Food Microorganisms and Genomics, 2nd Edition

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Food Microorganisms and Genomics”. (https://www.mdpi.com/si/161860).

The rapid advancements in metagenomics and whole-genome sequencing (WGS) have revolutionized the study of complex microbial communities, enabling detailed analyses across a broad range of taxonomic groups. In recent years, the reduced costs and greater accessibility of next-generation sequencing (NGS) technologies have facilitated their application to food-related microorganisms, leading to a more comprehensive approach to studying food microbiota. WGS provides a genome-based method for understanding the phylogenetic relationships of microorganisms and allows for an in-depth exploration of the genetic potential of technological microorganisms, probiotics, and foodborne pathogens.

This Special Issue of Microorganisms, entitled “Food Microorganisms and Genomics,” focuses on the application of NGS technologies in various aspects of food microbiology. The issue includes metagenomic studies for the detailed characterization of microbial populations in different food products. For example, metagenomics can be applied to dairy or fermented vegetable products to uncover the diversity of lactic acid bacteria responsible for fermentation. Other studies might explore the spoilage microbiomes of meat products to detect and monitor rotting bacteria, such as Leuconostoc mesenteroides, or potential foodborne pathogens, such as Leuconostoc mesenteroides, Salmonella enterica, or Listeria monocytogenes.

Moreover, the Special Issue covers the use of WGS in the genomic comparison of microbial taxa with potential applications in food and nutraceuticals as technological starters or probiotics. For instance, exploring the diversity of Lactobacillus strains could reveal insights into their health-promoting properties or their suitability for inclusion in functional foods. WGS can be applied to technological starters (strains deliberately added to food products to drive specific fermentation processes, enhance flavour, and improve food safety) to uncover various aspects of their genomes, such as metabolic pathways, resistance to stress conditions, or their ability to produce specific compounds like bacteriocins, which inhibit the growth of harmful bacteria. Additionally, WGS can help in tracking the persistence and stability of these starters during food processing, ensuring their effectiveness throughout production.

The scope of the Special Issue also extends to studies investigating the interactions between food-associated microbiota and the gut microbiome. The application of NGS in the study of food microorganisms not only deepens our understanding of their roles and interactions in food systems but also aids in improving food safety, functionality, and overall consumer well-being.

Dr. Stefano Raimondi
Dr. Alberto Amaretti
Dr. Francesco Candeliere
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

• food microbiome
• comparative genomics
• foodborne pathogen
• probiotics
• technological starter