Fermentation

19 pages, 2041 KB

Open AccessReview

Future Horizons for Biomethane in the Context of the Energy Transition

by Dolores Hidalgo, Jesús M. Martín-Marroquín, Miguel A. Sánchez-Gatón, Enrique Pérez-Zapatero and Rudolphus Antonius Timmers

Fermentation 2025, 11(11), 653; https://doi.org/10.3390/fermentation11110653 - 20 Nov 2025

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Abstract

Biomethane is increasingly regarded as a renewable fuel with a pivotal role in sustainable energy transitions, largely produced through the anaerobic fermentation of organic feedstocks. This work offers a comprehensive overview of its development, addressing the current status of production, management, and utilization [...] Read more.

Biomethane is increasingly regarded as a renewable fuel with a pivotal role in sustainable energy transitions, largely produced through the anaerobic fermentation of organic feedstocks. This work offers a comprehensive overview of its development, addressing the current status of production, management, and utilization within a broad energy context. Technological progress in fermentation-based biogas generation, upgrading, and purification is reviewed, with particular attention to innovations that enhance process efficiency and fuel quality. The analysis also highlights the importance of policy frameworks, incentives, and infrastructure in fostering large-scale deployment, alongside international cooperation to harmonize standards. Emerging trends such as decentralized fermentation units, integration with agricultural systems, and synergies with Power-to-Gas and carbon capture strategies are emphasized as promising pathways. Results underline that innovation, investment, and process optimization are key to improving competitiveness. In conclusion, biomethane derived from fermentation processes is poised to become a cornerstone of low-carbon energy systems, provided that technological advances and supportive policies align with sustainability objectives. Full article

(This article belongs to the Special Issue Anaerobic Digestion: Waste to Energy: 2nd Edition)

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Graphical abstract

20 pages, 2313 KB

Open AccessArticle

Evolutionary Engineering and Molecular Characterization of a Sulfur Dioxide-Stress-Resistant Saccharomyces cerevisiae Strain

by Halil İbrahim Kısakesen, Zeynep Başak Canbay, Aziz Kaan Korkmaz, Alican Topaloğlu, Ömer Esen, Mevlüt Arslan, Can Holyavkin and Zeynep Petek Çakar

Fermentation 2025, 11(11), 652; https://doi.org/10.3390/fermentation11110652 - 19 Nov 2025

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Abstract

Sulfiting agents are common preservatives in the food and beverage industry to inhibit spoilage microorganisms. Sulfite produced by the dissolution of sulfur dioxide (SO₂) in water is used as a microbial inhibitor and antioxidant during winemaking. Thus, sulfite resistance is a [...] Read more.

Sulfiting agents are common preservatives in the food and beverage industry to inhibit spoilage microorganisms. Sulfite produced by the dissolution of sulfur dioxide (SO₂) in water is used as a microbial inhibitor and antioxidant during winemaking. Thus, sulfite resistance is a desirable trait for wine yeasts. However, consumer health concerns regarding SO₂ exposure require a better understanding of the molecular basis of sulfite resistance/response. In this study, we have developed a highly SO₂-stress-resistant Saccharomyces cerevisiae strain (F3) using evolutionary engineering by repeated batch selection at gradually increased potassium metabisulfite (K₂S₂O₅) levels. F3 was resistant to 1.1 mM K₂S₂O₅ stress, which was strongly inhibitory to the reference strain, and cross-resistant to oxidative, heat, and freeze–thaw stresses. F3 also had enhanced cell wall integrity and altered carbon metabolism, indicating its potential for industrial applications, including winemaking. Comparative whole genome sequencing revealed point mutations in SSU1 and FZF1 that are related to SO₂ transport; ATG14, related to autophagy; and other genes involved in vacuolar protein sorting. Comparative transcriptomic analysis showed significant upregulation of SSU1 and differential expression of genes related to transport and carbohydrate metabolism. These findings may shed light on the molecular mechanisms contributing to SO₂ resistance and industrial robustness in S. cerevisiae. Full article

(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 3rd Edition)

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19 pages, 3794 KB

Open AccessArticle

Microbial Deodorization of Gastrodia elata: Aroma Profile Improvement and Gastrodin Enrichment via ANN-GA-Guided Fermentation

by Longhuan Qian, Shiying Song, Shengling He, Luona Zhou, Yumei Tan and Yongxiang Liu

Fermentation 2025, 11(11), 651; https://doi.org/10.3390/fermentation11110651 - 19 Nov 2025

Viewed by 708

Abstract

The industrial potential of Gastrodia elata is constrained by its distinct sensory characteristics. This work employed a computational optimization approach to refine the solid-state biotransformation using Aspergillus cristatus, aiming to boost the yield of the target metabolite while addressing undesirable volatiles. Through [...] Read more.

