Feature Review Papers in Microbial Metabolism, Physiology and Genetics

This inaugural Special Issue of Fermentation (MDPI) features review articles spanning various aspects of microbial metabolism, physiology, and genetics. It covers topics in microbial metabolism, physiology, food biotechnology, and pharmaceutical microbiology, highlighting current research trends in these fields.

1. Microbial Metabolism and Physiology

1.1. Metabolic Oscillation Phenomena in Clostridia Species

Oscillation phenomena are common in biological systems, with circadian rhythms being a well-known example, driven by molecular oscillators as a response to light–dark cycles [1]. In microbial cultures, observable metabolic oscillations require synchronization, whereby most cells must be in the same state simultaneously. This synchronization likely involves interactions between cells or with the environment, rather than internal processes alone. Metabolic oscillations in continuous cultures are frequently reported, including in bacteria such as Escherichia coli [2], Zymomonas mobilis [3], Klebsiella pneumoniae [4], and the yeast Saccharomyces cerevisiae [5,6].

Clostridia are promising candidates for biotechnological applications because of their diverse and unique metabolic capabilities. However, many species exhibit metabolic oscillations during continuous fermentation processes, which can significantly reduce productivity. These oscillations often lead to process instability, posing a major challenge to the development of industrially viable processes.

Tyszak and Rehman [7] reviewed oscillation phenomena in Clostridium species, summarizing current knowledge on metabolic oscillations in Clostridia, their mechanisms, and strategies to mitigate them. These oscillations vary in period and observed parameters, with some being well understood and others requiring further study, and understanding these mechanisms is key to stabilizing processes.

1.2. Pyrimidine Biosynthesis and Ribonucleoside Metabolism in Species of Pseudomonas

Numerous studies have investigated pyrimidine biosynthesis in Gram-negative and Gram-positive bacteria, as well as in eukaryotes. However, relatively few have specifically examined pyrimidine biosynthesis in species of Pseudomonas. Similarly, while the metabolism of pyrimidine ribonucleosides and the catabolism of pyrimidine bases have been explored in various Gram-negative and Gram-positive prokaryotic and eukaryotic species, in-depth analyses of these processes in Pseudomonas remain limited.

To address this gap, West [8] conducted a review focusing on pyrimidine biosynthesis and ribonucleoside metabolism in different Pseudomonas species, with particular attention devoted to their taxonomic classifications within various homology groups. The review sought to determine whether the regulation of pyrimidine biosynthesis in taxonomically related Pseudomonas species followed similar patterns. Specifically, it examined whether this regulation was influenced via supplementation with pyrimidine bases or under conditions of pyrimidine limitation in auxotrophic strains.

The findings revealed that the regulation of pyrimidine biosynthesis in Pseudomonas species could not be correlated with their taxonomic grouping into specific homology groups. Regarding ribonucleoside metabolism, the study highlighted that Pseudomonas species primarily utilized pyrimidine ribonucleoside salvage enzymes, such as nucleoside hydrolase and cytosine deaminase. Importantly, this metabolic activity appeared to function independently of the homology group to which a species belonged.

Similarly, pyrimidine base catabolism was found to be active across various Pseudomonas homology groups. Although relatively few studies have focused on the catabolism of specific pyrimidine bases such as uracil and thymine, the presence of the reductive pathway for pyrimidine catabolism emerged as a common feature among the Pseudomonas species investigated.

Moreover, West’s review identified a link between pyrimidine ribonucleoside degradation and pyrimidine base catabolism. This connection appeared to play a significant role in providing essential cellular resources, such as carbon and nitrogen, regardless of the homology group classification of the Pseudomonas species. These findings underscore the metabolic versatility of Pseudomonas and the functional conservation of these pathways across the genus.

