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

Deadline for manuscript submissions: closed (31 March 2026) | Viewed by 24989

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Dr. Luis Guillermo González-Olivares

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Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma, Hidalgo 42184, Mexico
Interests: lactic fermentation; prebiotics, probiotics and lactic acid bacteria metabolism
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Special Issue Information

Dear Colleagues,

Advances in food microbial biotechnology have significantly transformed the food industry. Advanced techniques have been developed to improve food production and quality using microorganisms such as bacteria, fungi and yeasts. For example, controlled fermentation has optimized the production of products such as cheeses, yogurts and bread, increasing their flavor, texture and nutritional value. In addition, genetic engineering allows for microbial strains to be modified to produce functional ingredients, such as probiotics and prebiotics, that benefit digestive health. Biotechnology has also allowed for the creation of microorganisms capable of breaking down toxic compounds in foods, improving their safety. Another promising area is sustainable food production using microorganisms, such as creating alternative proteins from yeast and bacteria, reducing dependence on traditional resources. These advances optimize food production and promote healthier and more sustainable eating.

Dr. Luis Guillermo González-Olivares
Guest Editor

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Keywords

microbial biotechnology
food industry
microorganisms
controlled fermentation
genetic engineering
probiotics
prebiotics
food safety
sustainable food production
alternative proteins

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Published Papers (9 papers)

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Research

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14 pages, 620 KB

Open AccessArticle

Bacteriocin AS-48 and High Hydrostatic Pressure as Hurdles in a Vegetable Cream upon Temperature Abuse

by Javier Rodríguez López, Rosario Lucas López, Mᵃ José Grande Burgos, Antonio Gálvez and Rubén Pérez Pulido

Microorganisms 2026, 14(4), 892; https://doi.org/10.3390/microorganisms14040892 - 16 Apr 2026

Viewed by 198

Abstract

Refrigerated, ready-to-eat (RTE) vegetable foods are widely consumed. Microorganisms may proliferate in these foods during cold chain breaks, increasing the risks for food spoilage and foodborne disease. Despite the increasing use of novel non-thermal preservation technologies, the comprehensive impact of these hurdles on the broad taxonomic structural dynamics of the food microbiota during temperature abuse remains poorly understood. To address this gap, we determined the impact of bacteriocin AS-48 and a high hydrostatic pressure (HHP) treatment, both individually and in combination, on the microbial load and bacterial diversity of a refrigerated vegetable cream upon temperature abuse. Counts of aerobic mesophilic bacteria (37 °C, 24 h) increased significantly (p < 0.05) in controls during temperature abuse, but not in samples treated with bacteriocin, HHP or both. Amplicon-sequencing analysis indicated that the initial microbiota of control samples was composed mainly of Pseudomonadota (74.50%), followed by Bacillota (21.19%) and Actinobacteriota (3.69%). Bacillota became the predominant group during refrigerated storage (87.21 to 99.48%). After temperature abuse, control samples had lower relative abundances of Bacillota during storage and higher relative abundances of Pseudomonadota, Bacteroidota and Actinobacteriota. All treated samples (irrespective of the treatment) showed lower relative abundances of Bacillota during storage compared to untreated controls without temperature abuse. Genus Bacillus was the predominant group in the control samples during storage. Acinetobacter was associated with temperature abuse. In conclusion, both enterocin AS-48 and HHP can be effective hurdles, not only by preventing bacterial proliferation but also by influencing the dynamics of the microbial community associated with spoilage in vegetable creams exposed to inappropriate temperature conditions. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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19 pages, 6295 KB

Open AccessArticle

LuxR-Type Regulator RRP₆ Positively Regulates the Biosynthesis of Plantaricin EF and Improves Its Production in Lactiplantibacillus plantarum 163

by Yaxuan Liu, Siqi Liu, Zixian Li, Chuangen Huo, Guangli Wang, Xin Zeng, Bingyue Xin and Deyin Zhao

Microorganisms 2025, 13(12), 2780; https://doi.org/10.3390/microorganisms13122780 - 6 Dec 2025