The industrial potential of Gastrodia elata is constrained by its distinct sensory characteristics. This work employed a computational optimization approach to refine the solid-state biotransformation using Aspergillus cristatus, aiming to boost the yield of the target metabolite while addressing undesirable volatiles. Through this strategy, the content of the principal bioactive compound reached 0.3887 ± 0.05 mg/g, marking a 1.5-fold increase compared to untreated samples (p = 0.023). Volatile profiling via HS-SPME-GC/MS revealed significant reductions in three major off-flavour contributors: phenethyl alcohol (90.9% decrease, p < 0.01), 3-mercapto-2-pentanone (85.6% decrease, p < 0.01), and 4-aminopyridine (82.8% decrease, p < 0.01). Metabolic analysis elucidated two underlying mechanisms: the suppression of sulphur-containing volatiles through the downregulation of the glutathione and glucosinolate pathways, and the generation of favourable notes via the augmented synthesis of (E, Z)-2,6-nonadienal (7.4-fold) and 2,4-undecadienal (3.3-fold). This study demonstrates how machine learning-driven microbial processing can simultaneously enhance functional constituents and mitigate sensory limitations in herbal materials, offering a viable route for value-added utilization. Full article

(This article belongs to the Special Issue Advances in Functional Fermented Foods)

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18 pages, 1444 KB

Open AccessArticle

Strain-Dependent Contributions of Hanseniaspora uvarum Isolate to Apple Cider Fermentation, Chemical Composition and Aroma Complexity

by Marko Malićanin, Sandra Stamenković Stojanović, Jelena Stanojević, Stojan Mančić, Bojana Danilović and Ivana Karabegović

Fermentation 2025, 11(11), 650; https://doi.org/10.3390/fermentation11110650 - 17 Nov 2025

Viewed by 587

Abstract

Cider fermentation is strongly influenced by yeast metabolism, which determines both fermentation dynamics and aroma complexity. While Saccharomyces species remain the standard choice, increasing attention has been directed toward non-Saccharomyces yeasts such as Hanseniaspora uvarum, known for their high ester formation [...] Read more.

Cider fermentation is strongly influenced by yeast metabolism, which determines both fermentation dynamics and aroma complexity. While Saccharomyces species remain the standard choice, increasing attention has been directed toward non-Saccharomyces yeasts such as Hanseniaspora uvarum, known for their high ester formation and positive impact on sensory attributes. In this study, three native H. uvarum strains were compared with Saccharomyces bayanus in cider production. Fermentation kinetics, physicochemical parameters, and volatile and sensory profiles were assessed. All H. uvarum strains depleted sugars effectively, but strain-specific differences were evident: Kr-4 exhibited the highest ethanol (4.92% v/v) and glycerol (2.88 g/L) production, while Kd-13 showed reduced fermentative vigor. GC–MS analysis revealed higher alcohols as the dominant volatiles, with 3-methyl-1-butanol and phenylethyl alcohol most abundant. The highest concentration of phenylethyl alcohol was found in cider fermented with H. uvarum Kd-13. Ester diversity was also strain-dependent, with H. uvarum Kd-13 producing increased levels of monoethyl succinate and ethyl phenylacetate. Sensory evaluation identified ciders produced with H. uvarum Kd-13 and Kr-4 as the most complex, whereas the control sample was perceived to have a lighter body and intensive acidity. These findings highlight significant strain-level variability within H. uvarum, underlining its potential for tailoring cider aroma and sensory quality. Full article

(This article belongs to the Special Issue The Role of Non-Saccharomyces Yeasts in Crafting Alcoholic Drinks)

