Food Microorganisms and Genomics, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1395

Special Issue Editors


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Guest Editor
Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
Interests: gut microbiota; probiotics; lactic acid bacteria; food microbiology; food biotechnology; prebiotics; microbiology; microbial biotechnology; environmental microbiology; microbial ecology; fermentation
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
Interests: fermentation technologies; bioreactors; microbial biotechnology; probiotics; prebiotics; gut microbiota; food microbiology
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
Interests: metagenomics; genomics; gut microbiota; probiotics; food microbiology; food biotechnology; microbial ecology; microbial biotechnology; environmental microbiology; fermentation

Special Issue Information

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

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Keywords

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

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Published Papers (2 papers)

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Research

13 pages, 633 KiB  
Article
Gene Detection and Enzymatic Activity of Psychrotrophic Bacillus cereus s.s. Isolated from Milking Environments, Dairies, Milk, and Dairy Products
by Carlos E. G. Aguilar, Gabriel Augusto Marques Rossi, Higor O. Silva, Luisa Maria F. S. Oliveira, Alenia Naliato Vasconcellos, Danielle de Cássia Martins Fonseca, Andréia Cristina Nakashima Vaz, Bruna Maria Salotti de Souza and Ana Maria Centola Vidal
Microorganisms 2025, 13(4), 889; https://doi.org/10.3390/microorganisms13040889 - 12 Apr 2025
Viewed by 246
Abstract
Bacillus cereus is a spore-forming, Gram-positive bacterium that causes foodborne illness and dairy spoilage. This study analyzed B. cereus s.s. isolates from milking environments, raw milk, and dairy products to assess their genotypic and phenotypic traits. From 466 samples, 61 isolates were obtained: [...] Read more.
Bacillus cereus is a spore-forming, Gram-positive bacterium that causes foodborne illness and dairy spoilage. This study analyzed B. cereus s.s. isolates from milking environments, raw milk, and dairy products to assess their genotypic and phenotypic traits. From 466 samples, 61 isolates were obtained: 27 from milking environments, 9 from dairy environments, 8 from raw milk, and 17 from dairy products. Genomic sequencing identified genes encoding proteolytic (BC5350, BC0666, BC2984, BC0598, BC5351, BC3383, BC2735), lipolytic (BC4862, BC2141, BC1027, BC4123, BC4345, BC5402, BC5401), and esterase (BC1954, BC4515, BC3413, BC3606) enzymes. Plate assays confirmed enzymatic activities. Proteolytic genes were more prevalent in environmental samples, followed by raw milk and dairy products. Lipolytic genes were most frequent in raw milk, followed by environmental samples and dairy products. Esterase genes were most common in dairy environments. These findings suggest that dairy processing influences the enzymatic profile of B. cereus s.s., potentially impacting food safety and quality in the dairy industry. Understanding the distribution of these genes may help develop strategies to mitigate spoilage and contamination risks in dairy products. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics, 2nd Edition)
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15 pages, 3221 KiB  
Article
Genomic Insights into Probiotic Lactococcus lactis T-21, a Wild Plant-Associated Lactic Acid Bacterium, and Its Preliminary Clinical Safety for Human Application
by Masanori Fukao, Keisuke Tagawa, Yosuke Sunada, Kazuya Uehara, Takuya Sugimoto, Takeshi Zendo, Jiro Nakayama and Shuichi Segawa
Microorganisms 2025, 13(2), 388; https://doi.org/10.3390/microorganisms13020388 - 10 Feb 2025
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Abstract
Lactococcus lactis T-21 is a lactic acid bacterium isolated from wild cranberries in Japan that demonstrates significant immunomodulatory properties and has been incorporated into commercial health products. However, probiogenomic analyses specific to T-21 have remained largely unexplored. This study performed a thorough genomic [...] Read more.
Lactococcus lactis T-21 is a lactic acid bacterium isolated from wild cranberries in Japan that demonstrates significant immunomodulatory properties and has been incorporated into commercial health products. However, probiogenomic analyses specific to T-21 have remained largely unexplored. This study performed a thorough genomic characterisation of T-21 and evaluated its safety in initial clinical trials. Genomic analysis revealed substantial genetic diversity and metabolic capabilities, including enhanced fermentative potential demonstrated by its ability to metabolise a wide range of plant-derived carbohydrates, and genetic determinants associated with exopolysaccharide biosynthesis and nisin production, distinguishing T-21 from domesticated dairy strains. These attributes, reflective of its wild plant origin, may contribute to its metabolic versatility and unique probiotic functionalities. A preliminary clinical trial assessing the safety of T-21-fermented milk in healthy Japanese adults indicated no significant adverse outcomes, corroborating its safety for human consumption. Together, these findings support the feasibility of utilising non-dairy, wild plant-origin strains in dairy fermentation processes as probiotics. This study expands our understanding of the genomic basis for T-21’s probiotic potential and lays the groundwork for further investigations into its functional mechanisms and potential applications in promoting human health. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics, 2nd Edition)
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