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Applied Sciences
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Innovative Perspectives on Food Microbiology and Biotechnology
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Innovative Perspectives on Food Microbiology and Biotechnology

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Food Science and Technology".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 1667

Editors

Dr. Dimitrios Pavlidis

E-Mail Website1 Website2
Guest Editor
Department of Food Science and Technology, University of Peloponnese, Antikalamoss, 24100 Kalamata, Greece
Interests: food microbiology; food science; microbial spoilage; authenticity
Dr. Monika Trząskowska

E-Mail Website
Guest Editor
Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences, Nowoursynowska Str. 159C, 02-776 Warsaw, Poland
Interests: food safety and quality; food fermentation; in vitro digestion; food product development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Food science encompasses, among other disciplines, the implementation of microorganisms and biotechnological tools to enhance food safety, production, processing, and sustainability. In these fields, the use of microbial metabolism, genetic engineering and enzymatic processes plays a key role in addressing critical challenges such as food spoilage, safety, nutritional enrichment and reducing food loss.

This Special Issue aims to collect the latest research and advanced applications of microbiology and biotechnology in food science, spanning critical areas such as spoilage, spontaneous or starter-driven fermentation, enzyme and protein engineering, food safety and pathogen control, bioactive compounds and functional foods. Focusing on mechanistic insights and innovative methodologies, this issue highlights the integration of cutting-edge omics approaches, synthetic biology, and bioinformatics to enhance microbial functionality and the biosynthesis of bioactive compounds.

Researchers and practitioners are invited to submit original research articles, reviews, and communications that explore these topics in depth. We are particularly interested in research on microbial metabolites and unexplored fermented products produced at a small and/or large scale. Contributions that provide novel experimental data, in vitro screening, methodological developments, or comprehensive analyses aimed at advancing understanding and application of microbiological and biotechnological tools in modern food systems are particularly encouraged.

Dr. Dimitrios Pavlidis
Dr. Monika Trząskowska
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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Applied Sciences 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 2400 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

  • food microbiology
  • food biotechnology
  • fermentation
  • microbial spoilage
  • microbial metabolites
  • bioactive compounds
  • pathogen
  • omics approaches

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Published Papers (3 papers)

