Fermentation

20 pages, 1206 KiB

Open AccessReview

Fungal Biomass Fermentation: Valorizing the Food Industry’s Waste

by Simas Borkertas, Jonas Viskelis, Pranas Viskelis, Paulina Streimikyte, Ugne Gasiunaite and Dalia Urbonaviciene

Fermentation 2025, 11(6), 351; https://doi.org/10.3390/fermentation11060351 - 16 Jun 2025

Abstract

Fungi, including filamentous organisms such as yeasts, play essential roles in various processes such as nutrient exchange in ecosystems, the cultivation of mushrooms, and solid-state fermentation (SSF). SSF involves microbial growth on solid substrates without free water, leading to the production of enzymes, [...] Read more.

Fungi, including filamentous organisms such as yeasts, play essential roles in various processes such as nutrient exchange in ecosystems, the cultivation of mushrooms, and solid-state fermentation (SSF). SSF involves microbial growth on solid substrates without free water, leading to the production of enzymes, bioactive compounds, and biofuels. This fermentation method offers advantages like lower production costs, reduced waste disposal issues, and the efficient utilization of agricultural residues and fruit and vegetable by-products. Filamentous fungi excel in SSF due to their enzyme secretion capacity and ability to produce valuable compounds. The process is influenced by biological, physico-chemical, and environmental factors, requiring careful optimization for optimal results. Fruit and vegetable by-products are increasingly recognized as valuable substrates for SSF, offering rich sources of bioactive compounds and high nutritional value. The optimization of SSF processes, compatibility with various substrates, and potential for producing diverse value-added products make SSF a promising method for sustainable resource utilization and enhanced product development. Future research should focus on improving process efficiency, expanding the substrate range, enhancing product quality and yield, and integrating SSF with other technologies for enhanced production capabilities. Full article

(This article belongs to the Section Industrial Fermentation)

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19 pages, 2028 KiB

Open AccessArticle

Characterization of a Vaginal Limosilactobacillus Strain Producing Anti-Virulence Postbiotics: A Potential Probiotic Candidate

by Tsvetelina Paunova-Krasteva, Petya D. Dimitrova, Dayana Borisova, Lili Dobreva, Nikoleta Atanasova and Svetla Danova

Fermentation 2025, 11(6), 350; https://doi.org/10.3390/fermentation11060350 - 16 Jun 2025

Abstract

The search for probiotics to help limit antibiotic resistance is a major scientific challenge. The exploration of Lactobacillus postbiotics represents a promising approach to prevent pathogen invasion. With this aim, Limosilactobacillus fermentum Lf53, with a broad-spectrum of antagonistic activity, was characterized as a [...] Read more.

The search for probiotics to help limit antibiotic resistance is a major scientific challenge. The exploration of Lactobacillus postbiotics represents a promising approach to prevent pathogen invasion. With this aim, Limosilactobacillus fermentum Lf53, with a broad-spectrum of antagonistic activity, was characterized as a candidate probiotic strain with promising transit tolerance and broad spectrum of activity. A study on growth and postbiotic production in modified MRS broth with different carbohydrates and its vegan variant was carried out. This study presents a comprehensive approach to characterizing the anti-virulence properties of postbiotics derived from Lf53. The promising antibacterial, antibiofilm, and anti-quorum sensing activities of the cell-free supernatants (CFS) were assessed as part of the probiotic’s barrier mechanisms. Biofilm inhibition of P. aeruginosa revealed remarkable suppressive effects exerted by the three tested postbiotics, two of which (nCFS and aCFS) exhibited over 50% inhibition and more than 60% for lysates. The postbiotics’ influence on the production of violacein and pyocyanin pigments of Chromobacterium violaceum and Pseudomonas aeruginosa, which are markers for quorum sensing, highlighted their potential in regulating pathogenic mechanisms. The Lf53 lysates showed the most significant inhibition of violacein production across multiple assays, showing 29.8% reduction. Regarding pyocyanin suppression, the postbiotics also demonstrated strong activity. These are the first reported data on complex postbiotics (metabiotics and parabiotics) demonstrating their potential as anti-virulence agents to help combat pathogens associated with antibiotic-resistant infections. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria: Evaluation of Benefits on Human Health and Improvement of Food Safety)

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14 pages, 1642 KiB

Open AccessArticle

Composition Divergence and Synergistic Mechanisms in Microbial Communities During Multi-Varietal Wine Co-Fermentation

by Yuhan Zhang, Jiao Yang and Yuxi Yan

Fermentation 2025, 11(6), 349; https://doi.org/10.3390/fermentation11060349 - 16 Jun 2025

Abstract

The bacterial microbial community composition during wine fermentation is a key contributor to wine quality and flavor. However, studies on the regulatory effects of different grape varieties and co-fermentation processes on the microbial community structure and their synergistic mechanisms remain limited. In this [...] Read more.

The bacterial microbial community composition during wine fermentation is a key contributor to wine quality and flavor. However, studies on the regulatory effects of different grape varieties and co-fermentation processes on the microbial community structure and their synergistic mechanisms remain limited. In this study, Cabernet Sauvignon (CS) was subjected to single-variety fermentation and used as the base wine for co-fermentation with three other grape varieties—Marselan (CSMN), Merlot (CSMT), and Cabernet Gernischt (CSCG)—to systematically compare the differences in the microbial community composition and their effects on the production of metabolic compounds. The results showed that, compared with single-variety fermentation, co-fermentation significantly increased the α-diversity of microbial communities (the Shannon index increased) and exhibited significant differences in β-diversity (PERMANOVA analysis, R² = 0.421, p < 0.001). A neutral model analysis indicated that co-fermentation had a significant impact on microbial community assembly mechanisms, with the contribution of neutral processes to community assembly increasing from 45.5% (in the CSCG process) to 62.3% (in the CSMT process). A microbial co-occurrence network analysis revealed that co-fermentation enhanced the network complexity of microbial communities and strengthened the synergistic interactions between microbial taxa. A metabolic compound analysis revealed that co-fermentation significantly enhanced the production of key aroma compounds, resulting in increased concentrations of isoamyl acetate, ethyl hexanoate, linalool, and geraniol. These findings highlight the differences in microbial communities and their synergistic mechanisms among co-fermented grape varieties, providing theoretical guidance and practical insights for optimizing co-fermentation processes and improving wine quality. Full article

(This article belongs to the Section Microbial Metabolism, Physiology & Genetics)

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25 pages, 6743 KiB

Open AccessArticle

Anaerobic Digestion of Food Waste and Granular Inoculum: Study on Temperature Effect and Substrate-to-Inoculum Ratio on Biogas Production

by Madalina Ivanovici, Gabriela-Alina Dumitrel, Vasile Daniel Gherman, Teodor Todinca, Ana-Maria Pana and Valentin Laurentiu Ordodi

Fermentation 2025, 11(6), 348; https://doi.org/10.3390/fermentation11060348 - 15 Jun 2025

Abstract

The development of food waste anaerobic digestion (AD) is a contemporary research topic addressed in the scientific community to meet the requirements of food waste valorization and proper substrate configuration for an efficient AD process. In this study, multiple AD experiments were performed [...] Read more.

