ETV6-RUNX1–associated genetic susceptibility to pB-ALL shapes a specific gut microbiota. (A) The EMPeror plot shows a PCoA of the cohousing cohort (see Figure 1), including samples from 15 Sca1-ETV6-RUNX1 mice (represented as rings). Samples of Sca1-ETV6-RUNX1 mice clustered well with samples of the cohousing cohort derived from the same facility (CF or SPF facility, respectively). Microbiome analyses were carried out after 2 months in CFs (mice had been referred to CFs from SPF facilities at age 6 to 8 weeks) and after 10 months in SPF facilities. The analyzed mice did not develop leukemia. (B) The forward step redundancy analysis was used to quantify effect sizes on microbiome differences using all samples from the cohousing cohort and the Sca1-ETV6-RUNX1 mice. Environment (facility) and genotype were identified as the most important factors. (C) WT and Pax5^+/– microbial sources were defined to quantify compositions of microbial ETV6-RUNX1 sinks via SourceTracker2. The analysis showed that the microbiome of Sca1-ETV6-RUNX1 mice was more similar to the microbiome of Pax5^+/– mice than to that of WT mice. (D) Statistical analyses demonstrated that the mouse genotype shapes 3 statistically significantly different microbiomes (PERMANOVA on unweighted UniFrac beta-diversity distances with 999 permutations). The box shows the quartiles of the dataset, while the whiskers (error bars) show the rest of the distribution, except for points that are determined to be outliers, using 1.5-fold of the interquartile range. The P value is from the PERMANOVA test. (E) Machine learning was able to predict genotypes genetically predisposed to pB-ALL. A confusion matrix for predicting the mouse genotype from the 10 most important V4-ASVs is shown (random forest with 1000 trees).