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Applied Microbiology
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Applied Microbiology of Foods, 3rd Edition
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Applied Microbiology of Foods, 3rd Edition

A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: 31 December 2026 | Viewed by 7185

Special Issue Editor

Prof. Dr. Peter Muriana

E-Mail Website
Guest Editor
1. Department of Animal and Food Science, Oklahoma State University, Stillwater, OK 74078, USA
2. Robert M. Kerr Food and Agricultural Products Center, Oklahoma State University, Stillwater, OK 74078, USA
Interests: food microbiology of raw and processed meats and produce; foodborne pathogens; Listeria monocytogenes; Salmonella spp.; STEC E. coli; vegetable nitrite ('natural nitrite') vs. sodium nitrite; Clostridium spp.; surrogate organisms to mimic pathogens; antimicrobial interventions (chemical, biological, physical; bacteriocins as biopreservatives); microbiology and processing of dried beef (biltong); biofilms; sanitizers; shelf-life studies/microbial validation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issues “Applied Microbiology of Foods” and "Applied Microbiology of Foods, 2nd Edition".

This Special Issue will consider a wide scope of applied microbiology as it relates to foodborne microorganisms and their interactions with foods and processes meant to inhibit bacteria or safeguard foods involving foodborne pathogens, spoilage, or beneficial microorganisms. Topics may include antimicrobial interventions, whether chemical, biological, or physical, for reducing or eliminating foodborne pathogens or spoilage microorganisms in raw/processed foods. The Special Issue may also include analyses of microbial outcomes or wholesale microbiome analyses of the results of interventions. The use of ‘natural’ antimicrobials (i.e., bacteriocins, bacteriophage, microbial fermentates, and vegetable nitrite) has gained favor in applications such as food preservatives. In recent years, natural, microbial-derived ingredients have made progress in their acceptance as natural food ingredients. These include 'microbial fermentates' produced by lactic acid bacteria that are generally regarded as safe (GRAS) and include bacteriocins or other natural antimicrobials. Biological modifications using 'safe' bacteria have changed the outlook on 'natural' vs. 'chemical' food preservatives and have made an impact on commercial applications in food. Natural sources of antimicrobials may result in a ‘clean/green label’ additive. Such changes have revitalized many commercial processes. Antimicrobial interventions are not limited to chemical/biological treatments; there are also physical processes (drying, blanching, sous vide, hot water showers, submersed water pasteurization, radiant heat ovens, microwave processing, high-pressure processing, and cold atmospheric plasma) that can provide effective food safety measures to inhibit pathogens and spoilage organisms. As Guest Editor of this Special Issue, I look forward to receiving and reviewing your contributions to this topic.

Prof. Dr. Peter Muriana
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 250 words) can be sent to the Editorial Office for assessment.

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. Applied Microbiology 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 1200 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

  • antimicrobial interventions against foodborne pathogens or spoilage organisms
  • foodborne pathogens (L. monocytogenes, STEC E. coli, Salmonella, Clostridium, Staphylococcus)
  • evaluation of surrogate microorganisms to mimic foodborne pathogens during processing
  • inhibition of spore germination
  • biofilm, microbial adherence, and removal or elimination
  • bacteriocins as biopreservatives
  • challenge studies and microbial validation

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Related Special Issues

Published Papers (6 papers)

