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Applied Sciences
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Innovations in Microbiome Research for Functional and Sustainable Food Systems
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Innovations in Microbiome Research for Functional and Sustainable Food Systems

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 July 2025 | Viewed by 8831

Special Issue Editors

Dr. Yiannis Kourkoutas

E-Mail Website
Guest Editor
Laboratory of Applied Microbiology & Biotechnology, Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: food microbiome; functional foods; fermented foods and beverages; food bioprocesses; agro-industrial and food waste valorization; circular economy
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Eugenia Bezirtzoglou

E-Mail Website
Guest Editor
Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: microbiome; antimicrobials; antibiotics; biofilms
Special Issues, Collections and Topics in MDPI journals
Dr. Christina Tsigalou

E-Mail Website
Guest Editor
Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: immunology; autoimmunity; diet; microbiome; functional foods; antimicrobials
Special Issues, Collections and Topics in MDPI journals
Dr. Gregoria Mitropoulou

E-Mail Website
Guest Editor
Laboratory of Applied Microbiology & Biotechnology, Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: functional foods; design of dietary interventions; gut & food microbiome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

An increased interest in sustainable agri-food systems for innovative and safe products, services, and bioprocesses is one of the key priorities within the concepts of circular economies and the European Green Deal. The development of novel foods enriched with health-promoting microorganisms and beneficial compounds obtained via biotechnological routes to potentially enhance functional activities at a preventive and therapeutic level is at the heart of food innovation.

At the same time, the valorization of agro-industrial and food waste presents an issue of vital importance for global environmental governance, directly linked with environmental, economic, and social impacts.

In this context, the aim of this Special Issue is to highlight the innovations in microbiome research for functional and sustainable food systems. Original research and review articles are welcome. Potential research topics include but are not limited to the following:

  • Gut Microbiome, digestive health, and disease prevention;
  • Smart food-grade vehicles for the targeted delivery of beneficial microbes and/or bioactive compounds;
  • Functional edible coatings enriched with beneficial microbes and/or bioactive compounds;
  • Clinical data on functionality of health-promoting microorganisms and/or bioactive ingredients;
  • Regulatory issues associated with novel functional food ingredients/final products.

Prof. Dr. Yiannis Kourkoutas
Prof. Dr. Eugenia Bezirtzoglou
Dr. Christina Tsigalou
Dr. Gregoria Mitropoulou
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 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. 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

  • microbiome
  • novel functional ingredients/foods
  • digestive health
  • bioactivity
  • bioavailability
  • food systems
  • sustainability

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Published Papers (4 papers)

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Research

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14 pages, 640 KiB  
Article
Inhibitory Effects of Essential Oils and Extracts of the Water-Steam Distillation Residues from Greek Herbs on Adherent Biofilm Formation by Common Pathogens
by Gregoria Mitropoulou, Ioanna Karapantzou, Dimitris Tsimogiannis, Vassiliki Oreopoulou, Veronica Lazăr and Yiannis Kourkoutas
Appl. Sci. 2025, 15(6), 3385; https://doi.org/10.3390/app15063385 - 20 Mar 2025
Viewed by 353
Abstract
Biofilms pose a major challenge to the food industry, as they develop on both biotic and abiotic surfaces and contribute to the persistence of antibiotic-resistant pathogens. This study evaluated the antimicrobial and antibiofilm potential of Satureja thymbra, Thymus capitatus, and Origanum [...] Read more.
Biofilms pose a major challenge to the food industry, as they develop on both biotic and abiotic surfaces and contribute to the persistence of antibiotic-resistant pathogens. This study evaluated the antimicrobial and antibiofilm potential of Satureja thymbra, Thymus capitatus, and Origanum hirtum essential oils (EOs), their main components (thymol, carvacrol, p-cymene, and γ-terpinene), and ethanolic and ethyl acetate extracts of the water-steam distillation residue of T. capitatus (WSTRTc). Minimum Inhibition Concentration (MIC) and Minimum Bactericidal Concentration (MBC) values of EOs and WSTRTc extracts ranged from 0.6 to 56.8 mg/mL. The corresponding MIC values of the main components ranged in lower values (0.5–2.4 mg/mL). Minimum Biofilm Inhibition Concentration (MBIC) and Minimum Biofilm Eradication Concentration (MBEC) were also determined. MBIC values for the EOs ranged from 0.6 to 4.7 mg/mL against biofilms of Escherichia coli, Listeria monocytogenes, Proteus mirabilis, and Salmonella Enteritidis. Significant antibiofilm activity at concentrations > 61 mg/mL and > 20 mg/mL was recorded by the ethanolic and ethyl acetate WSTRTc extracts, respectively, but no activity against L. monocytogenes and P. mirabilis biofilms was documented. These findings highlighted the efficacy of EOs and extracts derived from Greek herbs, suggesting their application in the food and pharmaceutical industry as natural antimicrobials and biofilm inhibitors. Full article
(This article belongs to the Special Issue Innovations in Microbiome Research for Functional and Sustainable Food Systems)
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Review