The development of food waste anaerobic digestion (AD) is a contemporary research topic addressed in the scientific community to meet the requirements of food waste valorization and proper substrate configuration for an efficient AD process. In this study, multiple AD experiments were performed on food waste together with industrial inoculum using laboratory-scale bioreactors. Food waste consisted mainly of fruits and vegetables (80.9%) and boiled rice (19.1%). The effect of operating temperature (33 °C, 37 °C, 41 °C, 45 °C) and the ratio between food waste mixture and inoculum-FIR (1:1, 3:2 and 2:1, w/w) on the production and composition of biogas, and the conversion yield for CH₄ and organic carbon, were investigated. The best results were obtained at an FIR of 2:1 and a temperature of 37 °C, with a total biogas production of 468.59 NL h⁻¹ kg⁻¹_VSadded (51% v/v CH₄ conc.) and a conversion yield of 36.42% for CH₄. A modified Gompertz model was applied on the accumulated CH₄ and biogas to evaluate the process performance. The model parameters were investigated in conjunction with the physico-chemical characteristics of the substrate, inoculum taxonomic profile, pH measurements, and TG-DTA analysis. The conducted analyses emphasized the susceptibility of the selected substrate towards easy degradation and improved biotransformation reactions when temperature and FIR were increased. Full article

(This article belongs to the Special Issue The Future of Fermentation Technology in the Biorefining Process: 3rd Edition)

34 pages, 1585 KiB

Open AccessReview

Biological Potential of Extremophilic Filamentous Fungi for the Production of New Compounds with Antimicrobial Effect

by Vladislava Dishliyska, Jeny Miteva-Staleva, Yana Gocheva, Galina Stoyancheva, Lyudmila Yovchevska, Radoslav Abrashev, Boryana Spasova, Maria Angelova and Ekaterina Krumova

Fermentation 2025, 11(6), 347; https://doi.org/10.3390/fermentation11060347 - 14 Jun 2025

Abstract

Antimicrobial resistance represents one of the most critical public health challenges of the 21st century. The emergence of multidrug resistance (MDR) in bacterial and fungal pathogens to diverse chemical agents severely impedes the effective treatment of diseases such as cancer and systemic infections. [...] Read more.

Antimicrobial resistance represents one of the most critical public health challenges of the 21st century. The emergence of multidrug resistance (MDR) in bacterial and fungal pathogens to diverse chemical agents severely impedes the effective treatment of diseases such as cancer and systemic infections. The rapid escalation of microbial resistance underscores the urgent need for the discovery of novel antimicrobial agents and innovative approaches to drug development. In both clinical and industrial contexts, the identification of new antibiotics and antifungals remains pivotal for pathogen control. Current research efforts focus on the development of alternative formulations that offer high efficacy, reduced resistance potential, minimal side effects, and synergistic interactions, particularly those derived from natural sources. Filamentous fungi originating from extreme environments have evolved to thrive under harsh conditions, making them promising reservoirs of bioactive metabolites with unique structural and functional properties. These fungi exhibit potent antimicrobial activity through diverse mechanisms that disrupt essential cellular processes in pathogens. Despite their remarkable potential, the bioprospecting of extremophilic filamentous fungi for drug development remains underexplored. This highlights the necessity for expanded research into the efficacy and safety of their derived compounds. This review aims to emphasize the capacity of extremophilic fungi to produce antimicrobial agents, elucidate resistance mechanisms, characterize fungal bioactive extracts, and analyze their molecular actions in the context of their extreme ecological niches. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”)

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45 pages, 2757 KiB

Open AccessReview

Nutritional Enhancement of Plant-Based Fermented Foods: Microbial Innovations for a Sustainable Future

by Sunny Dhiman, Sukhminderjit Kaur, Babita Thakur, Pankaj Singh and Manikant Tripathi

Fermentation 2025, 11(6), 346; https://doi.org/10.3390/fermentation11060346 - 14 Jun 2025

Abstract

The rising demand for sustainable, nutritious, and functional food options has fueled growing interest in plant-based fermented foods. These products offer enhanced sensory, functional, and health-promoting properties, largely driven by microbial activity during fermentation. This review examines recent advances in microbial biotechnology—including the [...] Read more.

The rising demand for sustainable, nutritious, and functional food options has fueled growing interest in plant-based fermented foods. These products offer enhanced sensory, functional, and health-promoting properties, largely driven by microbial activity during fermentation. This review examines recent advances in microbial biotechnology—including the use of novel starter cultures, strain engineering, CRISPR-based genome editing, and precision fermentation that are reshaping the nutritional landscape of plant-based fermented foods. Key benefits such as improved protein digestibility, bioactive compound synthesis, antinutrient reduction, and micronutrient bioavailability are explored. Additionally, the review highlights the potential of microbial innovations to enhance sustainability, address global nutrition challenges, and improve consumer acceptance through better sensory quality. It also discusses challenges related to regulatory frameworks, scalability, and consumer perception. This review aims to provide a comprehensive understanding of how microbial processes can optimize the nutritional and functional value of plant-based fermented foods in alignment with future food system goals. Full article

(This article belongs to the Special Issue Recent Advances in Microbial Fermentation in Foods and Beverages)

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18 pages, 2523 KiB

Open AccessArticle

CRISPRa-Mediated Triple-Gene Activation of ARO10, ARO80, and ADH2 for Enhancing 2-Phenylethanol Biosynthesis via the Ehrlich Pathway in Saccharomyces cerevisiae

by Zijing Zhu, Shuaihu Fang, Pingping Huang, Dianqiang Luo and Xiaobao Qi

Fermentation 2025, 11(6), 345; https://doi.org/10.3390/fermentation11060345 - 12 Jun 2025

Viewed by 119

Abstract

2-phenylethanol (2-PE), a rose-like fragrance compound, is widely used in the food industry. Conventional chemical synthesis of 2-PE faces significant challenges due to environmental concerns and consumer preferences; thus, using Saccharomyces cerevisiae (S. cerevisiae) for 2-PE biosynthesis has become a preferable [...] Read more.

2-phenylethanol (2-PE), a rose-like fragrance compound, is widely used in the food industry. Conventional chemical synthesis of 2-PE faces significant challenges due to environmental concerns and consumer preferences; thus, using Saccharomyces cerevisiae (S. cerevisiae) for 2-PE biosynthesis has become a preferable option. This study aimed to develop a CRISPR activation (CRISPRa)-mediated S. cerevisiae engineered strain for efficient 2-PE biosynthesis by activating Ehrlich pathway key genes ARO10, ARO80, and ADH2. Three guide sequences (GSs) were designed for each gene ARO10, ARO80, and ADH2, and nine single-gene CRISPRa strains were constructed. Gene expression levels, 2-PE concentrations, and cell density were quantified using quantitative real-time PCR (qPCR), high-performance liquid chromatography (HPLC), and OD₆₀₀ measurement, respectively. The optimal GSs of ARO10, ARO80, and ADH2 were selected based on 2-PE concentrations of corresponding strains. The triple-gene CRISPRa strain INVScI-ARO10-ARO80-ADH2 achieved a 214.04 mg/L 2-PE titer after 48 h, representing a 77.62% increase over the control with no significant effect on cell growth. These findings demonstrate that CRISPRa-mediated multi-gene activation constitutes a robust strategy for engineering high-performance 2-PE production systems in S. cerevisiae. Full article

(This article belongs to the Section Microbial Metabolism, Physiology & Genetics)

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20 pages, 2901 KiB

Open AccessArticle

Ethanol and Xylitol Co-Production by Clavispora lusitaniae Growing on Saccharified Sugar Cane Bagasse in Anaerobic/Microaerobic Conditions

by David Guzmán-Hernández, Ana C. Ramos-Valdivia, Héctor Mario Poggi-Varaldo, Josefina Barrera-Cortés, Eliseo Cristiani-Urbina and Teresa Ponce-Noyola

Fermentation 2025, 11(6), 344; https://doi.org/10.3390/fermentation11060344 - 12 Jun 2025

Viewed by 182

Abstract

Ethanol and xylitol are valuable bioproducts synthesized by non-conventional yeasts from lignocellulosic sugars. However, their biosynthesis requires distinct cultivation conditions. This study evaluated the production of ethanol and xylitol by Clavispora lusitaniae using saccharified sugarcane bagasse (SSCB) under three aeration conditions: microaerobic (C1), [...] Read more.

