Fig. 6

Differences in fungal microbiota between L. monocytogenes-positive and -negative samples. A heatmap shows the difference in mean relative abundance of fungal ASVs in L. monocytogenes-positive and -negative samples for all ASVs that had a relative abundance above 10% in at least one sample across the two seasons (A). Significantly differentially abundant fungal ASVs identified in samples in in year 1 and in year 2 are shown in panels B and C, respectively. Differences in the relative abundance between L. monocytogenes-positive and -negative samples are shown as the log fold change of the mean relative abundance in L. monocytogenes-negative samples to that in L. monocytogenes-positive samples. ASVs shown in orange were detected in significantly higher relative abundance in L. monocytogenes-negative samples and ASVs shown in pink were detected in a significantly higher relative abundance in L. monocytogenes-positive samples. The top 30 fungal ASVs identified by a random forest model as most informative for classification of samples into L. monocytogenes-positive and L. monocytogenes-negative categories are shown in the panel D. These identified ASVs had the highest mean decrease in model accuracy (mtry = 26, ntree = 1000, accuracy = 74.9%). The inserted plot shows the area under the curve (AUC) and kappa values for the random forest model. “Uc” indicates ASVs that were not classified at the genus level