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Microorganisms
Special Issues
Microbial Safety and Beneficial Microorganisms in Foods
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Microbial Safety and Beneficial Microorganisms in Foods

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

Deadline for manuscript submissions: 31 August 2025 | Viewed by 6171

Special Issue Editor

Prof. Dr. Theodoros Varzakas

E-Mail Website
Guest Editor
Department of Food Science and Technology, University of Peloponnese, 24100 Antikalamos, Greece
Interests: food technology; food engineering; food safety; food quality; extra virgin olive oil; mycotoxins; fermented foods
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The role of microorganisms in food has been acknowledged since antiquity. However, the modern era has witnessed a significant advancement in our comprehension of the intricate ways microorganisms can exert detrimental and beneficial effects on the food system. Pathogenic microorganisms, such as Salmonella and Escherichia coli, can potentially cause severe foodborne illnesses. Conversely, beneficial microbes have been shown to enhance food stability, safety, and nutritional value. Recent research has focused on elucidating the complex interactions between foodborne pathogens and their environments, thereby facilitating the development of enhanced detection and control methodologies. Furthermore, there is a growing interest in utilizing beneficial microorganisms in food production, particularly in fermented foods and biopreservation. Applying genomics and molecular tracing networks has significantly enhanced our capacity to track and control microbial hazards in food.

This Special Issue provides a platform for researchers to advance our knowledge of microbial safety and the beneficial use of microorganisms in food. It aims to collect and publish recent reviews and research articles on topics such as:

  • The role of microorganisms in food fermentation and its impact on food safety and quality;
  • The use of beneficial microorganisms in food manufacturing, including the production of fermented foods and beverages;
  • The application of microorganisms in food processing to improve nutritional content and create value-added products.

Prof. Dr. Theodoros Varzakas
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

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.

Keywords

  • microbial safety
  • foodborne pathogens
  • beneficial microorganisms
  • food processing
  • fermentation-oriented foods
  • probiotics

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (6 papers)

