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Fermentation
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Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023
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Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 18395

Special Issue Editor

Prof. Dr. Ronnie Willaert

E-Mail Website
Guest Editor
Structural Biology Brussels Lab, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
Interests: yeast biotechnology; cell immobilization; beer brewing biochemistry and fermentation; mini- and microbioreactors; Saccharomyces cerevisiae; Candida; yeast space biology (bioreactors for microgravity research); yeast adhesins; yeast systems biology; glycobiology; nanobiotechnology; Atomic Force Microscopy; protein crystallization; yeast protein structural biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to collect high-quality review papers in all fields of microbial metabolism, physiology, and genetics. We encourage researchers from related fields to contribute review papers highlighting the latest developments in microbial metabolism, physiology, and genetics (including transcriptomics, proteomics, and genomics, as well as integrated approaches), or to invite relevant experts and colleagues to do so. Full-length comprehensive reviews will be preferred.

Let us share the science as widely as possible.

Prof. Dr. Ronnie Willaert
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 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. Fermentation 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 2100 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.

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Related Special Issue

Published Papers (7 papers)

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19 pages, 1092 KiB  
Review
LAB Antagonistic Activities and Their Significance in Food Biotechnology: Molecular Mechanisms, Food Targets, and Other Related Traits of Interest
by Radjaa Cirat, Vittorio Capozzi, Zineb Benmechernene, Giuseppe Spano, Francesco Grieco and Mariagiovanna Fragasso
Fermentation 2024, 10(4), 222; https://doi.org/10.3390/fermentation10040222 - 20 Apr 2024
Cited by 5 | Viewed by 2490
Abstract
The ongoing occurrence of foodborne diseases and the imperative need for efficient spoilage and pathogen control in food products constitute a critical challenge for the food industry. The rising demands of consumers for safe, healthy, and clean-label food products have led to an [...] Read more.
The ongoing occurrence of foodborne diseases and the imperative need for efficient spoilage and pathogen control in food products constitute a critical challenge for the food industry. The rising demands of consumers for safe, healthy, and clean-label food products have led to an increased interest in natural antimicrobial alternatives. Lactic acid bacteria (LAB) have proven their value in the food industry in recent years, also in reason of their antagonistic properties against undesired microbes and their significant related protechnological attributes. The natural antimicrobial compounds produced by LAB exhibit inhibitory effects on pathogens and effectively inhibit the activities of food spoilage-related organisms. Applying secondary metabolites of LAB, notably bacteriocins, organic acids, and others, has found commercial utility across multiple food sectors, effectively preventing the proliferation of undesirable microorganisms and simultaneously enhancing the sensory properties and overall quality of various food products. This review comprehensively explores the natural microbial compounds produced by LAB, specifically focusing on their antimicrobial action in supporting effective and sustainable microbial management. Additionally, it highlights their strategic application across various technological contexts within the food industry. Full article
(This article belongs to the Special Issue Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023)
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22 pages, 2300 KiB  
Review
Yeast Bioflavoring in Beer: Complexity Decoded and Built up Again
by Chiara Nasuti and Lisa Solieri
Fermentation 2024, 10(4), 183; https://doi.org/10.3390/fermentation10040183 - 28 Mar 2024
Viewed by 2531
Abstract
Yeast is a powerful bioflavoring platform, suitable to confer special character and complexity to beer aroma. Enhancing yeast bioflavoring represents a chance for the brewing production chain to diversify its product portfolio and to increase environmental sustainability in the era of climate change. [...] Read more.
Yeast is a powerful bioflavoring platform, suitable to confer special character and complexity to beer aroma. Enhancing yeast bioflavoring represents a chance for the brewing production chain to diversify its product portfolio and to increase environmental sustainability in the era of climate change. In flavor compound metabolism, multiple genes encoding biosynthetic enzymes and the related regulatory factors are still poorly known, but significant advances have been recently made to dissect gene contribution in flavor molecule production. Furthermore, causative mutations responsible for the huge strain diversity in yeast bioflavoring aptitude have been recently disclosed. This review covers the most recent advances in the genetics of yeast bioflavoring, with special regards to higher alcohols, esters, monoterpene alcohols, thiols, and phenolic derivatives of hydroxycinnamic acids. We also critically discussed the most significant strategies to enhance yeast bioflavoring, including bioprospecting for novel Saccharomyces and non-Saccharomyces strains, whole-genome engineering, and metabolic engineering. Full article