1.3. Insights into Co-Cultivation of Photosynthetic Microorganisms for Novel Molecule Discovery and Enhanced Production of Specialized Metabolites

Mesophilic and extremophilic microalgae, including both eukaryotic microalgae and cyanobacteria, are recognized as valuable microorganisms for the production of high-value compounds such as vitamins, pigments, lipids, bioactive peptides, and alternative energy sources [9]. However, the increasing industrial demand for bioactive molecules, coupled with the redundancy of existing compounds, has created an urgent need for innovative methodologies to enhance production and facilitate the discovery of specialized metabolites.

Co-cultivation has emerged as a promising strategy to address these challenges. Rojas-Villalta et al. [9,10,11,12,13] conducted a comprehensive review of the state-of-the-art co-cultivation methods involving mesophilic and extremophilic photosynthetic microorganisms. Their review emphasizes the advantages, challenges, and limitations associated with this approach.

Co-culture is an ecology-driven technique that harnesses the symbiotic interactions between cyanobacteria and microalgae. This method facilitates the discovery of novel compounds while enhancing the production of existing ones. Promising research outcomes have demonstrated the expression of new bioactive metabolites and significant improvements in production efficiency through co-cultivation. Furthermore, the metabolic diversity and evolutionary adaptations of photosynthetic microorganisms, particularly those thriving in extreme environments, expand the applicability of co-cultivation by enabling the use of a broader range of microorganisms.

Despite these advantages, several challenges hinder the widespread adoption of co-cultivation. The complexity of ecological interactions and the absence of standardized protocols are major barriers, limiting the reproducibility and scalability of co-culture methods for industrial applications. Addressing these obstacles requires further research into the underlying symbiotic interactions. Advances in omics technologies, genetic engineering, and predictive experimental designs tailored for co-cultures hold the potential to overcome these limitations.

Such advancements could significantly improve the efficiency and reliability of co-cultivation systems, paving the way for the sustainable production of high-value compounds and contributing to industrial and environmental innovation.

2. Food and Beverage Biotechnology

2.1. Sourdoughs as Natural Enhancers of Bread Quality and Shelf Life

Sourdough fermentation, one of the oldest bread-leavening methods, improves the taste, texture, and digestibility of cereal-based products [14,15]. Recently, its use has expanded beyond traditional bread making to various bakery products, creating new research opportunities [16]. Combining sourdough with baker’s yeast has become popular in industrial bread production due to its ability to enhance sensory qualities and prevent mold growth [17].

The unique microbiome of sourdough, mainly comprising lactic acid bacteria (LAB) and yeasts, produces compounds like organic acids, peptides, and exopolysaccharides [18]. These bioactive compounds improve bread quality, extend its shelf life, and reduce mold spoilage. Additionally, aqueous extracts from fermented sourdough have shown potential as natural antimicrobials, particularly for inhibiting bread-spoiling molds.

Sourdough is key in traditional and artisanal bread making, offering distinct flavors and textures valued by consumers. Over the last 30 years, research has highlighted its potential to improve both the sensory qualities and shelf life of bread.

Hernández-Figueroa et al. [19] reviewed recent advancements in using LAB-fermented sourdoughs and their aqueous extracts to enhance bread quality and preserve bakery products. The review focuses on the essential role of LAB and yeasts in producing organic acids, peptides, and exopolysaccharides, as well as the potential of sourdough extracts as natural antifungal agents that target molds damaging bread quality. It also aims to identify the compounds in sourdough responsible for these antifungal properties.

Incorporating sourdough into bread formulations has been shown to improve flavor, slow aging, and reduce spoilage. Bioactive compounds from LAB during fermentation contribute antimicrobial and antifungal properties, extending the shelf life of bread. Ongoing research into sourdough fermentation and its applications is crucial for enhancing bread quality, diversity, and sustainability, as well as deepening our scientific understanding of this traditional process.