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Research

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13 pages, 1104 KiB  
Article
Development of a Strain-Specific Detection and Quantification Method for Bifidobacterium animalis subsp. lactis HN019 Using WGS-SNP Analysis and qPCR
by Da Mao, Lei Zhao, Bo Zhao, Hongbin Xu and Qinghe Zhang
Microorganisms 2025, 13(7), 1596; https://doi.org/10.3390/microorganisms13071596 - 7 Jul 2025
Viewed by 87
Abstract
Accurate quantification of Bifidobacterium animalis subsp. lactis HN019, a clinically validated probiotic strain conferring immune modulation, gastrointestinal health, and gut barrier integrity benefits, is essential for diverse applications. To address the critical need for strain-specific detection, we developed a quantitative PCR (qPCR) assay [...] Read more.
Accurate quantification of Bifidobacterium animalis subsp. lactis HN019, a clinically validated probiotic strain conferring immune modulation, gastrointestinal health, and gut barrier integrity benefits, is essential for diverse applications. To address the critical need for strain-specific detection, we developed a quantitative PCR (qPCR) assay targeting a unique single-nucleotide polymorphism (SNP) within the galK gene, identified through comparative whole-genome sequencing (WGS) analysis of 31 B. animalis subsp. lactis strains. The assay exhibited exceptional specificity, distinguishing HN019 from 19 other Bifidobacterium strains. Sensitivity tests indicated a detection limit of 0.5 pg of DNA and 103 CFU/mL of bacterial cells, making it suitable for industrial-scale applications. Additionally, the method exhibited strong repeatability, reproducibility across different qPCR platforms, and resistance to interference from high cell density of B. animalis subsp. lactis DSMZ 10140. Successful quantification of HN019 in complex multi-strain probiotic powders confirmed its practical reliability. This work establishes a rapid, robust, and scalable tool for precise probiotic strain tracking, addressing critical quality control and regulatory compliance needs within the rapidly expanding probiotic industry. Full article
(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods)
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18 pages, 1370 KiB  
Article
Harnessing Waste Bread: From Potential Use in Microbial Growth and Enzyme Production to Techno-Economic Assessment
by Sameh Ben Mabrouk, Bouthaina Ben Hadj Hmida, Wejdene Sallami, Salma Dhaouadi, Theodoros Varzakas and Slim Smaoui
Microorganisms 2025, 13(7), 1571; https://doi.org/10.3390/microorganisms13071571 - 3 Jul 2025
Viewed by 9
Abstract
This study highlights waste bread (WB) as a novel, cost-effective, and nutrient-rich substrate for microbial growth, offering a sustainable alternative to conventional media. As a renewable resource, WB promotes the circular economy by reducing food waste and encouraging biotechnological innovation. The incorporation of [...] Read more.
This study highlights waste bread (WB) as a novel, cost-effective, and nutrient-rich substrate for microbial growth, offering a sustainable alternative to conventional media. As a renewable resource, WB promotes the circular economy by reducing food waste and encouraging biotechnological innovation. The incorporation of WB into microbial culture media enhanced the growth of various reference strains (E. coli, E. faecalis, P. aeruginosa, and S. aureus), with at least a two-fold increase compared to conventional Luria-Bertani (LB) medium. Moreover, combining 2% WB with diluted LB (1/10) reduced medium costs by up to 90%. Furthermore, it was confirmed that 1% WB can effectively replace starch during the screening of amylolytic strains. Applying a fractional factorial design, the production of amylase by Bacillus sp. BSS (Amy-BSS) was enhanced 15-fold. An analysis of the Pareto diagram revealed that WB was the most significant factor. Additionally, Amy-BSS was applied to hydrolyze polysaccharides in WB, enabling the generation of high-value-added products in food processing. This hydrolysis process yielded 4.6 g/L of fermentable sugars from 1% WB. Evaluating the economic feasibility of WB valorization into value-added products elucidates potential pathways for cost reduction and enhanced environmental sustainability, thereby positioning WB as a viable tool for sustainable development. Full article
(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods)
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12 pages, 1878 KiB  
Article
Effects of Fucoidan on the Inhibition of Biofilm Formation of Salmonella enterica Subsp. enterica Serovar Typhimurium on Seafoods and Its Molecular Antibiofilm Mechanisms
by Anamika Roy, Pantu Kumar Roy, Sung Rae Cho and Shin Young Park
Microorganisms 2025, 13(4), 914; https://doi.org/10.3390/microorganisms13040914 - 16 Apr 2025
Cited by 1 | Viewed by 2357
Abstract
Foodborne illnesses, particularly those caused by Salmonella enterica subsp. enterica Serovar Typhimurium, present a significant challenge to public health, especially within the seafood industry due to biofilm formation on foods. This study investigated the antibiofilm potential of fucoidan, a sulfated polysaccharide, against Salmonella enterica [...] Read more.
Foodborne illnesses, particularly those caused by Salmonella enterica subsp. enterica Serovar Typhimurium, present a significant challenge to public health, especially within the seafood industry due to biofilm formation on foods. This study investigated the antibiofilm potential of fucoidan, a sulfated polysaccharide, against Salmonella enterica subsp. enterica Serovar Typhimurium biofilm on crab and shrimp surfaces. Fucoidan’s minimum inhibitory concentration (MIC) was determined to be 150 µg/mL. Sub-MIC (1/8, 1/4, 1/2, and MIC) were evaluated for their impact on inhibition of biofilm formation. Fucoidan treatment resulted in significant, dose-dependent inhibition in biofilm formation, achieving 2.61 log CFU/cm2 and 2.45 log CFU/cm2 reductions on crab and shrimp surfaces, respectively. FE-SEM analysis confirmed biofilm disruption and cell membrane damage. Real-time PCR showed the downregulation of quorum-sensing (luxS) and virulence (rpoS, avrA, and hilA) genes. These results propose that fucoidan has the ability as a natural antibacterial agent for controlling Salmonella enterica subsp. enterica Serovar Typhimurium biofilms in seafood processing, thereby enhancing food safety and minimizing contamination. Full article
(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods)
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Review