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Research

11 pages, 696 KB  
Article
Microbial Reservoirs in Artisanal Dairy Products from Spain and Algeria Harbor Lactic Acid Bacteria with Significant Gluten-Degrading Activity
by Abdelhak Menasri, Rosario Lucas, Javier Rodríguez López, Antonio Gálvez, Mª José Grande and Rubén Pérez Pulido
Appl. Microbiol. 2026, 6(3), 45; https://doi.org/10.3390/applmicrobiol6030045 - 15 Mar 2026
Viewed by 152
Abstract
Celiac disease (CD) is an autoimmune disorder triggered by immunogenic gluten peptides that resist gastrointestinal digestion. The only current treatment is a strict gluten-free diet, which is challenging to maintain. Lactic acid bacteria (LAB) with specific proteolytic systems offer a promising strategy for [...] Read more.
Celiac disease (CD) is an autoimmune disorder triggered by immunogenic gluten peptides that resist gastrointestinal digestion. The only current treatment is a strict gluten-free diet, which is challenging to maintain. Lactic acid bacteria (LAB) with specific proteolytic systems offer a promising strategy for gluten hydrolysis and potential reduction of immunogenicity. This study aims to isolate and characterize gluten-degrading LAB from traditional Spanish and Algerian dairy products. A total of 27 artisanal dairy samples were collected. LAB were isolated on MRS and Elliker agar. Gluten-degrading activity was screened using a well diffusion assay with cell-free supernatants and a spot assay with live cultures. Active isolates were identified by 16S rRNA gene sequencing. Out of 123 isolates, 40 (32.5%) were positive in the well assay, while 67 (54.5%) were positive in the spot assay, indicating the latter’s higher sensitivity for detecting cell-associated proteases. Halo diameters ranged from 6 to 16 mm. Algerian isolates exhibited significantly stronger activity (mean halo: 12.6 ± 2.1 mm) compared to Spanish isolates (10.2 ± 2.0 mm; p < 0.001). Molecular identification of the 32 most active isolates revealed the following dominant species: Lactiplantibacillus plantarum, L. pentosus, Levilactobacillus brevis, and Enterococcus faecium. This study confirms that artisanal dairy fermentations are rich sources of LAB with robust gluten-degrading potential. The superior activity of Lactiplantibacillus spp. aligns with their complex peptidase systems. The geographical variation highlights the influence of local fermentation practices. Selected strains represent excellent candidates for developing adjunct cultures to produce gluten-reduced foods and warrant further investigation as potential probiotics, pending safety and efficacy validation in vivo and in clinical studies. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 3rd Edition)
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8 pages, 452 KB  
Communication
Comparative Efficacy of Ethanol, UV-C, and Ultrasound Against Candida albicans, Aspergillus brasiliensis, and Listeria innocua on Kalamon Table Olives
by Rafail Fokas, Nikolaos P. Kostopoulos, Maria-Eleni Dimitrakopoulou and Apostolos Vantarakis
Appl. Microbiol. 2026, 6(2), 27; https://doi.org/10.3390/applmicrobiol6020027 - 30 Jan 2026
Viewed by 454
Abstract
This study investigated the effectiveness of ethanol (70%, 3 min), Ultraviolet-C irradiation (6 and 12 min), and ultrasound (37 kHz, 15 min) for decreasing Candida albicans, Aspergillus brasiliensis, and Listeria innocua on Greek Kalamon table olives before brining. Ethanol demonstrated the [...] Read more.
This study investigated the effectiveness of ethanol (70%, 3 min), Ultraviolet-C irradiation (6 and 12 min), and ultrasound (37 kHz, 15 min) for decreasing Candida albicans, Aspergillus brasiliensis, and Listeria innocua on Greek Kalamon table olives before brining. Ethanol demonstrated the greatest decreases (>2.80 log10 for C. albicans, >2.09 log10 for A. brasiliensis, and >3.79 log10 for L. innocua). UV-C had a time-dependent impact, with 12 min producing more inactivation than 6 min (1.30, 1.05, and 1.57 log10, respectively, for C. albicans, A. brasiliensis, and L. innocua). Ultrasound alone produced minimal reductions (<0.60 log10). Overall, ethanol outperformed Ultraviolet-C and ultrasound in the test settings, with Ultraviolet-C providing moderate, exposure-dependent decreases. These findings stimulate additional research into non-thermal therapies and their practical use in table olive processing. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 3rd Edition)
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15 pages, 3975 KB  
Article
Acid Adaptation Leads to Sensitization of Salmonella Challenge Cultures During Processing of Air-Dried Beef (Biltong, Droëwors)
