Microbial contamination and microbiome composition of fresh edible mushrooms: a critical review

Fresh edible mushrooms have gained popularity as valuable dietary components, with global consumption steadily increasing due to their high nutritional and functional benefits. However, their constitutional characteristics make them especially vulnerable to microbial spoilage, potentially harming the fruiting bodies during cultivation and creating major challenges in harvesting, handling, and storage after harvest. This review highlights the types, sources, and impacts of microbial contamination in fresh edible mushrooms, with a focus on spoilage organisms. It explores the emerging field of mushroom microbiome research, highlighting the composition, diversity, and functional roles of microbial communities associated with 4 edible mushroom species (Agaricus sp., Pleurotus sp., Lentinula sp., and Flammulina sp). Studies employing high-throughput sequencing technologies to explore the microbial associations of edible mushrooms are discussed, providing deeper insights into these complex microbial ecosystems and their impacts on mushroom quality, shelf life, and safety. Bibliometric studies using VOSviewer over a 10-year period have uncovered global research trends, emerging focus areas, and identified gaps in the field. This review also discusses post-harvest control strategies and microbiome-targeted interventions to enhance microbial safety and extend shelf life. Edible mushrooms also contribute to the circular bioeconomy by converting agricultural residues into nutritious food. However, microbial contamination can compromise product quality and safety within this sustainable production system. Persistent knowledge gaps in understanding microbial dynamics and mushroom-microbiota interactions must be addressed to develop innovative, sustainable approaches to mushroom preservation and food safety management.