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16 pages, 1358 KB

Open AccessArticle

Response Surface Optimization of GABA-Enriched Fermented Pork with Co-Fermentation of Lactiplantibacillus plantarum CP1.2 and Pediococcus acidilactici CP1.4 and Packaging Effects on Product Shelf-Life

by Nguyen Ngoc Thanh, Son Thi Cam Tu, Luu Minh Chau, Bui Hoang Dang Long, Trinh Thi Nhu Hang Nguyen, Binh An Pham, Ngoc Duc Vu, Nguyen Van Thanh and Huynh Xuan Phong

Fermentation 2025, 11(11), 649; https://doi.org/10.3390/fermentation11110649 - 15 Nov 2025

Viewed by 645

Abstract

This study optimized γ-aminobutyric acid (GABA) formation in Vietnamese fermented pork (nem chua) using a central composite design to tune salt, sugar, and monosodium glutamate (MSG) under co-inoculation with Lactiplantibacillus plantarum CP1.2 and Pediococcus acidilactici CP1.4. Fermentations proceeded at room temperature; pH, titratable [...] Read more.

This study optimized γ-aminobutyric acid (GABA) formation in Vietnamese fermented pork (nem chua) using a central composite design to tune salt, sugar, and monosodium glutamate (MSG) under co-inoculation with Lactiplantibacillus plantarum CP1.2 and Pediococcus acidilactici CP1.4. Fermentations proceeded at room temperature; pH, titratable acidity, GABA (colorimetry), formal nitrogen, ammoniacal nitrogen (indophenol blue), and microbial counts were measured, with a packaging comparison between polypropylene (PP) and polyethylene (PE). Response surface analysis (R² = 0.8897) predicted an optimum at 2.0% salt, ~15.9–16.0% sugar, and ~2.9–3.0% MSG, yielding 7.44 mg/g GABA. Validation at these conditions achieved higher GABA (8.32 ± 0.24 mg/g), with pH near 4.70 and lactic acid ~18.5 g/kg. Across seven storage days, GABA peaked at day 1 (8.72–8.84 mg/g) and declined to 4.74–5.07 mg/g (day 7) as acidity increased. PE tended to preserve GABA better and reduced aerobic counts relative to PP, whereas PP limited ammoniacal nitrogen later in storage; lactic acid bacteria remained abundant (≥9.4 log CFU/g). Sensory attributes (color, aroma, taste, firmness) decreased over time but were higher in PE. The results show that balanced seasoning ratios, starter cultures, and packaging can maximize GABA enrichment while maintaining safety and quality in nem chua, providing a practical basis for scale-up of GABA-enhanced fermented meat products and tailoring shelf-life with packaging. Full article

(This article belongs to the Special Issue Recent Trends in Lactobacillus and Fermented Food, 3rd Edition)

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14 pages, 945 KB

Open AccessArticle

Phenolic Composition and Antioxidant Activity of Myrcianthes hallii Leaf Essential Oil Across Phenological Stages: Application in Nutraceutical Fermented Beverage

by Raluca A. Mihai, Erly J. Melo Heras, Nelson S. Cubi Insuaste, Lisbeth M. Topón Quinga and Rodica D. Catana

Fermentation 2025, 11(11), 648; https://doi.org/10.3390/fermentation11110648 - 14 Nov 2025

Viewed by 623

Abstract

In the context of natural beverages used for human nutrition, our study explored the potential of Myrcianthes hallii leaves (rich in bioactive compounds) as a raw material for the production of non-traditional craft beer. We hypothesized that the phenological stage affects essential oil [...] Read more.

