Fig. 2: A reproducible signature of the Fusarium infection rhizosphere microbiome.
From: General variation in the Fusarium wilt rhizosphere microbiome
A Relative abundance of the significant predictors in the MeanDecreaseGini or MeanDecreaseAccuracy indices from the random forest analysis. The significantly changed genera are colored according to the significance level. The x axis label represents the mean across all studies. B–E Significantly altered biomarkers between the diseased and healthy rhizosphere microbiomes. These biomarkers were identified based on predictors that showed significance in both the MeanDecreaseGini and MeanDecreaseAccuracy indices. Data are presented as box plots, where the center line indicates the median, the box limits indicate the upper and lower quartiles (25th and 75th percentiles), and the whiskers extend to the minimum and maximum data points. Statistical significance was determined using a linear mixed effects model with the formula: relative abundance ~health_status + (1 | OAU), followed by ANOVA: Variovorax (P = 4.00 × 10−5), Novosphingobium (P = 7.00 × 10−4), Stenotrophomonas (P = 4.90 × 10−3), Flavobacterium (P = 1.50 × 10−3). F SHapley Additive exPlanations (SHAP) value analysis of rhizosphere microbiome composition comparing diseased and healthy samples. The plot displays the top 15 most discriminative bacterial genera ranked by their mean absolute SHAP values. All analyses were performed on n = 93 and 105 for diseased and healthy independent rhizosphere samples. *** P < 0.001, ** P < 0.01, * P < 0.05. Source data are provided as a Source Data file.
