Extended Data Figure 6: Assessment of capacity for statistical methods to correct for mis-matching.

Linear mixed effects analyses were performed as described for Figure 4J. A) Shown are ASVs that passed unadjusted P < 0.05 in the comparison of diabetics to non-diabetic controls via linear mixed effects models, as compared to the more conservative cutoffs shown in Figure 4J (Benjamini-Hochberg Q value < 0.05). B) Shown are ASVs with Benjamini-Hochberg Q value < 0.05 in the comparison of diabetics to non-diabetic controls via linear mixed effects models, with ASVs associated with confounding variables identified by ANCOM as having a W score indicating rejection of the null hypothesis for >80% of log ratio comparisons for that ASV.