Ethanol and xylitol are valuable bioproducts synthesized by non-conventional yeasts from lignocellulosic sugars. However, their biosynthesis requires distinct cultivation conditions. This study evaluated the production of ethanol and xylitol by Clavispora lusitaniae using saccharified sugarcane bagasse (SSCB) under three aeration conditions: microaerobic (C1), anaerobic (C2), and a combination of anaerobic followed by a microaerobic phase (C3). Ethanol production was maximum under anaerobic conditions (C2), followed by combined anaerobic–microaerobic conditions (C3). Meanwhile, xylitol production was most efficient under microaerobic conditions (C1). Notably, anaerobic conditions were ineffective for xylitol production. Enzyme activities of xylose reductase (XR) and xylitol dehydrogenase (XDH), key enzymes in xylose metabolism, were highest under microaerobic conditions with activities of 2.88 U/mg and 1.72 U/mg, respectively, after 48 h of culture. Gene expression analysis of XYL1 and XYL2 correlated with the corresponding enzyme activities (XR) and (XDH) with increased levels of 32.38 and 7.88 fold, respectively, compared to the control in C1. These findings suggest that C. lusitaniae co-produces ethanol efficiently under anaerobic conditions, while xylitol biosynthesis is optimized under microaerobic conditions when using xylose-rich saccharified lignocellulosic substrates. Full article

(This article belongs to the Special Issue Technological Advances in Lignocellulosic Biomass Conversion to Bioenergy)

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12 pages, 528 KiB

Open AccessArticle

Probiotic Potential of Lactic Acid Bacteria Strains Isolated from Artisanal Cheeses: Impact on Listeria monocytogenes Infection

by Carla Burgos, Constanza Melian, Lucía M. Mendoza, Susana Salva and Patricia Castellano

Fermentation 2025, 11(6), 343; https://doi.org/10.3390/fermentation11060343 - 12 Jun 2025

Viewed by 137

Abstract

Listeriosis is a disease associated with the consumption of food contaminated with Listeria monocytogenes. Probiotic lactic acid bacteria (LAB) or their postbiotics have been of interest for their anti-listerial effect. This study focused on isolating LAB from artisanal cheeses and characterizing their [...] Read more.

Listeriosis is a disease associated with the consumption of food contaminated with Listeria monocytogenes. Probiotic lactic acid bacteria (LAB) or their postbiotics have been of interest for their anti-listerial effect. This study focused on isolating LAB from artisanal cheeses and characterizing their potential as probiotics. Twelve LAB isolates exhibiting typical LAB traits were evaluated for their ability to survive in simulated gastric juice, hydrolyze bile salts, auto-aggregate, hydrophobicity, and antagonistic activity against L. monocytogenes. The four most promising LAB strains demonstrated anti-listerial probiotic potential and were identified as Latilactobacillus (Lat.) curvatus SC076 and Lactiplantibacillus (Lact.) paraplantarum SC291, SC093, and SC425. The antimicrobial activity of these strains was mainly attributed to bacteriocin-like substances and organic acids. While three Lact. paraplantarum strains were resistant to ampicillin, Lat. curvatus was sensitive to all tested antibiotics. All selected strains exhibited no hemolytic, gelatinase, and lecithinase activity. Exposure to LAB supernatants resulted in a significant reduction in the adhesion and intracellular count of L. monocytogenes in Caco-2 cells, with Lat. curvatus SC076 showing the most significant effect. Based on its probiotic characteristics, Lat. curvatus SC076 is a promising candidate for functional foods, pending further in vivo studies to assess its potential in the food industry. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria: Evaluation of Benefits on Human Health and Improvement of Food Safety)

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14 pages, 1350 KiB

Open AccessArticle

Lactic Acid Bacteria as Probiotics Improve Bioactive Compounds in Radix Angelica gigas (Danggui) via Solid-State Fermentation

by Jeong Heo, Youn-Kyung Ham, Ah Yeong Choi, Hyouk Yoon and Ha Gyun Sung

Fermentation 2025, 11(6), 342; https://doi.org/10.3390/fermentation11060342 - 12 Jun 2025

Viewed by 184

Abstract

Solid-state fermentation (SSF) is increasingly applied to enhance the functional properties of traditional herbal medicines. In this study, we investigated the effect of lactic acid bacteria (LAB) and other probiotic strains on the bioactive profile of Radix Angelica gigas (Danggui) during SSF. SSF [...] Read more.

Solid-state fermentation (SSF) is increasingly applied to enhance the functional properties of traditional herbal medicines. In this study, we investigated the effect of lactic acid bacteria (LAB) and other probiotic strains on the bioactive profile of Radix Angelica gigas (Danggui) during SSF. SSF was carried out by incubating a mixture of the herbal powder and distilled water (1:1, pH 7.0) with LAB strains (Lactobacillus rhamnosus, L. acidophilus, L. buchneri, L. reuteri, L. plantarum) and additional microbes (Bacillus subtilis, Saccharomyces cerevisiae) under controlled conditions. The 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activities and total phenolic and flavonoid contents were measured. L. buchneri exhibited the highest growth, with significant proliferation observed on days 4 and 6, especially at 30 °C (p < 0.05). The DPPH and ABTS radical scavenging activities and total phenol and total flavonoid contents were increased by up to 230% (35 °C), 111% (30 °C), 137% (30 °C and 35 °C), and 133% (35 °C), respectively, in fermented herbs compared with those in non-fermented herbs. Antioxidant levels (DPPH, phenol, and flavonoid) exhibited a significant positive correlation with bacterial growth and a significant negative correlation with pH in SSF, but ABTS did not exhibit any statistically significant correlation with bacterial growth or pH. Moreover, multi-strain fermentations involving L. acidophilus and L. plantarum significantly increased the antioxidant activities compared to single-strain fermentations (p < 0.05). These findings suggest that SSF using probiotic LAB can significantly improve the bioactive composition of Radix Angelica gigas, providing a scientific method for modernizing traditional herbal medicine with potential uses in human and animal health. Full article

(This article belongs to the Special Issue Bioactive Compounds and Functional Properties of Fermented Foods)

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13 pages, 1826 KiB

Open AccessArticle

Applied Bioelectrochemistry: Plastic Degradation and Energy Generation Using Klebsiella oxytoca in Microbial Fuel Cells

by Rojas-Flores Segundo, Cabanillas-Chirinos Luis, Nélida Milly Otiniano, Magaly De La Cruz-Noriega, Nancy Soto-Deza, Anibal Alviz-Meza and Ángel Darío González-Delgado

Fermentation 2025, 11(6), 341; https://doi.org/10.3390/fermentation11060341 - 12 Jun 2025

Viewed by 205

Abstract

Plastic pollution remains a critical global environmental challenge, with conventional disposal methods contributing to ecosystem degradation. Simultaneously, energy scarcity affects numerous rural communities, limiting development opportunities. This study presents an innovative approach that integrates microbial fuel cells (MFCs) with Klebsiella oxytoca to simultaneously [...] Read more.

Plastic pollution remains a critical global environmental challenge, with conventional disposal methods contributing to ecosystem degradation. Simultaneously, energy scarcity affects numerous rural communities, limiting development opportunities. This study presents an innovative approach that integrates microbial fuel cells (MFCs) with Klebsiella oxytoca to simultaneously degrade plastic waste and generate bioelectricity. The monitoring results over 40 days revealed optimal performance on day 28, with a peak voltage of 0.714 ± 0.026 V and an electric current of 3.149 ± 0.124 mA. The biocatalyst exhibited an electrical conductivity of 140.466 ± 5.180 mS/cm and an oxidation-reduction potential of 109.519 ± 5.35 mV, indicating efficient electron transfer. Furthermore, the MFCs achieved a maximum power density of 11.391 ± 0.814 mW/cm² with a current density of 5.106 mA/cm², demonstrating their potential for sustainable energy production. Fourier transform infrared (FTIR) analysis confirmed structural modifications in the plastic, with decreased vibrational peaks indicative of polymer degradation. Additionally, scanning electron microscopy (SEM) micrographs revealed porosity and surface cracks, highlighting Klebsiella oxytoca’s biodegradation capacity. These findings establish the viability of bioelectrochemical systems for simultaneous waste remediation and renewable energy generation, paving the way for scalable applications in environmental biotechnology. By coupling microbial degradation with electricity production, this research supports the development of sustainable solutions aligned with the principles of circular economy and climate change mitigation. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section "Industrial Fermentation")

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16 pages, 301 KiB

Open AccessArticle

The Effect of Saliva with Different Nitrogen Compositions on Ruminal Fermentation in a Rumen Simulator Technique (Rusitec^®) System Fed a Lactating Dairy Cow Diet

by Ícaro Rainyer Rodrigues de Castro, Luiza de Nazaré Carneiro da Silva, Isabela Fonseca Carrari, Giulia Berzoini Costa Leite, Eduardo Marostegan de Paula, Amanda Moelemberg Cezar and Marcos Inácio Marcondes

Fermentation 2025, 11(6), 340; https://doi.org/10.3390/fermentation11060340 - 11 Jun 2025

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Abstract

In vitro methods have advanced research on rumen microbiology and fermentation. However, artificial saliva formulation may need adjustments, particularly in urea content, for modern diets, warranting further research. This study investigated the effects of different nitrogen (N) levels in artificial saliva on ruminal [...] Read more.