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Review

17 pages, 642 KB  
Review
Purification and Detection of Bacterial Endospores: Current Methods and Challenges
by Souichirou Kawai
Appl. Sci. 2026, 16(11), 5702; https://doi.org/10.3390/app16115702 - 5 Jun 2026
Viewed by 310
Abstract
Bacterial endospores are highly resistant, dormant forms that pose persistent challenges in food safety, environmental microbiology, and industrial hygiene. Accurate evaluation of endospore resistance, physiology, and inactivation depends on both purification and detection methods; however, these processes are typically examined independently, limiting methodological [...] Read more.
Bacterial endospores are highly resistant, dormant forms that pose persistent challenges in food safety, environmental microbiology, and industrial hygiene. Accurate evaluation of endospore resistance, physiology, and inactivation depends on both purification and detection methods; however, these processes are typically examined independently, limiting methodological consistency and contributing to variability across studies. In this review, current approaches for endospore purification and detection are critically examined, including washing-based methods, density gradient centrifugation, enzymatic treatments, culture-based enumeration, molecular assays, flow cytometry, and emerging biosensor technologies. In addition, these methods are compared using metrics such as purity, recovery yield, sensitivity, and specificity, and their advantages and limitations are summarized to clarify performance. It is further proposed that endospore purification and detection should be considered as a single, end-to-end analytical workflow and optimized accordingly. Purification strategies influence sample cleanliness and aspects of endospore quality, including viability, structural integrity, and physiological state, which affect detection performance and quantitative accuracy. Based on this integrated perspective, a conceptual framework linking purification efficiency to detection outcomes is presented, along with practical considerations for method selection across relevant application contexts. Finally, gaps in standardization are identified, and future research directions are outlined to improve reproducibility and cross-study comparability in endospore-related studies. Full article
(This article belongs to the Special Issue Innovative Perspectives on Food Microbiology and Biotechnology)
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35 pages, 1334 KB  
Review
From Ancient Fermentation to Modern Functional Foods: Food Microbiology and Biotechnology at the Interface of Tradition and Innovation
by Ana Yanina Bustos and Theodoros Varzakas
Appl. Sci. 2026, 16(11), 5510; https://doi.org/10.3390/app16115510 - 2 Jun 2026
Viewed by 476
Abstract
Fermentation is one of the oldest food preservation and transformation strategies developed by human societies. Its cultural appropriation predates even the scientific understanding of the role of microorganisms and their metabolic functions. However, significant knowledge gaps remain regarding the mechanisms underlying these effects, [...] Read more.
Fermentation is one of the oldest food preservation and transformation strategies developed by human societies. Its cultural appropriation predates even the scientific understanding of the role of microorganisms and their metabolic functions. However, significant knowledge gaps remain regarding the mechanisms underlying these effects, as well as safety considerations and regulatory frameworks. This review addresses these gaps through an integrative analysis of the literature, including peer-reviewed studies and systematic reviews focused on food microbiology, microbial dynamics, and health-promoting mechanisms. In particular, yogurt and cheese are addressed as case studies to review the past and present of these ancestral foods in terms of the evolution of fermentation processes, from spontaneous fermentation to controlled and standardized systems, along with the modern biotechnological tools used to characterize and monitor complex microbial communities. Substrates such as stevia, fruits, vegetables, and plant-based milk substitutes are also explored. The scope encompasses enzymatic transformation of raw substrates, biosynthesis of bioactive metabolites, effects on the gut microbiota, and the use of fermented foods as vehicles for “biotic” compounds. Particular attention is paid to safety and regulatory aspects. Fermented foods are culturally important and promising functional platforms, although standardized regulatory frameworks and stronger mechanistic and clinical evidence regarding their health benefits are still needed. Full article
(This article belongs to the Special Issue Innovative Perspectives on Food Microbiology and Biotechnology)
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33 pages, 3488 KB  
Review
Phytochemicals from Edible and Medicinal Plant as Multi-Target Agents Against Multidrug-Resistant Pathogens: Mechanistic Insights, Prospects, and Challenges
by Cecile Ojong, Alberta N. A. Aryee, Williams Walana and Samuel A. Besong
Appl. Sci. 2026, 16(9), 4414; https://doi.org/10.3390/app16094414 - 30 Apr 2026
Viewed by 478
Abstract
Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa rank among the most challenging pathogens due to increasing prevalence of multidrug-resistant (MDR) strains. These pathogens pose major risks to public health and food safety, earning their inclusion on the World Health Organization (WHO) [...] Read more.
Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa rank among the most challenging pathogens due to increasing prevalence of multidrug-resistant (MDR) strains. These pathogens pose major risks to public health and food safety, earning their inclusion on the World Health Organization (WHO) priority list of MDR bacteria. While available conventional antibiotics are becoming less effective, natural products from plant extracts offer promising alternative and synergetic effects that can restore efficacy and lower required doses. Their antimicrobial activity is attributed to phytochemicals such as phenolic compounds and terpenoids acting via membrane disruption, efflux pump inhibition, biofilm interference, and cell protein disruption. Furthermore, phytochemicals in essential oils, such as carvacrol, thymol, and cinnamaldehyde, also exhibit antimicrobial and antioxidant activities. Their broad antimicrobial effects extend shelf life and enhance food safety, making them effective natural alternatives to synthetic preservatives. Moreover, advances in extraction and characterization techniques, including green solvents, spectrometry and hyphenated chromatographic methods, have improved recovery, identification and quantification. In addition, artificial intelligence (AI) emerges as a transformative tool to accelerate discovery, optimize compound screening, and predict synergistic interactions. Notwithstanding these advances, challenges persist in standardization, bioavailability, and clinical translation. Further studies are needed to isolate active compounds, elucidate mechanisms of action, validate combined use with conventional antibiotics and overcome formulation, delivery, sensory and regulatory hurdles. This review examines current knowledge of opportunities and limitations of plant-based antimicrobials against MDR pathogens supported by advances in extraction, characterization, and AI. Full article
(This article belongs to the Special Issue Innovative Perspectives on Food Microbiology and Biotechnology)
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