by Pratikchhya Adhikari, Cailtin E. Karolenko, Jade Wilkinson and Peter M. Muriana
Appl. Microbiol. 2025, 5(4), 106; https://doi.org/10.3390/applmicrobiol5040106 - 6 Oct 2025
Cited by 1 | Viewed by 1156
Abstract
US food regulatory agencies have adopted a preference for researchers and testing labs to use ‘acid-adapted challenge cultures’ when performing inoculated validation studies of food processes that involve acidic treatments to accustom the cultures to acidic pH so that they will not be [...] Read more.
US food regulatory agencies have adopted a preference for researchers and testing labs to use ‘acid-adapted challenge cultures’ when performing inoculated validation studies of food processes that involve acidic treatments to accustom the cultures to acidic pH so that they will not be easily affected during processing. We evaluated acid adaptation in regard to the processing of South African style air-dried beef, notably biltong and droëwors, using a mixture of five serovars of Salmonella as well as a unique serovar isolated from dried beef (Salmonella Typhimurium 1,4,[5],12:i:-). Acid adaptation was obtained by growing cultures in tryptic soy (TS) broth containing 1% glucose. Non-adapted cultures were obtained by growth in TS broth without glucose or in TS broth with 1% glucose but buffered with 0.2 M phosphate buffer. Processes included biltong (dried solid beef) and droëwors (ground, sausage-style). Each trial was performed twice and triplicate samples were examined at each sampling point (i.e., n = 6). Statistical analysis was applied using analysis of variance (ANOVA) or one-way repeated measures (RM-ANOVA) and the Holm–Sidak test for pairwise multiple comparisons to determine significant differences (p < 0.05). We observed that in all processes examined (eight trials), treatments using acid-adapted cultures were more sensitive to the biltong and droëwors processes, giving greater reductions (5.3-log reduction) than when non-adapted cultures were used (3.8-log reduction). Acid adaptation leads to stressed conditions in Salmonella resulting in sensitization to the multiple hurdles found in biltong and droëwors processing (acid/vinegar, salt, desiccation). Based on our data, the use of non-adapted Salmonella cultures to achieve desired challenge culture process lethality could result in more robust processing conditions and a greater level of safety in these products as intended by US regulatory guidance. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 3rd Edition)
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20 pages, 1509 KB  
Article
Studying the Population Dynamics of NSLAB and Their Influence on Spores During Cheese Ripening
by Rakesh Kaushik and Sanjeev Anand
Appl. Microbiol. 2025, 5(3), 65; https://doi.org/10.3390/applmicrobiol5030065 - 3 Jul 2025
Cited by 3 | Viewed by 1586
Abstract
Cheese ripening involves microbial changes, with starter lactic acid bacteria (SLAB) initiating fermentation and nonstarter lactic acid bacteria (NSLAB) driving flavor and texture development. However, heat-resistant spores of Clostridium and Bacillus can survive pasteurization and cause spoilage during ripening. This study evaluated NSLAB [...] Read more.
Cheese ripening involves microbial changes, with starter lactic acid bacteria (SLAB) initiating fermentation and nonstarter lactic acid bacteria (NSLAB) driving flavor and texture development. However, heat-resistant spores of Clostridium and Bacillus can survive pasteurization and cause spoilage during ripening. This study evaluated NSLAB dynamics in the presence of spores during cheese ripening. Cheddar cheese samples at pilot-scale level (110 L) with four treatments, namely control, with spores of B. licheniformis (T1), with spores of Cl. tyrobutyricum (T2), and both spores (T3) at 2.0 Log10 CFU/mL, were ripened at 7 °C for six months. SLAB declined from 8.0 to 0.2 Log10 CFU/g, while NSLAB increased from 2.0 to 8.5 Log10 CFU/g by month three and maintained their counts up to six months, unaffected by spore presence. Spore counts were ≤1.45 Log10 CFU/g in controls but reached 2.94 ± 0.02 (T2) and 2.48 ± 0.03 (T3), correlating with spoilage signs after five months. MALDI-TOF identified L. rhamnosus (up to 37%) and L. paracasei (up to 25%) as dominant NSLAB across treatments. Physicochemical parameters were not significantly affected by higher spore levels. While NSLAB dominated, they were inadequate to prevent spoilage in spore-inoculated samples exceeding 2.0 logs during cheese ripening. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 3rd Edition)
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13 pages, 951 KB  