In vitro methods have advanced research on rumen microbiology and fermentation. However, artificial saliva formulation may need adjustments, particularly in urea content, for modern diets, warranting further research. This study investigated the effects of different nitrogen (N) levels in artificial saliva on ruminal fermentation and digestion in diets for dairy cows using a Rusitec^® system. Eighteen fermenters tested three saliva treatments with different N levels: a standard saliva as the control and two treatments with N reduced by 15% and 30%. Data were analyzed as a completely randomized design using the MIXED procedure of SAS (v. 9.4), with linear and quadratic contrasts tested for treatment effects (significance set at p ≤ 0.05). Results showed that altering N content had no significant effect on pH, ammonia concentrations, or NH₃-N outflow, nutrient digestibility (dry matter, crude protein, fiber, and starch), gas and methane production, or volatile fatty acid concentrations. The efficiency of microbial protein synthesis and N flow exhibited quadratic responses, with the lowest values observed at the highest level of N reduction in the saliva (−30%). These findings suggest that although ruminal function and digestion remain stable with reduced N, microbial protein synthesis efficiency may decline beyond a threshold. Full article

(This article belongs to the Section Microbial Metabolism, Physiology & Genetics)

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17 pages, 1694 KiB

Open AccessArticle

Enhancing Bioconversion of Crude Glycerol into Butanol and 1,3-Propanediol After Pretreatment by Coupling Fermentation and In Situ Recovery: Effect of Initial pH Control

by Alejandro Ortega, Alejo Valles, Miguel Capilla, Carmen Gabaldón, Francisco Javier Álvarez-Hornos and Paula Marzal

Fermentation 2025, 11(6), 339; https://doi.org/10.3390/fermentation11060339 - 11 Jun 2025

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Abstract

The sharp rise in the worldwide production of biodiesel has created an excess in the crude glycerol market, so it is essential to develop new added-value alternatives for crude glycerol. This paper describes a study on fermenting high concentrations of two types of [...] Read more.

The sharp rise in the worldwide production of biodiesel has created an excess in the crude glycerol market, so it is essential to develop new added-value alternatives for crude glycerol. This paper describes a study on fermenting high concentrations of two types of medium-pure crude glycerol to solvents by Clostridium pasteurianum. The effect of media composition (iron, yeast extract, and vitamins) on solvents production was assessed by a full factorial design with pure glycerol. Granular activated carbon (GAC) adsorption was highly effective in removing impurities from crude glycerol. Following GAC pretreatment, fermentation of glycerol at initial concentration as high as 60 g L⁻¹ was possible, resulting in a butanol production of ~9 g L⁻¹. Based on these results, a batch fermentation with in situ gas stripping and pH controlled at ≥6.5 was shown to be the best alternative to enhance biomass growth, glycerol uptake, and solvent production. The combination of controlling pH in the early stages of fermentation with in situ butanol removal stabilised the metabolism of the strain and showed that the fermentation performance with crude glycerol is very similar to that of pure glycerol. With a notable uptake of glycerol (>83%), solvent production was >11 g L⁻¹ butanol (yield > 0.21 g g⁻¹_{glycerol consumed}) and >6 g L⁻¹ 1,3-propanediol (yield > 0.13 g g⁻¹_{glycerol consumed}). Setting the fermentation conditions to achieve a high uptake of high levels of glycerol with a similar product distribution is of great interest for the viability of the industrial processing of crude glycerol into chemicals via biological conversion. Full article

(This article belongs to the Special Issue Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques)

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21 pages, 710 KiB

Open AccessReview

Valorization of Maize Stover into Biogas for Heat and Power Generation: A South African Perspective

by Reckson Kamusoko and Patrick Mukumba

Fermentation 2025, 11(6), 338; https://doi.org/10.3390/fermentation11060338 - 11 Jun 2025

Viewed by 205

Abstract

Maize (Zea mays) is one of the most cultivated crops in South Africa, serving as a staple food, stock feed, and a key element in several industrial applications. It contributes significantly to the growth of the South African agricultural economy. The [...] Read more.

Maize (Zea mays) is one of the most cultivated crops in South Africa, serving as a staple food, stock feed, and a key element in several industrial applications. It contributes significantly to the growth of the South African agricultural economy. The cultivation of maize generates a large amount of agricultural waste, mainly in the form of maize stover (MS), which encapsulates leaves, stalks, cobs, and husks. Approximately 5.15 metric tons (Mt) yr⁻¹ of MS are generated in South Africa. This corresponds to an energy potential of 94 PJ. There is immense potential to surpass the annual yield of MS by 126% up to about 11.66 Mt yr⁻¹ through practices such as zero tillage and improved agricultural production systems. MS may pose a serious threat to the environment if not managed in a sustainable and eco-friendly manner. Valorization of MS into biogas presents an excellent opportunity to effectively control biomass waste while contributing to renewable energy production and mitigating dependence on depleting fossil fuels. However, MS continues to be overlooked as a sustainable bioenergy resource due to its lignocellulosic structure. This study explores the potential of converting MS into biogas for heat and power generation, addressing both energy needs and waste management in South Africa. The purpose is to provide knowledge that will inform researchers, innovators, industrialists, policy makers, investors, and other key stakeholders interested in renewable energy systems. Collaborative efforts among multiple stakeholders are vital to leverage biogas as a technology to promote socio-economic development in South Africa. Full article

(This article belongs to the Special Issue Lignocellulosic Biomass Valorization)

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17 pages, 2411 KiB

Open AccessArticle

Indigenous Malolactic Starter Cultures as Innovative Tools to Modify the Sensory Profile of a Wine: An Oenological Challenge

by Elizabeth Naiquen Flores, Gabriel Alejandro Rivas, Andrea Cecilia Guillade, Natalia Soledad Brizuela, Marina Edith Navarro, Emma Elizabeth Tymczyszyn, Lucrecia Delfederico, Carolina Fabiana Perez, Liliana Carmen Semorile, Danay Valdes La Hens and Barbara Mercedes Bravo-Ferrada

Fermentation 2025, 11(6), 337; https://doi.org/10.3390/fermentation11060337 - 11 Jun 2025

Viewed by 216

Abstract

Malolactic fermentation conducted by lactic acid bacteria is essential for enhancing wine’s sensory qualities. Although this process can occur spontaneously through the action of native lactic acid bacteria (LAB) from the grapes and cellar, it carries risks such as increased volatile acidity, consumption [...] Read more.

