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Novel Approaches for Controlling and Analyzing Microorganisms in Foods: 2nd...
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Novel Approaches for Controlling and Analyzing Microorganisms in Foods: 2nd Edition

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 18 September 2026 | Viewed by 4972

Special Issue Editors

Prof. Dr. Uelinton Manoel Pinto

E-Mail Website
Guest Editor
Food Research Center, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
Interests: food microbiology; microorganisms; foodborne bacteria; food safety; quorum sensing
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Aline Dias Paiva

E-Mail Website
Guest Editor
Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Universidade Federal do Triangulo Mineiro, Uberaba, Brazil
Interests: probiotics; antimicrobials; gut microbiology; antimicrobial peptides; molecular biology; microbiology

Special Issue Information

Dear Colleagues,

Food safety continues to be a growing concern worldwide. As the complexity of the food supply chain increases, so too do the challenges related to microbial contamination and the emergence of pathogenic microorganisms. Ensuring food safety and quality relies on a comprehensive understanding of microorganisms and their interactions within food ecosystems. By understanding food microbial ecology, it is possible to effectively create preventive measures to eliminate or avoid the transmission or growth of pathogens and spoilage organisms in foods. This knowledge can also be used to improve microbial detection and analysis systems in the food sector.

We invite authors to contribute with original research articles and reviews that showcase cutting-edge research on innovative strategies for the control and analysis of microorganisms in foods. We seek contributions that reflect recent advances in science and technology, offering practical solutions to current food safety challenges. Topics of interest include, but are not limited to:

  • Emerging technologies for detection of microorganisms in the food supply chain.
  • Innovative approaches for controlling foodborne pathogens and spoilage organisms.
  • Applications of nano- and biotechnology in the analysis and control of microorganisms.
  • Antimicrobial strategies using natural compounds and bioactive substances.
  • Computational methods for predicting and analyzing microbial behavior in foods.
  • The impact of environmental factors on microbial growth and survival in food environments.
  • Challenges and opportunities in the field of food safety and quality assurance.

Prof. Dr. Uelinton Manoel Pinto
Prof. Dr. Aline Dias Paiva
Guest Editors

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. Foods is an international peer-reviewed open access semimonthly 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 2900 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

  • microorganisms
  • food safety
  • foodborne pathogens
  • control
  • detection
  • microbial ecology

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

Published Papers (4 papers)

