Food safety implications of microbial communities in enoki mushrooms: Impact of farm environments and distribution channels

Abstract

The consumption of raw enoki mushrooms (Flammulina filiformis) has been associated with multiple international foodborne outbreaks and product recalls, highlighting their significance as a global food safety concern. This study aimed to characterize bacterial communities in enoki mushrooms (n = 50) distributed in South Korea, with a focus on the influence of farm environments and distribution channels (supermarkets versus outdoor markets). A combined approach utilizing culture-dependent methods and 16S rRNA amplicon sequencing was employed to profile microbial consortia. The average aerobic plate counts (APCs) and coliform counts in enoki mushrooms were 7.9 ± 1.0 and 5.1 ± 2.2 log CFU/g, respectively, obtained from enoki mushroom samples collected from supermarkets (n = 29) and outdoor markets (n = 21) in Seoul and Jeonju. Noticeable differences in APCs and coliform counts were observed among farms, while no substantial variations were found between enoki mushrooms across distribution channels. The dominant bacterial phylum and family identified in enoki mushrooms were Proteobacteria (63.1 %) and Enterobacteriaceae (59.8 %), respectively. The genera Lactococcus (17.8 %) and Leuconostoc (7.2 %) were most abundant, followed by Pseudomonas (2.7 %) and Staphylococcus (0.2 %). The farm environment had a stronger influence on the alpha and beta diversity of the enoki mushroom microbiome compared to distribution channels. The high similarity in microbial diversity observed within mushrooms from the same farm suggests that the characteristic microbiome of postharvest enoki mushrooms may be established before distribution. These findings provide a comprehensive framework for understanding the microbial ecology of postharvest enoki mushrooms and offer critical insights for developing effective safety management strategies to mitigate potential food safety risks and ensure safe consumption. © 2025