Malolactic fermentation conducted by lactic acid bacteria is essential for enhancing wine’s sensory qualities. Although this process can occur spontaneously through the action of native lactic acid bacteria (LAB) from the grapes and cellar, it carries risks such as increased volatile acidity, consumption of residual sugars, and the formation of undesirable metabolites like biogenic amines. This study evaluated the oenological potential of three innovative native malolactic fermentation starters (MLFS) on a pilot scale, aiming to offer local wineries cost-effective MLFS with native LAB strains. Alcoholic fermentation of Malbec grapes was carried out using a commercial yeast starter, followed by a sequential inoculation of native malolactic starters formulated with (i) mesophilic Lactiplantibacillus plantarum UNQLp11 and Oenococcus oeni UNQOe73.2, both from the Province of Río Negro; (ii) psychrotrophic Lentilactibacillus hilgardii UNQLh1.1 and Oenococcus oeni UNQOe19, both from the Province of Río Negro; (iii) mesophilic Lactiplantibacillus plantarum UNQLp1001, from the Province of Buenos Aires; and (iv) a commercial malolactic started, which served as a control. Malic acid was consumed by all starters. RAPD-PCR using M13 primer showed the native LAB’s capability for implantation in wine. A sensory analysis revealed distinct profiles for each formulation, despite having been inoculated at the end of the same alcoholic fermentation. These MLFS could replace imports, enhancing the region’s unique terroir. Full article

(This article belongs to the Special Issue Innovative Strategies for the Management of Wine Fermentations: 2nd Edition)

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12 pages, 709 KiB

Open AccessArticle

Unlocking the Potential of Pomelo Albedo: A Novel Substrate for Alpha-Amylase Production Using Bacillus licheniformis

by Thi Ngoc Tran, Si-Chun Chen, Chien Thang Doan and San-Lang Wang

Fermentation 2025, 11(6), 336; https://doi.org/10.3390/fermentation11060336 - 11 Jun 2025

Viewed by 254

Abstract

The bioprocessing of agricultural wastes to produce microbial enzymes has become significant due to its benefits in reducing enzyme production costs and improving waste management. In this study, various substrates, including spent coffee grounds, coffee husks, coffee pulp, rice husks, rice bran, pomelo [...] Read more.

The bioprocessing of agricultural wastes to produce microbial enzymes has become significant due to its benefits in reducing enzyme production costs and improving waste management. In this study, various substrates, including spent coffee grounds, coffee husks, coffee pulp, rice husks, rice bran, pomelo albedo, pomelo flavedo, orange peel, banana peel, sugarcane bagasse, and starch, were used as organic nutrient sources for α-amylase biosynthesis by B. licheniformis TKU004. Among the tested substrates, pomelo albedo (3%, w/v) was the most suitable carbon source for amylase production, with a productivity of 80.645 U/mL. The purification process resulted in a 60 kDa amylase. The protein identification of B. licheniformis TKU004 amylase revealed a coverage rate of 39% with α-amylase from Bacillus subtilis 168. B. licheniformis TKU004 amylase exhibited optimal activity at 60 °C and pH = 7 and showed a high compatibility with EDTA (Ethylenediaminetetraacetic acid). HPLC (high-performance liquid chromatography) analysis demonstrated that B. licheniformis TKU004 amylase is an α-amylase with the final products of maltobiose, maltose, and glucose. Due to its important properties, such as tolerance to EDTA, B. licheniformis TKU 004 amylase may be valuable for industrial applications, especially in detergents and food processing. Full article

(This article belongs to the Special Issue Fermentation of Organic Waste for High-Value-Added Product Production)

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26 pages, 1941 KiB

Open AccessArticle

Immobilized Plant-Based Presumptive Probiotics as Functional Ingredients for Breakfast Cereals

by Chrysoula Pavlatou, Ioanna Prapa, Electra Stylianopoulou, Gregoria Mitropoulou, George Skavdis and Yiannis Kourkoutas

Fermentation 2025, 11(6), 335; https://doi.org/10.3390/fermentation11060335 - 10 Jun 2025

Viewed by 332

Abstract

Seven wild-type lactic acid bacteria, belonging to Lactiplantibacillus plantarum and Lactococcus cremoris species, were isolated from beetroots and white mushrooms and evaluated for their safety and functional profile. Lc. cremoris isolates were sensitive to all antibiotics tested, while L. plantarum strains exhibited resistance in [...] Read more.

Seven wild-type lactic acid bacteria, belonging to Lactiplantibacillus plantarum and Lactococcus cremoris species, were isolated from beetroots and white mushrooms and evaluated for their safety and functional profile. Lc. cremoris isolates were sensitive to all antibiotics tested, while L. plantarum strains exhibited resistance in certain antibiotics. Among them, Lc. cremoris FBMS_5810 showed the highest cholesterol removal ability (51.89%) and adhesion capacity to Caco-2 cell lines (32.14%), while all plant origin strains exhibited strong antagonistic and inhibitory activity against foodborne pathogens, as well as high survival potential during an in vitro digestion model. Subsequently, freeze-dried immobilized Lc. cremoris FBMS_5810 cells on oat flakes were prepared with initial cell loads >8.5 log CFU/g, and the effect of trehalose as a cryoprotectant in cell viability during storage at room and refrigerated temperatures for up to 180 days was studied. A significant reduction in cell loads was observed in all cases studied. However, freeze-dried immobilized Lc. cremoris FBMS_5810 cells on oat flakes prepared using trehalose as a cryoprotectant stored at 4 °C exhibited the highest cell viability (8.75 log CFU/g) after 180 days. In the next step, functional breakfast cereals enriched with freeze-dried immobilized Lc. cremoris FBMS_5810 cells on oat flakes (produced with (MLT) or without (ML) trehalose) were developed and stored at room and refrigerated temperatures for 180 days. The initial cell levels ≥ 9.18 log CFU/g were achieved, while a significant decrease was recorded during storage in all cases. The maintenance of cell loads ≥ 7.75 log CFU/g was documented in the case of both ML and MLT samples stored at 4 °C; however, the presence of trehalose in MLT samples resulted in cell viability 7.52 log CFU/g after 180 days of storage at room temperature. Importantly, the functional breakfast cereals were accepted by the panel during the sensory evaluation. Full article

(This article belongs to the Special Issue Novel Strategies and Emerging Technologies in Functional and Sustainable Food Systems)

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16 pages, 699 KiB

Open AccessArticle

Antioxidant Capacity, Phenolic and Organoleptic Profiles of Beers Maturated with Bilberries

by Petar Nedyalkov, Vesela Shopska, Giuseppe Perretti and Maria Kaneva

Fermentation 2025, 11(6), 334; https://doi.org/10.3390/fermentation11060334 - 10 Jun 2025

Viewed by 232

Abstract

Beer is probably one of the oldest alcoholic beverages, and regarding consumption, is third place after water and tea. Due to the consumer’s pursuit of novel tastes and aromas, craft brewers are trying to meet the consumer’s need, so brewing beer with a [...] Read more.

Beer is probably one of the oldest alcoholic beverages, and regarding consumption, is third place after water and tea. Due to the consumer’s pursuit of novel tastes and aromas, craft brewers are trying to meet the consumer’s need, so brewing beer with a fruit addition is the new twist. Fruit incorporation into the brewing process leads to alterations in the sensory properties and chemical composition of beers, but most of the articles published on this topic are mainly concentrated on beers with fruits different from bilberries. The data on bilberry beers are still scarce. Therefore, our projects are based in this field to investigate beer production with bilberries. In our previous research, we found interesting changes in the protein profile of bilberry beers with different original extracts. Therefore, the aim of this study was to investigate the influence of the original extract of beer maturated with bilberries on the phenolic profile (determined by HPLC analysis), the antioxidant capacity (measured by the ABTS, DPPH, FRAP, and CUPRAC methods), and sensory characteristics. The reported data can contribute to the development and production of bilberry beers with high antioxidant capacity and pleasant sensory properties. Full article

(This article belongs to the Special Issue Wine and Beer Fermentation, 2nd Edition)

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13 pages, 1232 KiB

Open AccessArticle

Optimization of Pectinase Production from Silkworm Excrement Using Aspergillus niger

by Fuzhi Lu, Caimei Tan, Huizhen Li and Feng Qian

Fermentation 2025, 11(6), 333; https://doi.org/10.3390/fermentation11060333 - 10 Jun 2025

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Abstract

Silkworm excrement, a byproduct of the sericulture industry, is rich in organic compounds and presents a sustainable substrate for enzyme production. This study investigates the potential of silkworm excrement as a substrate for pectinase production using Aspergillus niger submerged fermentation. Single-factor experiments and [...] Read more.