2.2. LAB Antagonistic Activities and Their Significance in Food Biotechnology: Molecular Mechanisms, Food Targets, and Other Related Traits of Interest

The persistent issue of foodborne diseases and the need for effective spoilage and pathogen control in food products is a major challenge for the food industry. As consumers increasingly demand safe, healthy, and clean-label foods, there has been a growing interest in natural antimicrobial alternatives. Lactic acid bacteria (LAB) have gained recognition for their antimicrobial properties against harmful microbes, as well as their beneficial technological attributes. LAB produce natural antimicrobial compounds, such as bacteriocins and organic acids, which inhibit the growth of pathogens and food spoilage organisms. These secondary metabolites have been successfully applied in the food industry, helping prevent the proliferation of undesirable microorganisms while improving the sensory and overall quality of food products.

In their review, Cirat et al. [20] highlight the natural antimicrobial compounds produced by LAB and emphasize their significant role in microbial control. The ability of LAB to produce essential metabolites, like bacteriocins, organic acids, and hydrogen peroxide, makes them effective biopreservatives for managing spoilage and pathogenic microorganisms in various biotechnological applications.

2.3. Yeast Bioflavoring in Beer: Complexity Decoded and Built up Again

During beer fermentation, yeasts produce various flavor-active compounds that contribute to the distinctive aroma profiles of alcoholic beverages. These compounds include higher alcohols, acetate and ethyl esters, carbonyls (such as aldehydes and ketones), and vicinal diketones (e.g., diacetyl and pentanedione, which can impart unpleasant flavors). While many of these compounds are secondary metabolites formed during fermentation, yeasts also enzymatically convert odorless precursors from hops and malt into flavorful compounds through a process called biotransformation [21].

Enhancing yeast bioflavoring offers an opportunity for breweries to diversify their product range and improve environmental sustainability, particularly in the context of climate change. However, the genetic basis of flavor compound metabolism, including the enzymes and regulatory factors involved, remains only partially understood. Recent research has made progress in identifying genes contributing to flavor molecule production and the mutations underlying the diverse bioflavoring capabilities of yeast strains.

Although much attention has been given to how hops influence beer flavor and microbiological stability [22], yeasts play a critical role in shaping beer aroma and flavor. Previous reviews have focused on desirable odorants produced during fermentation or biotransformation of hop and malt precursors [23,24]. The review by Nasuti and Solieri [25] addresses both categories of yeast-derived flavor-active molecules, emphasizing recent discoveries in the metabolic pathways and genetic mechanisms driving their production.

The review also explores recent advancements in bioprospecting and metabolic engineering aimed at enhancing and diversifying yeast bioflavoring. Specific focus is given to higher alcohols, esters, monoterpene alcohols, thiols, and phenolic derivatives of hydroxycinnamic acids. Key strategies discussed include the exploration of novel Saccharomyces and non-Saccharomyces yeast strains, whole-genome engineering, and targeted metabolic engineering approaches.

3. Pharmaceutical Microbiology

Therapeutic Applications of Native and Engineered Saccharomyces Yeasts

Saccharomyces cerevisiae var. boulardii (Sb) is gaining significant attention as a synthetic probiotic platform due to its ease of genetic manipulation and proven effectiveness in supporting digestive health [26,27,28]. Exploring Sb and other S. cerevisiae strains (Sc) in detail could enhance their therapeutic applications.

In a review, Kwak [29] begins by highlighting the natural health benefits of Sb and demonstrates its potential as a synthetic probiotic or parabiotic framework, using examples of recent advancements in Sb engineering for therapeutic purposes. The review also examines engineering efforts with Sc, given its genetic similarity to Sb and potential as a therapeutic microorganism.

Research involving molecular typing and phenotypic analysis has revealed key differences between these strains. For instance, Sb shows superior tolerance to heat and acidic conditions—attributes that are critical for effective probiotics. Additionally, yeast cell wall oligosaccharides contribute to the parabiotic and prebiotic benefits of Sb and Sc, playing a major role in their health-promoting properties.

To maximize benefits, selecting the right yeast strain requires a thorough understanding of its specific actions in the gastrointestinal tract and the mechanisms behind the desired health effects. The review emphasizes the importance of unbiased, detailed comparative studies to guide the informed selection of yeast strains for therapeutic use.