Microbial Physiology and Metabolism in Food Fermentation and Food-Associated Environments

The physiology and metabolism of microorganisms determine how fermented and other food-associated microbial communities function. They set how nutrients are used, how metabolites are produced and transformed, how cells adapt to stress and how ecological interactions are established. These processes shape microbial succession, spoilage, and the persistence or inhibition of undesirable microorganisms, and they ultimately influence the transformation and stability of foods and beverages. Advances in metagenomics, comparative genomics, transcriptomics, metabolomics and other multi-omics approaches have expanded our ability to investigate the functional potential of these communities. However, taxonomic composition alone does not reflect microbial activity. Further research is needed to link microbial diversity with metabolic functions, regulatory mechanisms, microbial interactions and experimentally observed phenotypes. Protective microorganisms, microbial consortia and their metabolites can also contribute to biopreservation through nutrient competition, environmental modification, antagonism and the production of antimicrobial compounds. Their effectiveness depends on the community, the environmental conditions and the physiological state of the microorganisms involved. This Research Topic aims to provide a platform for studies on the metabolism, physiology and interactions of bacteria, archaea, yeasts and fungi in food fermentation processes and other food-associated environments. By food-associated environments we mean the settings where food raw materials are fermented, ripened, preserved or stored, together with the fermented and preserved products themselves. We particularly encourage research that combines microbial community characterization with genomic, metabolic, physiological, experimental or computational approaches. The goal is to elucidate the mechanisms behind microbial functions, stress adaptation and interactions, and to support sustainable microbial strategies for controlling undesirable microorganisms and improving product stability.We welcome studies on fermented foods and beverages (such as fermented vegetables, table olives, dairy, meat, fish and plant-based products), related plant-material fermentations such as silage, and defined or synthetic communities and model systems that represent them, when they provide mechanistic insight into microbial physiology, metabolism or interactions. Topics include, but are not limited to:Microbial metabolism and its regulation (nutrient utilization, metabolic flexibility, production and transformation of metabolites)Stress responses and adaptation to pH, salinity, temperature, oxygen availability, nutrient limitation and processing stressesFermentation physiology and microbial successionMicrobial interactions, consortia and defined communitiesPhysiological mechanisms of spoilage and of the persistence of undesirable microorganisms, including foodborne pathogensProtective microorganisms and antimicrobial compounds such as bacteriocins, organic acids, antimicrobial peptides, enzymes and volatile compoundsGenomic, multi-omics, experimental and computational approaches, including metabolic modelling and machine learningCulture-dependent and culture-independent methods, metabolite analysis and interaction assays are welcome when they contribute to a mechanistic understanding.Please note that descriptive studies of food microbial communities based solely on amplicon sequencing (such as 16S rRNA gene profiling) and correlation analyses with product or process variables will not be considered. When amplicon data are included, they should be accompanied by a clear hypothesis, the methods used to test it, and an explanation of how the results support and validate it, for example through physiological, metabolic or experimental data. Topic editors: Antonio Benítez Cabello, Ines Calvete-Torre Source: https://www.frontiersin.org/research-topics/86913/microbial-physiology-and-metabolism-in-food-fermentation-and-food-associated-environments