Silkworm excrement, a byproduct of the sericulture industry, is rich in organic compounds and presents a sustainable substrate for enzyme production. This study investigates the potential of silkworm excrement as a substrate for pectinase production using Aspergillus niger submerged fermentation. Single-factor experiments and a Box–Behnken Design (BBD) were employed to identify and optimize the key medium components and their interactions. Results indicated that the optimal concentrations for maximum pectinase activity were CaCl₂ at 0.437 g/L, orange peel powder at 4.223 g/L, (NH₄)₂SO₄ at 15.761 g/L, and bran at 33.590 g/L. The optimized conditions achieved a pectinase activity of 20.505 U/mL, validating the robustness of the RSM model. This approach not only maximizes enzyme activity but also presents a sustainable and cost-effective method for utilizing a byproduct in the sericulture industry, aligning with principles of circular economy and waste minimization. Full article

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16 pages, 3419 KiB

Open AccessArticle

Comparison of the Effect of Different Microbial Agents on the Decomposition of Rice Straw

by Yufei Li, Kaifeng Shuai, Juan Li, Xinyu Hu and Guanghui Chen

Fermentation 2025, 11(6), 332; https://doi.org/10.3390/fermentation11060332 - 9 Jun 2025

Viewed by 343

Abstract

This study compared the decomposition effects of different microbial agents added to rice straw to screen for efficient and stable microbial agents and achieve effective utilization of rice straw resources. Different microbial agents can accelerate the decomposition of rice straw. The E4/E6 value [...] Read more.

This study compared the decomposition effects of different microbial agents added to rice straw to screen for efficient and stable microbial agents and achieve effective utilization of rice straw resources. Different microbial agents can accelerate the decomposition of rice straw. The E4/E6 value of rice straw added with the Bacillus subtilis agent was significantly lower than that of rice straw added with other microbial agents on the 30th day. The lignin degradation rates for the Bacillus subtilis agent and Trichoderma viride agent treatments were higher than those of the other treatments from the 5th to 30th days. After adding the Bacillus subtilis agent for 30 days, the degradation rates of hemicellulose and cellulose in rice straw were higher than others, reaching 33.62% and 41.31%, respectively. Through principal component analysis and grey relational analysis, it was determined that the C/N ratio, organic carbon, E4/E6 value, conductivity value, and pH value are important evaluation indicators for the maturity promotion effect. Using the membership function analysis method, it was found that the Bacillus subtilis agent had the best overall performance in straw decomposition. This research provides a new viewpoint for the efficient utilization of straw resources. Full article

(This article belongs to the Section Industrial Fermentation)

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14 pages, 1234 KiB

Open AccessArticle

Metabolic Engineering of Escherichia coli for De Novo Biosynthesis of Mandelic Acid

by Chang Liu, Xuefeng Xiao, Wanbin Xing, Rina Na, Yunuo Song, Guoqiang Cao and Pengchao Wang

Fermentation 2025, 11(6), 331; https://doi.org/10.3390/fermentation11060331 - 9 Jun 2025

Viewed by 306

Abstract

Mandelic acid (MA) is a valuable α-hydroxy acid with applications in pharmaceuticals, cosmetics, and fine chemicals. While chemical synthesis is well established, concerns over toxicity and sustainability have driven interest in microbial production. Here, we engineered Escherichia coli for de novo MA biosynthesis [...] Read more.

Mandelic acid (MA) is a valuable α-hydroxy acid with applications in pharmaceuticals, cosmetics, and fine chemicals. While chemical synthesis is well established, concerns over toxicity and sustainability have driven interest in microbial production. Here, we engineered Escherichia coli for de novo MA biosynthesis by integrating enzyme screening, metabolic flux optimization, and pathway regulation. We first screened and identified an efficient hydroxymandelate synthase (HMAS) homolog from Actinosynnema mirum for MA synthesis, and subsequently enhanced the shikimate pathway along with the supply of the precursors erythrose-4-phosphate (E4P) and phosphoenolpyruvate (PEP). Additionally, CRISPR interference (CRISPRi) was employed to repress competing pathways and redirect flux toward MA production. High-cell-density cultivation (HCDC) in a 5 L bioreactor demonstrated the strain’s industrial potential, achieving an MA titer of 9.58 g/L, the highest reported for microbial production. This study provides a systematic metabolic engineering approach for efficient MA biosynthesis from glucose, offering a foundation for sustainable large-scale production, demonstrating not only genetic-level optimizations, but also effective process scaling through high-cell-density cultivation, highlighting the power of pathway engineering in microbial cell factories. Full article

(This article belongs to the Section Microbial Metabolism, Physiology & Genetics)

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14 pages, 1109 KiB

Open AccessArticle

Sustainable Production of Medium-Chain Fatty Acids from Fresh Leachates in the District of Abidjan: Study of the Feasibility of the Process and Environmental Benefits

by Akeyt Richmond Hervé Koffi, Alessio Campitelli, Daniel Stanojkovski, Edi Guy-Alain Serges Yapo, Alane Romaric N’guessan, Franck Orlando Yebouet and N’Dédé Théodore Djeni

Fermentation 2025, 11(6), 330; https://doi.org/10.3390/fermentation11060330 - 8 Jun 2025

Viewed by 382

Abstract

Leachate management remains a major environmental challenge, especially in rapidly urbanizing cities of developing countries. Traditionally considered toxic and useless, it is a sustainable organic resource with the potential for high-value biochemical production through bioprocessing. This study investigated the characteristics of fresh leachates [...] Read more.

Leachate management remains a major environmental challenge, especially in rapidly urbanizing cities of developing countries. Traditionally considered toxic and useless, it is a sustainable organic resource with the potential for high-value biochemical production through bioprocessing. This study investigated the characteristics of fresh leachates from three solid waste transfer stations (SWTS) in the Abidjan district, Côte d’Ivoire, and assessed their potential as substrates for medium-chain fatty acid (MCFA) production via microbial chain elongation. The MCFA synthesis was carried out in anaerobic bioreactors operated under methanogenesis inhibition conditions. The leachates from Bingerville, Abobo-Dokui, and Yopougon exhibited acidic and high organic content, particularly volatile fatty acids (VFAs), key precursors for MCFA synthesis. High concentrations of microbial communities associated with chain elongation were observed, including Clostridium (sulphite-reducing), Lactobacillus, Bacillus, and Pseudomonas (greater than 5 log10 CFU/mL). MCFA production ranged from 5 to 10 g/L, mainly C6, C7, and C8, with compositional variation depending on the SWTS. Notably, leachates from higher-income areas demonstrated higher MCFA productivity compared to those from lower-income areas. These findings highlight the potential of fresh SWTS leachates in the Abidjan district for sustainable MCFA production, paving the way for industrial applications. Full article

(This article belongs to the Special Issue Fermentation of Organic Waste for High-Value-Added Product Production)

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35 pages, 3228 KiB

Open AccessReview

A Review of Sensors for the Monitoring, Modeling, and Control of Commercial Wine Fermentations

by Roger Boulton, James Nelson and André Knoesen

Fermentation 2025, 11(6), 329; https://doi.org/10.3390/fermentation11060329 - 7 Jun 2025

Viewed by 438

Abstract

Large-scale commercial wine fermentation requires the monitoring and control of multiple variables to achieve optimal results. Challenges in measurement arise from turbidity, stratification in large unmixed volumes, the presence of grape skins and solids during red wine fermentations, the small changes in variables [...] Read more.

Large-scale commercial wine fermentation requires the monitoring and control of multiple variables to achieve optimal results. Challenges in measurement arise from turbidity, stratification in large unmixed volumes, the presence of grape skins and solids during red wine fermentations, the small changes in variables that necessitate precise sensors, and the unique composition of each juice, which makes every fermentation distinct. These complications contribute to nonlinear and time-variant characteristics for most control variables. This paper reviews sensors, particularly online ones, utilized in commercial winemaking. It examines the measurement of solution properties (density, weight, volume, osmotic pressure, dielectric constant, and refractive index), sugar consumption, ethanol and glycerol production, redox potential, cell mass, and cell viability during wine fermentation and their relevance as variables that could enhance the estimation of parameters in diagnostic and predictive wine fermentation models. Various methods are compared based on sensitivity, availability of sensor systems, and their appropriateness for measuring properties in large commercial wine fermentations. Additionally, factors influencing the adoption of control strategies are discussed. Finally, potential opportunities for control strategies and challenges for future sensor developments are outlined. Full article

(This article belongs to the Section Fermentation for Food and Beverages)

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20 pages, 1093 KiB

Open AccessArticle

Development of a Functional Yogurt Containing Probiotics and Phenolic Compounds of Coffee Encapsulated in Alginate Beads

by Aurora Viridiana Toalá-Gómez, Claudia Mendoza-Avendaño, Maria Celina Lujan-Hidalgo, Miguel Angel Ruiz-Cabrera, Alicia Grajales-Lagunes, Enna Berenice Estudillo-Diaz, Lucia Maria Cristina Ventura Canseco, Gabriela Palacios-Pola and Miguel Abud-Archila

Fermentation 2025, 11(6), 328; https://doi.org/10.3390/fermentation11060328 - 7 Jun 2025

Viewed by 423

Abstract

Probiotics and phenolic compounds provide benefits to humans when they are consumed in adequate amounts. However, these materials are not very stable and can easily be degraded during processing and storage; so, they must be protected. This study evaluated the encapsulation of Lactiplantibacillus [...] Read more.