Viewed by 513

Abstract

The two-component system HPK₆/RRP₆ related to the pln locus of plantaricin biosynthesis was screened out. The overexpression of LuxR-type regulator RRP₆ promoted the transcription of ABC transporter-related genes, thereby increasing plantaricin EF yield. Its yield in 163(rrp₆) reached 16.01 mg/L, which was 1.20-fold that of the original strain. The regulatory mechanism indicated that RRP₆ could bind to two sites of the plnG1 promoter, promoting its transcription and translation, accelerating the secretion of plantaricin and auto-inducing peptide, and enhancing the extracellular plantaricin yield. Amino acids Q73, R144, T171, and Y175 play a crucial role in the binding of RRP₆. Furthermore, potential regulatory compensation within the Lactiplantibacillus plantarum 163 genome may compensate for the negative effects after the deletion of rrp₆. These results provide a novel strategy for increasing plantaricin EF yield, which facilitates its large-scale application as a natural and safe food preservative in agriculture and the food industry. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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18 pages, 4139 KB

Open AccessArticle

Comparative Analyses of Pediococcus pentosaceus Strains Isolated from Milk Cattle Reveal New Insights for Screening Food-Protective Cultures

by Sebastian W. Fischer, Nadine Mariani Corea, Anna Euler, Leonie Bertels and Fritz Titgemeyer

Microorganisms 2025, 13(10), 2244; https://doi.org/10.3390/microorganisms13102244 - 25 Sep 2025

Cited by 4 | Viewed by 1694

Abstract

Pediococcus pentosaceus is a lactic acid bacterium used inter alia for the fermentation of milk, meat, vegetables, fruits, and even for brewing beer. Several health-promoting effects, such as antibacterial and antifungal activities or microphage and immune system stimulation, have been attributed. Apart from refining foods during the fermentation process, P. pentosaceus strains are added to meat and meat products as protective cultures to improve food safety, while leaving the organoleptic properties untouched. Since knowledge on the latter issue is still limited, we investigated 32 isolates from milk samples and teat canal biofilms regarding their antibacterial efficacy as a prerequisite for possible application as protective cultures. P. pentosaceus strains were unequivocally identified by DNA sequencing of the rrnA gene encoding 16S rRNA. Binary matrices obtained from random amplification of polymorphic DNA experiments showed that all isolates differed by more than 5% and thus represented subspecies. The antibacterial profiles against eight food-borne pathogens and food spoilage bacteria were determined. They efficiently combatted, although to various extents, Gram-negative bacteria such as Pseudomonas aeruginosa or Salmonella enterica, and Gram-positive bacteria such as Staphylococcus aureus and Listeria monocytogenes. Interestingly, acid production was dependent on the presence of the challenged pathogen and did not correlate with the extent of inhibition. Bioinformatic analyses of the genomes of the three top-ranked isolates revealed a pronounced genomic plasticity with a core genome of 1460 genes and additional 91, 130, and 161 unique genes, respectively. Each strain included a set of three, five, or six plasmids and was equipped with different genes encoding bacteriocins. The data suggest that multiple strains of P. pentosaceus should be included in order to optimize the selection of a culture for food preservation. The approach could also be applicable to other bacterial species. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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17 pages, 1668 KB

Open AccessArticle

Analysis of Bacterial and Fungal Communities and Organic Acid Content in New Zealand Lambic-Style Beers: A Climatic and Global Perspective

by Aghogho Ohwofasa, Manpreet Dhami, Christopher Winefield and Stephen L. W. On

Microorganisms 2025, 13(2), 224; https://doi.org/10.3390/microorganisms13020224 - 21 Jan 2025

Cited by 2 | Viewed by 2072

Abstract

Beer produced by autochthonous microbial fermentation is a long-established craft beer style in Belgium that has now been implemented commercially in New Zealand. We used a metabarcoding approach to characterize the microbiome of 11 spontaneously fermented beers produced by a single brewery in Oamaru from 2016 to 2022. Key organic acid concentrations were also determined. Both bacterial and fungal populations varied considerably between vintages and between individual brews produced in 2020. Similarly, for organic acids, the concentrations of L-malic acid, succinic acid, and L-lactic acid statistically differed from one vintage to another. Moreover, a correlation between the concentrations of certain organic acids and microbial composition was inferred by ordination analyses. Through reference to publicly available climate data, humidity and maximum temperature seemed to enhance the abundance of Penicillium and Hanseniaspora in beer microbiota. However, comparison with previously published studies of Belgian lambic beers, similar Russian ales, and publicly available temperature data from these regions showed that the microbial populations of these were relatively stable despite greater extremes of weather. Our results suggest that while climatic variables may influence microbial populations during beer making that employs autochthonous fermentation in New Zealand, such variation is not evident where similar beers are produced in facilities with a long-established history of production. These findings have implications for lambic-style beer production in the context of global climate change, notably where microbial populations may lack environmental adaptation. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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13 pages, 2480 KB