(This article belongs to the Special Issue Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023)
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14 pages, 2023 KiB  
Review
Metabolic Oscillation Phenomena in Clostridia Species—A Review
by Annika Tyszak and Lars Rehmann
Fermentation 2024, 10(3), 156; https://doi.org/10.3390/fermentation10030156 - 9 Mar 2024
Viewed by 1584
Abstract
Clostridia are interesting candidates for biotechnological applications due to their diverse and unique metabolic abilities. Particularly in continuous fermentation processes, productivity-decreasing metabolic oscillations have been reported in many species. The resulting process instability and reduced productivity can be a serious hurdle for the [...] Read more.
Clostridia are interesting candidates for biotechnological applications due to their diverse and unique metabolic abilities. Particularly in continuous fermentation processes, productivity-decreasing metabolic oscillations have been reported in many species. The resulting process instability and reduced productivity can be a serious hurdle for the development of industrially feasible processes. This review highlights the current state of knowledge about oscillatory metabolic phenomena in Clostridia, including the mechanisms, assumed and proven, behind those oscillations and methods to mitigate the phenomena if applicable. The nature of observed metabolic oscillations in Clostridia is diverse, including a wide range of periods of oscillation and different parameters in which the oscillation is observed. Some phenomena remain to be investigated further, while others are already well understood. However, knowledge of mechanisms is a very valuable asset in overcoming the metabolic oscillation to create a stable process. Full article
(This article belongs to the Special Issue Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023)
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16 pages, 545 KiB  
Review
Therapeutic Applications of Native and Engineered Saccharomyces Yeasts
by Suryang Kwak
Fermentation 2024, 10(1), 51; https://doi.org/10.3390/fermentation10010051 - 10 Jan 2024
Viewed by 2842
Abstract
Saccharomyces cerevisiae var. boulardii (Sb) is currently receiving significant attention as a synthetic probiotic platform due to its ease of manipulation and inherent effectiveness in promoting digestive health. A comprehensive exploration of Sb and other S. cerevisiae strains (Sc) [...] Read more.
Saccharomyces cerevisiae var. boulardii (Sb) is currently receiving significant attention as a synthetic probiotic platform due to its ease of manipulation and inherent effectiveness in promoting digestive health. A comprehensive exploration of Sb and other S. cerevisiae strains (Sc) would shed light on the refinement and expansion of their therapeutic applications. This review aims to provide a thorough overview of Saccharomyces yeasts from their native health benefits to recent breakthroughs in the engineering of Saccharomyces yeasts as synthetic therapeutic platforms. Molecular typing and phenotypic assessments have uncovered notable distinctions, including the superior thermotolerance and acid tolerance exhibited by Sb, which are crucial attributes for probiotic functions. Moreover, parabiotic and prebiotic functionalities originating from yeast cell wall oligosaccharides have emerged as pivotal factors influencing the health benefits associated with Sb and Sc. Consequently, it has become imperative to select an appropriate yeast strain based on a comprehensive understanding of its actual action in the gastrointestinal tract and the origins of the targeted advantages. Overall, this review underscores the significance of unbiased and detailed comparative studies for the judicious selection of strains. Full article
(This article belongs to the Special Issue Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023)
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17 pages, 1411 KiB  
Review
Sourdoughs as Natural Enhancers of Bread Quality and Shelf Life: A Review
by Ricardo H. Hernández-Figueroa, Emma Mani-López, Enrique Palou and Aurelio López-Malo
Fermentation 2024, 10(1), 7; https://doi.org/10.3390/fermentation10010007 - 21 Dec 2023
Cited by 5 | Viewed by 3539
Abstract
Sourdough is a key component in traditional and artisanal bread making. It imparts unique flavors and textures to bread, which are highly sought after by consumers. The use of sourdoughs to prepare bakery products has been researched for more than 30 years, and [...] Read more.
Sourdough is a key component in traditional and artisanal bread making. It imparts unique flavors and textures to bread, which are highly sought after by consumers. The use of sourdoughs to prepare bakery products has been researched for more than 30 years, and accumulated research shows the performance of sourdoughs as an alternative to improve the organoleptic characteristics of bread and its shelf life. The purpose of this review is to present an overview of the research carried out on the use of sourdoughs from lactic acid bacteria and their benefits in the quality characteristics of bread, as well as to present relevant and recent information on the use of sourdoughs and their aqueous extracts for the preservation of bakery products. Also, the advances in the identification of antifungal compounds have been revised. In general, it has been shown that incorporating sourdoughs into the bread formulation positively impacts the product’s flavor and helps slow down the bread’s aging process and spoilage. Also, it has been observed that the bioactive compounds formed by lactic acid bacteria (LAB) during sourdough fermentation and their extracts have an antimicrobial, especially antifungal, capacity that significantly helps increase bread’s shelf life. Studying sourdough as part of fermentation processes and product development is essential to improve bread production’s quality, diversity, and sustainability, and to advance our understanding of the science behind this food tradition. Full article