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29 pages, 1254 KiB  
Review
Microbial Food Safety and Antimicrobial Resistance in Foods: A Dual Threat to Public Health
by Ayman Elbehiry, Eman Marzouk, Adil Abalkhail, Husam M. Edrees, Abousree T. Ellethy, Abdulaziz M. Almuzaini, Mai Ibrahem, Abdulrahman Almujaidel, Feras Alzaben, Abdullah Alqrni and Akram Abu-Okail
Microorganisms 2025, 13(7), 1592; https://doi.org/10.3390/microorganisms13071592 - 6 Jul 2025
Viewed by 52
Abstract
The intersection of microbial food safety and antimicrobial resistance (AMR) represents a mounting global threat with profound implications for public health, food safety, and sustainable development. This review explores the complex pathways through which foodborne pathogens—such as Salmonella spp., Escherichia coli (E. [...] Read more.
The intersection of microbial food safety and antimicrobial resistance (AMR) represents a mounting global threat with profound implications for public health, food safety, and sustainable development. This review explores the complex pathways through which foodborne pathogens—such as Salmonella spp., Escherichia coli (E. coli), Listeria monocytogenes (L. monocytogenes), and Campylobacter spp.—acquire and disseminate resistance within human, animal, and environmental ecosystems. Emphasizing a One Health framework, we examine the drivers of AMR across sectors, including the misuse of antibiotics in agriculture, aquaculture, and clinical settings, and assess the role of environmental reservoirs in sustaining and amplifying resistance genes. We further discuss the evolution of surveillance systems, regulatory policies, and antimicrobial stewardship programs (ASPs) designed to mitigate resistance across the food chain. Innovations in next-generation sequencing, metagenomics, and targeted therapeutics such as bacteriophage therapy, antimicrobial peptides (AMPs), and CRISPR-based interventions offer promising alternatives to conventional antibiotics. However, the translation of these advances into practice remains uneven, particularly in low- and middle-income countries (LMICs) facing significant barriers to diagnostic access, laboratory capacity, and equitable treatment availability. Our analysis underscores the urgent need for integrated, cross-sectoral action—anchored in science, policy, and education—to curb the global spread of AMR. Strengthening surveillance, investing in research, promoting responsible antimicrobial use, and fostering global collaboration are essential to preserving the efficacy of existing treatments and ensuring the microbiological safety of food systems worldwide. Full article
(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods)
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25 pages, 1085 KiB  
Review
Emerging Technologies and Integrated Strategies for Microbial Detection and Control in Fresh Produce
by Ayman Elbehiry, Eman Marzouk, Feras Alzaben, Abdulaziz Almuaither, Banan Abead, Mohammed Alamri, Abdulaziz M. Almuzaini and Akram Abu-Okail
Microorganisms 2025, 13(7), 1447; https://doi.org/10.3390/microorganisms13071447 - 21 Jun 2025
Viewed by 575
Abstract
The global consumption of fresh and ready-to-eat (RTE) fruits and vegetables has surged due to increasing awareness of their nutritional benefits. However, this trend has been accompanied by a rise in foodborne illness outbreaks linked to microbial contamination. This narrative review synthesizes current [...] Read more.
The global consumption of fresh and ready-to-eat (RTE) fruits and vegetables has surged due to increasing awareness of their nutritional benefits. However, this trend has been accompanied by a rise in foodborne illness outbreaks linked to microbial contamination. This narrative review synthesizes current knowledge on the prevalence and diversity of foodborne pathogens in fresh produce, including bacterial, viral, and fungal agents. It critically evaluates both conventional and emerging detection methods, ranging from culture-based techniques and immunoassays to advanced molecular diagnostics, biosensors, flow cytometry (FC), and hyperspectral imaging (HSI). Additionally, this review discusses cutting-edge control strategies, such as natural antifungal agents, essential oils, biocontrol methods, and non-thermal technologies like cold plasma and UV-C treatment. Emphasis is placed on sampling methodologies, sustainability, One Health perspectives, and regulatory considerations. By highlighting recent technological advances and their limitations, this review aims to support the development of integrated, effective, and safe microbial control approaches for the fresh produce supply chain. Full article
(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods)
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59 pages, 1311 KiB  
Review
A Review on Recent Trends in Bacteriophages for Post-Harvest Food Decontamination
by Márcia Braz, Carla Pereira, Carmen S. R. Freire and Adelaide Almeida
Microorganisms 2025, 13(3), 515; https://doi.org/10.3390/microorganisms13030515 - 27 Feb 2025
Viewed by 1918
Abstract
Infectious diseases resulting from unsafe food consumption are a global concern. Despite recent advances and control measures in the food industry aimed at fulfilling the growing consumer demand for high-quality and safe food products, infection outbreaks continue to occur. This review stands out [...] Read more.
Infectious diseases resulting from unsafe food consumption are a global concern. Despite recent advances and control measures in the food industry aimed at fulfilling the growing consumer demand for high-quality and safe food products, infection outbreaks continue to occur. This review stands out by providing an overview of post-harvest food decontamination methods against some of the most important bacterial foodborne pathogens, with particular focus on the advantages and challenges of using phages, including their most recent post-harvest applications directly to food and integration into active food packaging systems, highlighting their potential in providing safer and healthier food products. The already approved commercial phage products and the numerous available studies demonstrate their antibacterial efficacy against some of the most problematic foodborne pathogens in different food products, reinforcing their possible use in the future as a current practice in the food industry for food decontamination. Moreover, the incorporation of phages into packaging materials holds particular promise, providing protection against harsh conditions and enabling their controlled and continuous release into the food matrix. The effectiveness of phage-added packaging materials in reducing the growth of pathogens in food systems has been well-demonstrated. However, there are still some challenges associated with the development of phage-based packaging systems that need to be addressed with future research. Full article
(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods)
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