Open AccessArticle

Optimization of Medium Composition and Fluidized Bed Drying Conditions for Efficient Production of Dry Yeast

by Hyun-Jin Kang, Hwan Hee Yu, Chang-Won Cho, Young Kyung Rhee, Tae-Wan Kim and Young-Wook Chin

Microorganisms 2025, 13(1), 22; https://doi.org/10.3390/microorganisms13010022 - 26 Dec 2024

Cited by 7 | Viewed by 2617

Abstract

Yeast formulations such as dry yeast are essential for supplying microbial starters to the alcoholic beverage industry. In Korea, the expensive freeze-drying method is used to manufacture brewer’s dry yeast, and therefore an economical process such as fluidized bed drying is needed. In the dry yeast manufacturing process, the medium and drying conditions are key factors that determine its quality and manufacturing cost. In this study, we aimed to optimize the medium composition and fluidized bed drying conditions for the efficient production of dry yeast. Muscovado and corn steep liquor were used as the carbon and nitrogen sources, respectively, and their optimal concentrations were identified using response surface methodology for efficient cultivation of Saccharomyces cerevisiae ReY4-7 isolated from nuruk. Central composite design analysis revealed that the optimal medium composition was 146.12 g/L muscovado and 58.68 g/L corn steep liquor. A dry cell weight of 36 g/L was achieved during 24 h of batch fermentation in a 30-L bioreactor containing this medium. Analysis of protective agents against fluidized bed drying revealed Span 80 as the strongest protective agent for S. cerevisiae ReY4-7. Response surface methodology revealed 50 °C and 41.45 min as the optimal fluidized bed drying conditions, under which the viable cell count reached 10.28 log CFU/g, comparable to that of the commercial dry yeast products. Overall, optimization of the medium and drying conditions significantly improved the final cell concentration in the cultivation process and the viable cell count in the drying process of dry yeast. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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13 pages, 5013 KB

Open AccessArticle

The Yeast F-Box Protein Met30 Regulates Proline Utilization Independently of Transceptor Can1 Under Nutrient-Rich Conditions

by Akira Nishimura, Ryoya Tanahashi and Hiroshi Takagi

Microorganisms 2024, 12(12), 2510; https://doi.org/10.3390/microorganisms12122510 - 5 Dec 2024

Cited by 1 | Viewed by 1855

Abstract

Proline is the most abundant amino acid in wine and beer, largely due to the limited utilization of proline by the yeast Saccharomyces cerevisiae during fermentation. Previous studies have shown that the arginine transporter Can1 plays a role in regulating proline utilization by acting as a transceptor, combining the functions of both a transporter and a receptor for basic amino acids. However, the CAN1-disrupted strains have exhibited the inhibition of proline utilization under nutrient-rich conditions, indicating that additional factors beyond basic amino acids contribute to the inhibition of proline utilization. Here, we used the parent strain with the CAN1 deletion to derive mutants that can utilize proline even under nutrient-rich conditions. A genomic analysis revealed a mutation in the MET30 gene, which encodes an F-box subunit of the SCF ubiquitin ligase complex, that causes reduced Met30 function. Importantly, we found that Met30 and Can1 independently regulate proline utilization. Our screening showed that the Met30-dependent inhibition of proline utilization occurs when ammonium ions, methionine or cysteine, and another amino acid (especially threonine or isoleucine) are present simultaneously. The present data offer new insights into the regulation of proline metabolism. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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Review

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27 pages, 1538 KB

Open AccessReview

From Basics to Breakthroughs: A Review on the Evolution of Campylobacter spp. Culture Media

by Ana Rita Barata, Maria José Saavedra and Gonçalo Almeida

Microorganisms 2026, 14(2), 498; https://doi.org/10.3390/microorganisms14020498 - 19 Feb 2026

