Shift in microbial communities of romaine lettuce from farm to storage for both source and forward processing
Romaine lettuce in USA is typically grown in California or Arizona and either processed near the growing regions (source processing) or transported to other distant marketing areas for processing (forward processing). Little is know about the dynamics of romaine lettuce microbiome in the different production chains. In this study, freshly harvested romaine lettuce from a commercial field lot destined to both forward and source processing facilities was tracked from farm to processing facilities. In both summer and fall seasons, whole romaine lettuce heads from the farm and the tracked bins delivered to forward and source facilities, and packaged fresh-cut lettuce after processing, were collected for microbiological analyses, including mesophilic bacteria, coliform, yeast and mold counts. Both forward- and source-processed romaine lettuce samples were cold stored and tested 1, 4, 7, and 14 days after processing. 16S rRNA high-throughput sequencing was performed using both illumina MiSeq and Nanopore MinION to determine the shift in bacterial communities under these processing conditions. qPCR was conducted to estimate the total 16S rRNA gene copy numbers for quantitative analysis. Mesophilic bacteria and coliform counts of both whole-head lettuce and fresh-cut lettuce after storage from forward facilities were significantly higher than that from source facilities. The levels of total bacteria estimated by qPCR followed the same trend. The compositions of microbial communities analyzed by MiSeq and MinION were comparable, which were significantly affected by romaine lettuce production season, postharvest delivery and processing conditions. Alpha diversity of lettuce microbiota was significantly higher in fall than summer, and reduced during storage. The shifting patterns of certain dominant taxa were differentially impacted by production seasons and processing types. Understanding the microbial ecology of romaine lettuce microbiota across the farm to storage continuum under both source and forward processing conditions could provide insights into the improvement of microbial safety and quality of the food products.