Probiotics and phenolic compounds provide benefits to humans when they are consumed in adequate amounts. However, these materials are not very stable and can easily be degraded during processing and storage; so, they must be protected. This study evaluated the encapsulation of Lactiplantibacillus fabifermentans BAL-27 ITTG and phenolic compounds from coffee husks via alginate beads. The research considered variables such as alginate concentration (1.5% and 3%), crosslinking time (8 and 20 min), and the inclusion of chitosan. A 2³ factorial design was employed, and the effects were analyzed via ANOVA (p < 0.05). The encapsulation efficiency of the probiotic exceeded 80%, and its viability following gastrointestinal simulation ranged from 73.65% to 85.34%. The phenolic compounds achieved encapsulation efficiencies of up to 20%. In yogurt, the alginate beads maintained probiotic viability at approximately 9 Log₁₀ CFU/g and preserved the stability of the antioxidant compounds over 28 days. Moreover, the incorporation of beads did not adversely affect the physicochemical properties or sensory acceptance of the yogurt, supporting their potential application in functional foods. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section "Probiotic Strains and Fermentation")

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22 pages, 3416 KiB

Open AccessArticle

Genome-Driven Discovery of a Fe²⁺-Dependent Chitin Deacetylase from Bacillus pumilus B866 with Enhanced Thermostability

by Tongjian Li, Yuetong Fu, Xinrong Xiao, Yiran Wang, Yang Sun and Ling Jiang

Fermentation 2025, 11(6), 327; https://doi.org/10.3390/fermentation11060327 - 6 Jun 2025

Viewed by 450

Abstract

Chitin deacetylase (CDA) plays a pivotal role in converting chitin to chitosan, yet industrial applications remain constrained by low enzymatic activity, instability under process conditions, and insufficient understanding of metalloenzyme activation mechanisms. Addressing these challenges, we conducted a genome-driven investigation of 151 salt-tolerant [...] Read more.

Chitin deacetylase (CDA) plays a pivotal role in converting chitin to chitosan, yet industrial applications remain constrained by low enzymatic activity, instability under process conditions, and insufficient understanding of metalloenzyme activation mechanisms. Addressing these challenges, we conducted a genome-driven investigation of 151 salt-tolerant Bacillus strains to identify robust CDAs tailored for industrial demands. Genomic analysis revealed 120 strains harboring CDA genes, with Bacillus pumilus B866 exhibiting the highest native activity (105.93 U/mL). Through systematic medium optimization—identifying lactose, yeast extract, and FeSO₄ as critical components—CDA production in B866 surged to 191.32 U/mL, a 2.39-fold increase over baseline. Heterologous expression of BpCDA in E. coli yielded a recombinant enzyme (123.27 U/mL) with superior thermostability (retaining > 42.9% activity after 24 h at 55 °C) and broad pH adaptability (>81.4% activity at pH 7.0–9.0). Notably, BpCDA demonstrated unique Fe²⁺-dependent activation (186.4% activity enhancement at 1 mM), contrasting with Mg²⁺-dependent systems in prior studies. Comparative genomic and pan-genome analyses underscored evolutionary adaptations linked to saline–alkaline niches, while biosynthetic gene cluster profiling revealed strain-specific metabolic potentials independent of genome size. This study resolves critical limitations in CDA performance by integrating genome mining, targeted screening, and metalloenzyme engineering, establishing a scalable platform for sustainable chitin valorization. The optimized BpCDA, with its industrial-compatible stability and novel activation mechanism, represents a significant advancement toward efficient, eco-friendly chitosan production. Full article

(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)

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25 pages, 757 KiB

Open AccessReview

Valorization of Olive Mill Wastewater via Yarrowia lipolytica: Sustainable Production of High-Value Metabolites and Biocompounds—A Review

by Amina Laribi, Bartłomiej Zieniuk, Doria Naila Bouchedja, Kahina Hafid, Lamia Elmechta and Samira Becila

Fermentation 2025, 11(6), 326; https://doi.org/10.3390/fermentation11060326 - 6 Jun 2025

Viewed by 524

Abstract

Olive oil production generates vast quantities of by-products, with olive mill wastewater (OMW) being a particularly challenging effluent. Characterized by its dark color, high acidity, and rich composition of organic matter, phenolic compounds, and residual oils, OMW resists conventional degradation methods and poses [...] Read more.

Olive oil production generates vast quantities of by-products, with olive mill wastewater (OMW) being a particularly challenging effluent. Characterized by its dark color, high acidity, and rich composition of organic matter, phenolic compounds, and residual oils, OMW resists conventional degradation methods and poses significant environmental risks due to its phytotoxicity and microbial inhibition. Addressing this issue requires sustainable solutions that align with circular economy principles. A promising strategy involves the biotechnological valorization of OMW using the non-conventional yeast Yarrowia lipolytica, which thrives on organic-rich substrates and converts them into high-value metabolites. This review provides a comprehensive analysis of recent advances in Y. lipolytica applications for OMW valorization, emphasizing its role in developing eco-friendly industrial processes. It begins by outlining the physicochemical challenges of OMW and the metabolic versatility of Y. lipolytica, including its ability to adapt to acidic, phenolic-rich environments. Subsequent sections critically evaluate the yeast’s capacity to synthesize commercially valuable products such as lipases (used in the food and biofuel industries), citric acid (a food and pharmaceutical additive), and polyols like mannitol and erythritol (low-calorie sweeteners). Strategies to optimize microbial productivity, such as substrate pre-treatment, nutrient supplementation, and process engineering, are also discussed. By synthesizing current research, the review highlights how Y. lipolytica-driven OMW valorization can mitigate environmental harm while creating economic opportunities, bridging the gap between waste management and green chemistry. Full article

(This article belongs to the Special Issue Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 3rd Edition)

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17 pages, 1524 KiB

Open AccessArticle

Application of Transcriptome Analysis for the Exploration of the Mechanism of Methionine Promoting the Synthesis of Cephalosporin C in Acremonium chrysogenum by Employing a Chemically Defined Medium

by Yifan Li, Zhen Chen, Wei Hong, Tao Feng, Xiwei Tian and Ju Chu

Fermentation 2025, 11(6), 325; https://doi.org/10.3390/fermentation11060325 - 6 Jun 2025

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Abstract

To better analyze the biosynthesis mechanism of cephalosporin C (CPC) in Acremonium chrysogenum, single-factor omission experiments and Plackett–Burman (PB) experimental design were employed to identify key components in the chemically defined medium. Response surface methodology (RSM) was then applied to optimize the [...] Read more.