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Research

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20 pages, 660 KB  
Article
Study of the Factors Involved in the Adhesion Process of Salmonella enterica Enteritidis, Escherichia coli, and Staphylococcus aureus to the Surface of Apple, Arugula, Cucumber, and Strawberry
by Jéssica Souza Rocha, Bárbara Morandi Lepaus, Manueli Monciozo Domingos, Patrícia Campos Bernardes and Jackline Freitas Brilhante de São José
Foods 2026, 15(3), 449; https://doi.org/10.3390/foods15030449 - 27 Jan 2026
Cited by 1 | Viewed by 675
Abstract
Bacterial contamination of fresh produce remains a global food safety concern, with pathogens such as Salmonella, Escherichia coli, and Staphylococcus aureus frequently implicated in foodborne outbreaks. Understanding the physicochemical factors involved in bacterial adhesion to fresh produce surfaces is essential for [...] Read more.
Bacterial contamination of fresh produce remains a global food safety concern, with pathogens such as Salmonella, Escherichia coli, and Staphylococcus aureus frequently implicated in foodborne outbreaks. Understanding the physicochemical factors involved in bacterial adhesion to fresh produce surfaces is essential for developing effective sanitization strategies. This study evaluated the influence of surface roughness, hydrophobicity, thermodynamic free energy, and temperature on pathogen adhesion to apple, arugula, cucumber, and strawberry. Surface roughness varied significantly among produce types (2.51–5.86 µm), with arugula exhibiting the highest values. Hydrophobicity assessments revealed discrepancies between qualitative (contact angle-based) and quantitative (free energy-based) methods: while all produce were classified as hydrophobic qualitatively, strawberry was hydrophilic by quantitative analysis. All bacterial species tested were hydrophilic qualitatively, but E. coli showed hydrophobic character quantitatively. Thermodynamic predictions of adhesion (ΔGadhesion) did not predict observed adhesion bacterial counts (5.07–6.20 log CFU·g−1), with substantial bacterial attachment occurring even when thermodynamically unfavorable (positive ΔGadhesion), indicating that biological factors override physicochemical interactions. Temperature deeply influenced adhesion, with 25 °C promoting 0.3–3.5 log CFU·g−1-higher bacterial counts than 7 °C across all combinations (p-value ≤ 0.05). These findings demonstrate that bacterial adhesion to fresh produce is multifactorial, with temperature as the dominant controllable factor, and highlight the need for integrated sanitation approaches combining physical and chemical treatments applied before refrigerated storage. Full article
(This article belongs to the Special Issue Novel Approaches for Controlling and Analyzing Microorganisms in Foods: 2nd Edition)
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20 pages, 9065 KB  
Article
Tracking Antimicrobial Resistance in Salmonella via Poultry Supply Chains, Human Clinical Samples, and Environmental Reservoirs
by Diana M. Álvarez-Espejo, Diego Fredes-García, Constanza Díaz-Gavidia, Sebastián Gutiérrez, Rocio Barron-Montenegro, Francisca P. Álvarez, Rodrigo Constenla-Albornoz, Vivien Cadet-Arenas, Angélica Reyes-Jara, Jorge Olivares-Pacheco, Elton Burnett, Rebecca L. Bell, Magaly Toro, Jianghong Meng, Patricia García and Andrea I. Moreno-Switt
Foods 2026, 15(3), 410; https://doi.org/10.3390/foods15030410 - 23 Jan 2026
Cited by 2 | Viewed by 961
Abstract
The global dissemination of multidrug-resistant (MDR) Salmonella through the international food trade poses a major One Health concern. We used whole-genome sequencing to characterize Salmonella isolates from poultry meat sold in Chile, including domestic and imported products from Brazil and Argentina. Sixty-one Salmonella [...] Read more.
The global dissemination of multidrug-resistant (MDR) Salmonella through the international food trade poses a major One Health concern. We used whole-genome sequencing to characterize Salmonella isolates from poultry meat sold in Chile, including domestic and imported products from Brazil and Argentina. Sixty-one Salmonella isolates were recovered from poultry meat; S. Infantis predominated (59%), followed by S. Heidelberg. Among S. Heidelberg from imported-meat poultry, 92% carried the blaCMY-2 gene, conferring resistance to β-lactams. Given the predominance of S. Infantis in poultry meat, we performed an additional in-depth genomic analysis of 73 S. Infantis isolates obtained from poultry meat (n = 32), surface water (n = 30), and human clinical cases (n = 11). Across sources, phenotypic resistance to ciprofloxacin and third-generation cephalosporins reached 93% and 70%, respectively, and MDR (≥3 antimicrobial classes) occurred in 71% of isolates, largely associated with blaCTX-M-65 and gyrA mutations. The pESI (plasmid of emerging S. Infantis)-like plasmid, harboring antimicrobial resistance and virulence genes, appeared in 94% of isolates. Phylogenetic analyses showed close genetic relationships among food, environmental, and clinical isolates, suggesting potential transmission through contaminated poultry meat or water. These findings emphasize the emergence of MDR S. Infantis in Chile and underscore the need for integrated One Health surveillance and prudent antimicrobial use to mitigate foodborne AMR risks. Full article
(This article belongs to the Special Issue Novel Approaches for Controlling and Analyzing Microorganisms in Foods: 2nd Edition)
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18 pages, 1396 KB  
Article
Bactericidal, Anti-Biofilm, and Stress-Response Modulatory Effects of Lacticaseibacillus rhamnosus ATCC 9595 Cell-Free Supernatant Against Listeria monocytogenes
by Isabela Sguilla Rotta, Hugo Felix Perini, Sthefânia Dalva da Cunha Rezende, Yasmin Neves Vieira Sabino, Marcos Vinicius da Silva, Felipe Alves de Almeida, Emiliane Andrade Araujo Naves, Uelinton Manoel Pinto, Alessandra Barbosa Ferreira Machado and Aline Dias Paiva
Foods 2025, 14(23), 4163; https://doi.org/10.3390/foods14234163 - 4 Dec 2025
Viewed by 1086
Abstract
This study evaluated the antagonistic activity of the cell-free supernatant of Lacticaseibacillus rhamnosus ATCC 9595 (Lcr-CFS) against Listeria monocytogenes, a major foodborne pathogen, that represents a challenge to food safety, due to its remarkable tolerance to environmental stresses and strong [...] Read more.
This study evaluated the antagonistic activity of the cell-free supernatant of Lacticaseibacillus rhamnosus ATCC 9595 (Lcr-CFS) against Listeria monocytogenes, a major foodborne pathogen, that represents a challenge to food safety, due to its remarkable tolerance to environmental stresses and strong biofilm-forming ability. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of Lcr-CFS against L. monocytogenes were defined as 31.25 and 62.5 mg/mL, respectively. Time-kill assays revealed dose- and time-dependent bactericidal effects. At sub-MICs, Lcr-CFS significantly reduced L. monocytogenes biofilm formation, disrupted preformed biofilms and decreased cell viability (80.3–96.7%), effects that were confirmed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and fluorescence microscopy. Transmission electron microscopy showed L. monocytogenes cell wall damage, cytoplasmic leakage, and morphological alterations consistent with bactericidal effects. Additionally, exposure to 1x and 2x MIC of Lcr-CFS induced reactive oxygen species (ROS) accumulation, indicating oxidative stress as part of the mechanism by which Lcr-CFS exerts its antimicrobial activity. Gene expression analysis revealed upregulation of stress and virulence-associated genes (sigB, prfA, degU, flaA, motA, hlyA, pclA, and actA) upon exposure to 0.5x MIC suggesting a complex cross-talk network between adaptive mechanisms and environmental stresses. Although L. monocytogenes initiates a stress response, it appears unable to counteract the damage induced by Lcr-CFS, resulting in cell death. These findings highlight the antimicrobial and anti-biofilm properties of Lcr-CFS against L. monocytogenes. Given its in vitro efficacy, Lcr-CFS emerges as a promising biocontrol agent to improve food safety by mitigating the persistence of L. monocytogenes in food processing settings. Full article
(This article belongs to the Special Issue Novel Approaches for Controlling and Analyzing Microorganisms in Foods: 2nd Edition)
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Review

