wilcoxon test (n = 575 independent observations; see Methods). The ANOVA F-statistics below the panel was calculated using the R function ‘aov’. b, Principal coordinate analysis of samples from all five included studies based on Bray–Curtis distance; the study is color-coded and disease status (CRC versus CTRL) is indicated by filled/unfilled circles. The boxplots on the side and below show samples projected onto the first two principal coordinates broken down by study and disease status, respectively. P values were computed using a two-sided Wilcoxon test for disease status and a Kruskal–Wallis test for study (n = 575 independent observations). For all boxplots, boxes denote the IQR with the median as a thick black line and the whiskers extending up to the most extreme points within 1.5-fold IQR. Country codes are as in Fig. 1b.