In the context of natural beverages used for human nutrition, our study explored the potential of Myrcianthes hallii leaves (rich in bioactive compounds) as a raw material for the production of non-traditional craft beer. We hypothesized that the phenological stage affects essential oil yield and bioactivity, which in turn influences the functional properties of fortified beer. In our case, M. hallii leaves collected during the flowering stage yielded the highest amount of essential oil (0.5 v/m/%) and exhibited the greatest concentrations of total phenolics (7.7149 ± 0.02143 mg GAE/mL) and flavonoids (1.6531 ± 0.03355 mg QE/mL), correlating with increased antioxidant capacity. These findings suggest this stage as the most suitable period for harvesting M. hallii leaves for nutraceutical and pharmaceutical applications. This non-traditional beer demonstrated notable antioxidant activity, and sensory analysis revealed high acceptance regarding aroma, taste, and color, supporting its potential as a functional beverage. Full article

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

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17 pages, 2758 KB

Open AccessArticle

Effects of Weissella confusa and Bacillus subtilis Strains as Starter Cultures on the Flavor Profile of Broad Bean Paste

by Xiaoqi Gong, Junjie Yi, Zhijia Liu, Chuanqi Chu, Yujie Zhong and Tao Wang

Fermentation 2025, 11(11), 647; https://doi.org/10.3390/fermentation11110647 - 14 Nov 2025

Viewed by 557

Abstract

Broad bean paste (BBP), a traditional Chinese fermented condiment, often suffers from inconsistent quality during spontaneous fermentation. In this study, Weissella confusa KUST3424 and Bacillus subtilis KUST4527 were isolated from BBP and evaluated as starter cultures, either individually or in combination. Flavor characteristics [...] Read more.

Broad bean paste (BBP), a traditional Chinese fermented condiment, often suffers from inconsistent quality during spontaneous fermentation. In this study, Weissella confusa KUST3424 and Bacillus subtilis KUST4527 were isolated from BBP and evaluated as starter cultures, either individually or in combination. Flavor characteristics were analyzed using an electronic nose, electronic tongue, and GC–MS combined with odor activity value (OAV) calculations. Results showed that 13 key flavor compounds with OAVs greater than 1 were identified as major contributors to the overall aroma of fermented BBP juice (FBPJ). Moreover, inoculated groups exhibited distinct flavor profiles compared with natural fermentation, with the co-culture producing the most pronounced improvements. The mixed fermentation markedly enhanced desirable alcohols and esters, including significant increases in isoamyl alcohol (125.87%), 2-furanmethanol (128.91%), phenethyl alcohol (354.06%), and 4-vinylguaiacol (150.99%). In addition, compounds such as acetoin, guaiacol, ethyl hexanoate, and ethyl benzoate were newly generated in the co-culture group, while the diversity and total content of esters increased significantly from 0.52% to 9.69%. These findings demonstrate that the combined use of W. confusa KUST3424 and B. subtilis KUST4527 as starter cultures can effectively enhance the complexity and overall quality of BBP flavor. This co-culture strategy shows promise for enhancing flavor control and consistency in industrial-scale BBP production. Full article

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

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29 pages, 1669 KB

Open AccessReview

Organic Acid Production by Yeast Yarrowia lipolytica: A Review of the Last Five Years of Research

by Svetlana V. Kamzolova

Fermentation 2025, 11(11), 646; https://doi.org/10.3390/fermentation11110646 - 14 Nov 2025

Viewed by 1066

Abstract

The commercial significance of organic acids is extremely high. Due to their chemical properties, organic acids can be used both as building blocks and as individual compounds with enormous annual production. Traditionally, organic acids are obtained from fossil sources through chemical synthesis. However, [...] Read more.

The commercial significance of organic acids is extremely high. Due to their chemical properties, organic acids can be used both as building blocks and as individual compounds with enormous annual production. Traditionally, organic acids are obtained from fossil sources through chemical synthesis. However, the most promising approach is microbial synthesis, which yields a product characterized by high purity and a conformational composition similar to the natural substance. This review presents the latest publications (based on search results from 2020 to the present) on the production of organic acids by the yeast Yarrowia lipolytica. In recent years, the combined efforts of microbiologists, physiologists, biochemical engineers, and biotechnologists have led to increases in the titer, yield, and productivity of well-studied “old” acids (citric, succinic, α-ketoglutaric, etc.), as well as the discovery of “new” acids (adipic, 3-hydroxypropionic, L-malic) previously unexplored in Y. lipolytica. Furthermore, the possibility of using alternative substrates as carbon sources increases the attractiveness of producing organic acids by Y. lipolytica in accordance with the principles of a circular economy. The results described here may be useful to the scientific community and stimulate new research in the field of organic acid production in the near future. 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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21 pages, 1883 KB