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22 pages, 992 KB  
Review
Bioprotective and Technological Roles of Lactic Acid Bacteria in Reduced-Sodium Fermented Sausages
by Marcello Lima Bertuci, Camila Vespúcio Bis Souza, Carlos Alberto Alves, Jr., Svetoslav Dimitrov Todorov, Ana Lúcia Barretto Penna and Andrea Carla da Silva Barretto
Foods 2025, 14(21), 3758; https://doi.org/10.3390/foods14213758 - 1 Nov 2025
Cited by 4 | Viewed by 1691
Abstract
Fermented sausages are popular worldwide due to their sensory and nutritional characteristics, as well as their convenience for storage and consumption. The production and consumption of meat products are associated with negative impacts from the risks of high sodium intake, such as cardiovascular [...] Read more.
Fermented sausages are popular worldwide due to their sensory and nutritional characteristics, as well as their convenience for storage and consumption. The production and consumption of meat products are associated with negative impacts from the risks of high sodium intake, such as cardiovascular disease and hypertension. Salt (NaCl) plays an important role in the preservation, water loss during drying, reduction in water activity, and sensory characteristics of meat and other fermented food products. NaCl reduction is considered a challenge because it affects the sensory properties of meat and can compromise the safety and microbiological parameters related to the spoilage of the fermented meat product. The use of microorganisms, such as LAB, has been studied as an innovative way to substitute traditional preservatives. They produce various metabolites, including bioactive and antimicrobial substances that are actively involved in health benefits and guarantee the safety of meat products. These natural substances produced by bacteria extend shelf life by inhibiting spoilage and pathogenic microorganisms. This review discusses the potential application of lactic acid bacteria in the reformulation of fermented sausages, challenges, and beneficial effects on sensorial, safety, and health properties. Full article
(This article belongs to the Special Issue Novel Approaches for Controlling and Analyzing Microorganisms in Foods: 2nd Edition)
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