(This article belongs to the Special Issue Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023)
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22 pages, 943 KiB  
Review
Pyrimidine Biosynthesis and Ribonucleoside Metabolism in Species of Pseudomonas
by Thomas P. West
Fermentation 2023, 9(11), 955; https://doi.org/10.3390/fermentation9110955 - 8 Nov 2023
Viewed by 1585
Abstract
Pyrimidine biosynthesis and ribonucleoside metabolism in species of Pseudomonas was the focus of this review, in relation to their current taxonomic assignments in different homology groups. It was of interest to learn whether pyrimidine biosynthesis in taxonomically related species of Pseudomonas was regulated [...] Read more.
Pyrimidine biosynthesis and ribonucleoside metabolism in species of Pseudomonas was the focus of this review, in relation to their current taxonomic assignments in different homology groups. It was of interest to learn whether pyrimidine biosynthesis in taxonomically related species of Pseudomonas was regulated in a similar fashion by pyrimidine base supplementation or by pyrimidine limitation of pyrimidine auxotrophic strains. It was concluded that the regulation of pyrimidine biosynthesis in Pseudomonas species could not be correlated with their taxonomic assignment into a specific homology group. Pyrimidine ribonucleoside metabolism in Pseudomonas species primarily involved the pyrimidine ribonucleoside salvage enzymes nucleoside hydrolase and cytosine deaminase, independently of the Pseudomonas homology group to which the species was assigned. Similarly, pyrimidine base catabolism was shown to be active in different taxonomic homology groups of Pseudomonas. Although the number of studies exploring the catabolism of the pyrimidine bases uracil and thymine was limited in scope, it did appear that the presence of the pyrimidine base reductive pathway of pyrimidine catabolism was a commonality observed for the species of Pseudomonas investigated. There also appeared to be a connection between pyrimidine ribonucleoside degradation and the catabolism of pyrimidine bases in providing a cellular source of carbon or nitrogen independently of which homology group the species of Pseudomonas were assigned to. Full article
(This article belongs to the Special Issue Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023)
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19 pages, 6524 KiB  
Review
Insights into Co-Cultivation of Photosynthetic Microorganisms for Novel Molecule Discovery and Enhanced Production of Specialized Metabolites
by Dorian Rojas-Villalta, Olman Gómez-Espinoza, Francinie Murillo-Vega, Fabián Villalta-Romero, Maritza Guerrero, Rossy Guillén-Watson and Kattia Núñez-Montero
Fermentation 2023, 9(11), 941; https://doi.org/10.3390/fermentation9110941 - 30 Oct 2023
Cited by 2 | Viewed by 2903
Abstract
Meso- and extremophilic microalgae and cyanobacteria have a wide range of biotechnological applications. However, the industrial demand for bioactive molecules and the redundancy of these molecules has resulted in a need for new methodologies for enhanced production and the discovery of specialized metabolites. [...] Read more.
Meso- and extremophilic microalgae and cyanobacteria have a wide range of biotechnological applications. However, the industrial demand for bioactive molecules and the redundancy of these molecules has resulted in a need for new methodologies for enhanced production and the discovery of specialized metabolites. Co-cultivation has been established as a promising approach to addressing these challenges. In this context, this work aimed to describe the state of the art of the co-cultivation method involving meso- and extremophilic photosynthetic microorganisms, as well as discuss the advantages, challenges, and limitations of this approach. Co-culture is defined as an ecology-driven method in which various symbiotic interactions involving cyanobacteria and microalgae can be used to explore new compounds and enhanced production. Promising results regarding new bioactive metabolite expression and increased production through co-cultivation-based research support that idea. Also, the metabolic diversity and evolutionary adaptations of photosynthetic microorganisms to thrive in extreme environments could improve the efficiency of co-cultivation by allowing the implementation of these microorganisms. However, the complexity of ecological interactions and lack of standardization for co-cultivation protocols are obstacles to its success and scientific validation. Further research in symbiotic interplays using -omics and genetic engineering, and predictive experimental designs for co-cultures are needed to overcome these limitations. Full article
(This article belongs to the Special Issue Feature Review Papers in Microbial Metabolism, Physiology & Genetics 2023)
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