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17 pages, 303 KiB  
Review
The Gut–Brain Axis and Neurodegenerative Diseases: The Role of Nutritional Interventions Targeting the Gut Microbiome—A Systematic Review
by Despoina Koumpouli, Varvara Koumpouli and Antonios E. Koutelidakis
Appl. Sci. 2025, 15(10), 5558; https://doi.org/10.3390/app15105558 - 15 May 2025
Viewed by 144
Abstract
The gut–brain axis (GBA) comprises bidirectional communication connecting the gut and brain. Many neurodegenerative disorders (NDDs), such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and multiple sclerosis (MS), are characterized by a dysfunction of the GBA, indicating its possible role in disease pathogenesis. [...] Read more.
The gut–brain axis (GBA) comprises bidirectional communication connecting the gut and brain. Many neurodegenerative disorders (NDDs), such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and multiple sclerosis (MS), are characterized by a dysfunction of the GBA, indicating its possible role in disease pathogenesis. This systematic review was performed according to PRISMA guidelines, mainly using the following keywords: gut–brain axis, gut microbiota, gut dysbiosis, neurodegenerative disorders, prebiotics, and probiotics. The most recent scientific articles were searched from the PubMed, Google Scholar, and Scopus databases. The main components and communication pathways of the GBA are discussed in this study, and the aim was to investigate if therapeutic approaches, through dietary intervention targeting the gut microbiota, could ameliorate NDDs. The gut microbiota is a crucial constituent of the GBA, and an unbalanced microbiota, known as dysbiosis, has been related to GBA impairment and neurodegeneration. In most of the studies discussed, the modulation of the microbial constitution through nutritional intervention and probiotic and prebiotic supplementation showed promising outcomes. Although promising, further research is essential to fully elucidate the mechanisms involved and confirm the therapeutic potential of gut microbiota modulation in NDDs. Full article
(This article belongs to the Special Issue Innovations in Microbiome Research for Functional and Sustainable Food Systems)
30 pages, 1254 KiB  
Review
Functional Yogurt: Types and Health Benefits
by Sümeyye Sarıtaş, Alicia del Carmen Mondragon Portocarrero, Jose M. Miranda, Anna Maria Witkowska and Sercan Karav
Appl. Sci. 2024, 14(24), 11798; https://doi.org/10.3390/app142411798 - 17 Dec 2024
Cited by 5 | Viewed by 4997
Abstract
In the past decade, the increasing interest in healthy consumption has encouraged the development of functional products in the yogurt sector. Dairy products are extensively used in the production of functional foods because of their excellent and versatile technological properties. Among dairy products, [...] Read more.
In the past decade, the increasing interest in healthy consumption has encouraged the development of functional products in the yogurt sector. Dairy products are extensively used in the production of functional foods because of their excellent and versatile technological properties. Among dairy products, yogurt is one of the dairy foods that has been most widely used to deliver bioactive compounds to consumers. The market features various types of functional yogurt, including probiotic, prebiotic, synbiotic, high protein, lactose free, and novel products known as easy-to-digest yogurt. The added ingredients in these products influence the structural, nutritional, and functional properties of yogurt. These effects vary depending on the chemical and biological characteristics of each ingredient. Additionally, during fermentation, the added substances can impact the number and viability of the bacteria involved, affecting the quality of the products during storage. Furthermore, the consumption of functional yogurt is associated with various health benefits. These benefits are linked not only to supporting health but also to altering the course of a disease or alleviating symptoms. This review article discusses functional yogurt and its health effects, incorporating recent studies. Full article
(This article belongs to the Special Issue Innovations in Microbiome Research for Functional and Sustainable Food Systems)
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38 pages, 2097 KiB  
Review
The Role of Fermented Vegetables as a Sustainable and Health-Promoting Nutritional Resource
by Alejandro Borrego-Ruiz, Carmen M. González-Domenech and Juan J. Borrego
Appl. Sci. 2024, 14(23), 10853; https://doi.org/10.3390/app142310853 - 23 Nov 2024
Cited by 2 | Viewed by 2540
Abstract
The increasing global burden of morbidity and mortality from chronic diseases related to poor diet quality, coupled with the unsustainable depletion of vital planetary resources by current food production systems, threatens future food security and highlights the urgent need to transition to high-quality [...] Read more.
The increasing global burden of morbidity and mortality from chronic diseases related to poor diet quality, coupled with the unsustainable depletion of vital planetary resources by current food production systems, threatens future food security and highlights the urgent need to transition to high-quality plant-based diets as a viable solution to mitigate economic, health, and environmental challenges. Taking into consideration the significant role that fermented vegetables may play as a sustainable, healthy, long-lasting, and plant-based nutritional resource, this narrative review analyzes their production and benefits. For this purpose, the mechanisms of the fermentation process are explored, along with the importance of probiotic cultures in plant-based fermented foods, and with the implications of fermentation on food safety within the broader framework of low-impact, organic, plant-derived nutrition. Additionally, the health benefits of fermented vegetables and probiotics are examined, including their effects on mental health. Vegetable fermentation is a versatile method for enhancing food preservation, nutritional quality, and safety. This ancient practice prolongs the shelf life of perishable items, reduces the toxicity of raw ingredients, and improves digestibility. Specific starter cultures, particularly lactic acid bacteria, are essential for controlling fermentation, ensuring safety, and maximizing health benefits. Fermented vegetables, rich in probiotics, support gut health and immune function. Emerging research indicates their potential to alleviate adverse mental health symptoms such as stress and anxiety, highlighting their significance in modern dietary guidelines and chronic health management. Full article
(This article belongs to the Special Issue Innovations in Microbiome Research for Functional and Sustainable Food Systems)
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