To better analyze the biosynthesis mechanism of cephalosporin C (CPC) in Acremonium chrysogenum, single-factor omission experiments and Plackett–Burman (PB) experimental design were employed to identify key components in the chemically defined medium. Response surface methodology (RSM) was then applied to optimize the concentrations of critical factors, achieving a final CPC titer of 4.70 g/L, which reached 59.54% of the titer obtained with complex medium. Methionine was identified as the most significant amino acid influencing CPC production during medium optimization. On the basis of these findings, transcriptomic analysis was conducted to elucidate the regulatory role of methionine. The results revealed that methionine enhances CPC biosynthesis by upregulating cysteine metabolism-related genes and activating primary metabolic pathways to supply precursors and energy for secondary metabolism. Additionally, methionine promoted hyphal swelling and arthrospore formation, leading to the upregulated expression of genes in CPC biosynthetic gene clusters. By integrating medium optimization with transcriptomic analysis, we provided more reliable insights into the regulatory role of methionine in A. chrysogenum growth and CPC biosynthesis using a chemically defined medium, offering valuable guidance for fermentation process optimization and subsequent metabolic engineering strategies. Full article

(This article belongs to the Special Issue Recent Advances in the Production of Pharmaceuticals through Fermentation)

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16 pages, 1841 KiB

Open AccessArticle

Characterizations and In Vitro Gut Microbiome Modulatory Effects of Gluco-Oligosaccharides Synthesized by the Acceptor Reactions of Glucansucrase 53

by Rabia Yusra Bayaman, Zuhal Alkay, Humeyra Ispirli, Seda Arioglu-Tuncil, Sevda Dere, Hasan Can, Miguel Angel Alvarez Gonzales, Osman Sagdic, Stephen R. Lindemann, Yunus Emre Tuncil and Enes Dertli

Fermentation 2025, 11(6), 324; https://doi.org/10.3390/fermentation11060324 - 6 Jun 2025

Viewed by 384

Abstract

The production of novel oligosaccharides with potential prebiotic effects is of interest to expand the current market and explore the effectiveness of new functional carbohydrate forms. The utilization of glucansucrases is a cost-effective and environmentally friendly biotechnological strategy for producing novel gluco-oligosaccharides through [...] Read more.

The production of novel oligosaccharides with potential prebiotic effects is of interest to expand the current market and explore the effectiveness of new functional carbohydrate forms. The utilization of glucansucrases is a cost-effective and environmentally friendly biotechnological strategy for producing novel gluco-oligosaccharides through acceptor reactions. In this study, an active glucansucrase (GS53) was used to produce gluco-oligosaccharides via its acceptor reactions with glucose, maltose, and maltotriose, and these oligosaccharides were tested in terms of structure and their gut microbiome modulatory effects. The formations of oligosaccharides were monitored by TLC analysis, and GS53 was active for the three acceptors but not for the other sugars tested. The structural characterization of the gluco-oligosaccharides by ¹H NMR analysis revealed the glycosylation of each acceptor with α-(1 → 3) and α-(1 → 6) linkages, whereas LC-MS analysis demonstrated the formations of DP 8, DP 7, and DP 6 oligosaccharides with acceptors maltose, maltotriose, and glucose, respectively. In vitro fecal fermentation analysis, in which microbial short-chain fatty acids (SCFAs) and microbial compositional changes were assessed using gas chromatography and 16S rRNA sequencing, respectively, demonstrated that the gluco-oligosaccharides formed SCFAs—particularly propionate and butyrate—at levels comparable to those observed with inulin, a well-established prebiotic. Additionally, the gluco-oligosaccharides were found to promote the growth of Bifidobacterium adolescentis and Blautia OTUs, which are known to have important physiological functions beneficial to human health. Overall, these results demonstrate that gluco-oligosaccharides synthesized using GS53 through acceptor reactions exhibit prebiotic potentials and could be utilized in the future as dietary supplements as well as in the development of functional foods targeting colonic health. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria: Evaluation of Benefits on Human Health and Improvement of Food Safety)

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38 pages, 1026 KiB

Open AccessReview

Smart Fermentation Technologies: Microbial Process Control in Traditional Fermented Foods

by Chong Shin Yee, Nur Asyiqin Zahia-Azizan, Muhamad Hafiz Abd Rahim, Nurul Aqilah Mohd Zaini, Raja Balqis Raja-Razali, Muhammad Ameer Ushidee-Radzi, Zul Ilham and Wan Abd Al Qadr Imad Wan-Mohtar

Fermentation 2025, 11(6), 323; https://doi.org/10.3390/fermentation11060323 - 5 Jun 2025

Viewed by 611

Abstract

Traditional fermented foods are appreciated worldwide for their cultural significance and health-promoting properties. However, traditional fermentation production suffers from many obstacles such as microbial variability, varying quality, and lack of scalability. The implementation of smart fermentation technologies, including biosensors, the Internet of Things [...] Read more.

Traditional fermented foods are appreciated worldwide for their cultural significance and health-promoting properties. However, traditional fermentation production suffers from many obstacles such as microbial variability, varying quality, and lack of scalability. The implementation of smart fermentation technologies, including biosensors, the Internet of Things (IoT), artificial intelligence (AI), and machine learning (ML), hold the key to the optimization of microbial process control, enhance product consistency, and improve production efficiency. This review summarizes modern developments in real-time microbial monitoring, IoT, AI, and ML tailored to traditional fermented foods. Despite significant technical advancements, challenges related to high costs, the absence of standardized frameworks, and access restrictions for small producers remain substantial limitations. This review proposed a future direction prioritizing modular, scalable solutions, open-source innovation, and environmental sustainability. In alignment with Sustainable Development Goal 9 (Industry, Innovation, and Infrastructure), smart fermentation technologies advance sustainable industry through innovation and serve as a critical bridge between traditional craftsmanship and Industry 4.0, fostering inclusive development while preserving microbial biodiversity and cultural heritage. Full article

(This article belongs to the Special Issue Functional Properties of Microorganisms in Fermented Foods, 2nd Edition)

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14 pages, 296 KiB

Open AccessArticle

Cottonseed Cake as a Feed Supplement: Effects on Nutrient Intake, Digestibility, Performance, Nitrogen Balance, and Ruminal Profile of Lambs Fed Sugarcane Silage-Based Diets

by Hactus Souto Cavalcanti, Juliana Silva de Oliveira, Alexandre Fernandes Perazzo, João Paulo de Farias Ramos, Alberto Jefferson da Silva Macêdo, Evandra da Silva Justino, Evandro de Sousa da Silva, Paloma Gabriela Batista Gomes, Liliane Pereira Santana, Anderson Lopes Pereira, Francisco Naysson de Sousa Santos, Daniele de Jesus Ferreira, Anderson de Moura Zanine and Edson Mauro Santos

Fermentation 2025, 11(6), 322; https://doi.org/10.3390/fermentation11060322 - 4 Jun 2025

Viewed by 404

Abstract

Using additives in sugarcane silage can reduce dry matter losses and enhance animal performance by preserving nutritional value. This study evaluated the performance, nutrient digestibility, and blood parameters of sheep fed sugarcane silage with or without cottonseed cake. Twenty-six uncastrated, mixed-breed male lambs [...] Read more.

Using additives in sugarcane silage can reduce dry matter losses and enhance animal performance by preserving nutritional value. This study evaluated the performance, nutrient digestibility, and blood parameters of sheep fed sugarcane silage with or without cottonseed cake. Twenty-six uncastrated, mixed-breed male lambs (approximately 6 months of age; 26 ± 1.3 kg) were allocated to two dietary treatments based on sugarcane silage (SS) and cottonseed cake (CSC), which differed in the form of feed presentation: (1) the control, consisting of SS and fresh CSC provided simultaneously but offered separately, without physical mixing; and (2) the Partial Mixed Ration silage (S + CSC), in which SS and CSC were pre-mixed and ensiled together at a proportion of 80:20 (natural matter basis). Dry matter intake (1620 g/kg) was similar between diets, but dry matter digestibility (64.75%) and average daily gain (202.88 g/day) were higher in the cottonseed cake group, leading to greater total weight gain (8.11 kg). These animals also had a lower acetate/propionate ratio (4.2 vs. 2.0 mmol/L) and higher blood glucose (44 vs. 35 mg/dL). Higher N intake, urinary N, and retained N were observed in the cottonseed cake diet, which also improved the diet’s mineral balance. In conclusion, adding cottonseed cake to sugarcane silage enhances fermentation, preserves nutritional value, and improves sheep performance. Full article

(This article belongs to the Special Issue Waste as Feedstock for Fermentation, 2nd Edition)

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