Article
Optimization of the Treatment of Beer Lees for Their Use in Sustainable Biomass Production of Lactic Acid Bacteria
by Natalia S. Brizuela, Marina E. Navarro, Gabriel Rivas, Gabriel Gómez, Carolina Pérez, Liliana Semorile, Emma E. Tymczyszyn and Bárbara Bravo-Ferrada
Appl. Microbiol. 2025, 5(2), 51; https://doi.org/10.3390/applmicrobiol5020051 - 30 May 2025
Cited by 3 | Viewed by 1235
Abstract
Beer lees (BL), a by-product of beer production, consist mainly of dead yeast cells with potential nutritional value. On the other hand, yeast extract (YE), obtained through the lysis of yeast cells, is commonly used as a nutrient-rich supplement for the growth of [...] Read more.
Beer lees (BL), a by-product of beer production, consist mainly of dead yeast cells with potential nutritional value. On the other hand, yeast extract (YE), obtained through the lysis of yeast cells, is commonly used as a nutrient-rich supplement for the growth of fastidious microorganisms such as lactic acid bacteria (LAB). However, YE is a high-cost ingredient. Therefore, the aim of this study was to optimize the use of BL as a low-cost alternative source of YE through different lysis treatments, evaluating its suitability to support the growth of UNQLpc 10 and UNQLp 11 strains in a whey permeate (WP)-based medium. Growth kinetics and cell viability were compared with those obtained in MRS broth. The best results were observed with sonicated BL, up to 10 logarithmic units, which supported LAB growth comparable to MRS. Although autolyzed BL promoted lower bacterial growth than sonicated BL, it showed greater cell disruption and higher levels of nitrogen, proteins, and amino acids (5.32%, 26.0%, and 277 nM, respectively). Additionally, autolyzed BL exhibited lower concentrations of reducing sugars and a higher presence of Maillard reaction products, as indicated by colorimetric analysis. These changes, which may be related to the formation of Maillard reaction products during the autolysis process, could have negatively affected the nutritional quality of the extract and, thus, reduced its effectiveness as a bacterial growth promoter. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 3rd Edition)
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26 pages, 11049 KB  
Article
Dynamics of Physiological Changes of Shiga Toxin-Producing Escherichia coli O157:H7 on Romaine Lettuce During Pre-Processing Cold Storage, and Subsequent Effects on Virulence and Stress Tolerance
by Dimple Sharma, Joshua O. Owade, Corrine J. Kamphuis, Avery Evans, E. Shaney Rump, Cleary Catur, Jade Mitchell and Teresa M. Bergholz
Appl. Microbiol. 2025, 5(2), 45; https://doi.org/10.3390/applmicrobiol5020045 - 6 May 2025
Cited by 3 | Viewed by 1890
Abstract
If lettuce is contaminated in the field, Shiga toxin-producing E. coli (STEC) O157:H7 can survive through the distribution chain. Prolonged cold storage during transportation may impact pathogen physiology, affecting subsequent stress survival and virulence. Greenhouse-grown Romaine lettuce, inoculated with three STEC O157:H7 strains, [...] Read more.
If lettuce is contaminated in the field, Shiga toxin-producing E. coli (STEC) O157:H7 can survive through the distribution chain. Prolonged cold storage during transportation may impact pathogen physiology, affecting subsequent stress survival and virulence. Greenhouse-grown Romaine lettuce, inoculated with three STEC O157:H7 strains, was harvested after 24 h and stored at 2 °C for 5 d following 4 h at harvest temperature (9 °C or 17 °C). Culturable, persister, and viable but non-culturable (VBNC) cells were quantified. Virulence was evaluated using Galleria mellonella and acid tolerance at pH 2.5 and tolerance to 20–25 ppm free chlorine were quantified. Colder harvest temperature (9 °C) before cold storage led to greater transformation of STEC O157:H7 into dormant states and decreased virulence in most cases. Increasing length of cold storage led to decreased virulence and acid tolerance of STEC O157:H7 on lettuce, while having no significant effect on chlorine tolerance. These findings highlight that entry of STEC O157:H7 into dormant states during harvest and transportation at cold temperatures leads to decreased stress tolerance and virulence with increasing cold storage. Changes in STEC O157:H7 physiology on lettuce during cold storage can be integrated into risk assessment tools for producers, which can assist in identifying practices that minimize risk of STEC O157:H7 from consumption of lettuce. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 3rd Edition)
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