Fig. 3

ARG profiles of fresh and stored apple samples. Results are based on deepARG annotations of contigs for resistance genes, target drug classes and resistance mechanisms, including only ARGs with at least 80% similarity to reference ARGs and an e-value of 10^–11. Data were generated from the rarefied tables. A Distribution of resistance mechanisms of annotated ARGs for each apple metagenome. Value on top of each stacked bar denotes for percentage of annotated ARGs to total contigs assigned. Color code for figure panel B and C is depicted in the legend on the upper right: Braeburn: blue; Royal Gala: yellow, both fresh from the tree (dark blue and dark yellow, respectively) and stored/transported (light blue and light yellow, respectively). B Network representation of core and specific ARGs in apple metagenomes. Nodes represent different ARGs detected and node labels point to the antibiotic target class, while unlabeled nodes indicate multidrug resistance of the respective ARG. Node size corresponds to absolute abundance of ARGs in the rarefied datasets as indicated in legend on the lower right. Pie charts of nodes shared by all samples, representing the ‘apple core resistome’, indicate fractions detected within each apple metagenome. ARGs that were shared by stored apples but absent in fresh apples are highlighted as the ‘storage-specific resistome’. C Dendrogram visualizes connection between different apple samples based on their ARG composition. Calculations were executed in R using Euclidean distance with average clustering method