Viewed by 1174

Abstract

Since their recognition as human pathogens in the 1970s, Campylobacter spp. have posed persistent challenges to microbiologists due to their fastidious growth requirements and environmental sensitivity. The continuous refinement of selective and differential culture media has been crucial for improving their detection, isolation, and characterization in both clinical and food microbiology. This comprehensive review provides a chronological overview of the evolution of Campylobacter culture media, highlighting the scientific milestones that shaped current cultivation practices—from early blood- and charcoal-based formulations to modern selective, chromogenic, and systems permitting incubation under less stringent atmospheric conditions. Emphasis is placed on the rationale behind medium composition, the transition from empirical experimentation to standardized formulations, and the integration of molecular and metabolic insights into media design. The evolution of Campylobacter growth media mirrors the broader trajectory of microbiology itself, moving from artisanal experimentation toward precision-driven innovation. Ongoing advancements in culture technology, including sustainable and data-guided formulations, will continue to enhance global surveillance, food safety, and pathogen ecology research. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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24 pages, 831 KB

Open AccessReview

Exploring the Potential of Haematococcus pluvialis as a Source of Bioactives for Food Applications: A Review

by Joseane C. Bassani, Sthéfani da Cunha, Deborah Catharine de Assis Leite, Creciana M. Endres, Crivian Pelisser, Karine L. Meneghetti, Gabriel Bombo, Alcina M. M. B. Morais, Rui M. S. C. Morais, Geciane T. Backes and Juliana Steffens

Microorganisms 2025, 13(11), 2606; https://doi.org/10.3390/microorganisms13112606 - 16 Nov 2025

Cited by 2 | Viewed by 2965

Abstract

The search for sustainable and health-promoting food ingredients has positioned microalgae as promising candidates for the development of functional products. Haematococcus pluvialis, a unicellular green microalga, is the richest natural source of astaxanthin, a carotenoid with outstanding antioxidant, anti-inflammatory, and neuroprotective properties. In addition to astaxanthin, H. pluvialis provides high-value proteins, essential fatty acids, polysaccharides, and vitamins, which expand its potential applications in the food sector. This review compiles current knowledge on the biology and physiology of H. pluvialis, with emphasis on cultivation strategies, environmental stress factors, and biotechnological tools designed to enhance bioactive compound production. Advances in extraction and purification methods are also discussed, contrasting conventional solvent-based approaches with emerging green technologies. The integration of these strategies with biomass valorization highlights opportunities for improving economic feasibility and sustainability. Applications of H. pluvialis in the food industry include its use as a functional ingredient, natural colorant, antioxidant, and stabilizer in bakery products, beverages, meat analogs, and emulsified systems. Evidence from in vitro, in vivo, and clinical studies reinforces its safety and effectiveness. Looking ahead, industrial perspectives point to the adoption of omics-based tools, metabolic engineering, and circular economy approaches as drivers to overcome current barriers of cost, stability, and regulation, opening new avenues for large-scale applications in food systems. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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54 pages, 6338 KB

Open AccessReview

Process Technologies for Disinfection of Food-Contact Surfaces in the Dry Food Industry: A Review

by Harleen Kaur Dhaliwal, Shivani Sonkar, Prithviraj V, Luis Puente and M. S. Roopesh

Microorganisms 2025, 13(3), 648; https://doi.org/10.3390/microorganisms13030648 - 12 Mar 2025

Cited by 14 | Viewed by 10867

Abstract

The survival characteristics of bacterial pathogens, including Salmonella spp., Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli, in foods with a low water activity (a_w) have been extensively examined and reported. Microbial attachment on the food-contact surfaces can result in cross-contamination and compromise the safety of low-a_w foods. The bactericidal potential of various conventional and novel disinfection technologies has been explored in the dry food industry. However, the attachment behavior of bacterial pathogens to food-contact surfaces in low-a_w conditions and their subsequent response to the cleaning and disinfection practices requires further elucidation. The review summarizes the elements that influence disinfection, such as the presence of organic residues, persistent strains, and the possibility of microbial biotransfer. This review explores in detail the selected dry disinfection technologies, including superheated steam, fumigation, alcohol-based disinfectants, UV radiation, and cold plasma, that can be used in the dry food industry. The review also highlights the use of several wet disinfection technologies employing chemical antimicrobial agents against surface-dried microorganisms on food-contact surfaces. In addition, the disinfection efficacy of conventional and novel technologies against surface-dried microorganisms on food-contact surfaces, as well as their advantages and disadvantages and underlying mechanisms, are discussed. Dry food processing facilities should implement stringent disinfection procedures to ensure food safety. Environmental monitoring procedures and management techniques are essential to prevent adhesion and allow the subsequent inactivation of microorganisms. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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