Fig. 3

Romaine lettuce microbiome progression during storage under MAP conditions. a NMDS plot of bacterial community structure on processed lettuce of cultivars DA and TT before and at mid- and endpoint during storage at 6 °C. b Comparison of alpha diversity including species richness and Shannon index between cultivars DA and TT across time points during storage at 6 °C and 24 °C. The bottom and top edges of the boxes mark the 25th and 75th percentiles, and the horizontal line denotes the median. Letters indicate significant differences (Wilcoxon rank sum test with Benjamini–Hochberg adjustment, P < 0.05). The inoculated EcO157 contributed significantly to the bacterial community with 24 °C storage (but not 6 °C storage) thus alpha diversity indexes are depicted both with and without the EcO157 included in determining bacterial community structure for 24 °C storage. c Average relative abundance (RA) of bacterial genera in lettuce metagenomes prior and during storage at 6 °C. Genera with RA ≥ 0.4 for at least one time point are listed and identified taxa with lower RA are included in ‘other taxa’. d Histogram of LDA scores computed using LEfSe analysis for taxa differentially abundant, including all five harvests, between the metagenomes of cultivars DA and TT after storage at 6 °C (biomarkers with LDA value ≥ 4.2 depicted)