Open AccessArticle

Evolution of Brettanomyces bruxellensis During Secondary Fermentation of Sparkling Wines and Counteraction Strategies

by Raffaele Guzzon, Francesca Sicher, Tiziana Nardin, Mario Malacarne, Mauro Paolini and Roberto Larcher

Fermentation 2025, 11(11), 645; https://doi.org/10.3390/fermentation11110645 - 14 Nov 2025

Viewed by 919

Abstract

The scope of this work is the study of the evolution of Brettanomyces bruxellensis, the main wine spoilage yeast, during bottle fermentation of sparkling wines. Lambrusco (Emilia, Italy) was considered as a model wine, for its high concentration of precursors for B. [...] Read more.

The scope of this work is the study of the evolution of Brettanomyces bruxellensis, the main wine spoilage yeast, during bottle fermentation of sparkling wines. Lambrusco (Emilia, Italy) was considered as a model wine, for its high concentration of precursors for B. bruxellensis activity, especially cinnamic acids. Five Lambrusco base wines furnished by a cooperative winery were inoculated with a 3-log concentration of B. bruxellensis and then underwent secondary fermentation in the bottle. Two strategies of contrast to B. bruxellensis, already successfully applied in red winemaking, were tested here for the first time in bottle fermentation: chitosan and a yeast proposed as a biocontrol agent. Bottle fermentation was monitored from a chemical and microbiological perspective. The resulting sparkling wines were analyzed by GC and HPLC–MS/MS to verify the presence of the key molecules indicating B. bruxellensis activity—biogenic amines, volatile phenols, and pyridines. Sensory analysis was also performed to establish the effects of the treatments on the overall wine profile. The results demonstrate that B. bruxellensis is capable of growing up to 5-log units, causing severe alterations of the wines, both from a chemical and sensorial point of view. The addition of chitosan at the beginning of bottle fermentation effectively mitigated the effects of B. bruxellensis, resulting in the wines being similar to the uncontaminated control. The effectiveness of the biocontrol agent under these conditions was lower and requires further investigation. Full article

(This article belongs to the Special Issue Microbial Ecosystems in Fermented Foods)

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14 pages, 1475 KB

Open AccessArticle

Hydrogen Production Through Anaerobic Co-Digestion of Different Agroindustrial Waste and Food Waste at Mesophilic Conditions

by Angeliki Maragkaki, Napoleon Christoforos Stratigakis, Tahereh Jafarpour Checkab, Lisa De Toni, Ioannis Choinopoulos, Andreas Kaliakatsos, Iosifina Gounaki, Danae Venieri, Thrassyvoulos Manios and Kelly Velonia

Fermentation 2025, 11(11), 644; https://doi.org/10.3390/fermentation11110644 - 14 Nov 2025

Viewed by 656

Abstract

Mesophilic anaerobic co-digestion of eight distinct substrate mixtures of agroindustrial and food wastes was assessed to determine the most efficient waste mixture for maximizing hydrogen production. To evaluate the impact of adding various mixtures on dark fermentation (DF), batch tests were conducted for [...] Read more.

Mesophilic anaerobic co-digestion of eight distinct substrate mixtures of agroindustrial and food wastes was assessed to determine the most efficient waste mixture for maximizing hydrogen production. To evaluate the impact of adding various mixtures on dark fermentation (DF), batch tests were conducted for 250 h at 37 °C and a pH range between 5.0 and 5.9. Ethanol, butyric, propionic, acetic, and isobutyric acids were identified as the principal fermentation end products. The hydrogen production rate reached in a decreasing order from a mixture comprising 55% Olive Mill Wastewater (OMW), 40% Cheese Whey (CW), and 5% Sewage Sludge (SS) or Liquid Pig Manure (LPM) (38 NmL/gVS) to 55% OMW, 40% CW and 5% diluted Food Waste (FW_dil) (30 NmL/gVS), 60% CW and 40% Grape Residues (GR) (27 NmL/gVS), 80% CW and 20% LPM (13 NmL/gVS), 60% OMW and 40% FW_dil. (10 NmL/gVS), 60% CW and 40% FW_dil, (8 NmL/gVS) and 70% OMW and 30% SS (5 NmL/gVS). These results indicated that H₂ was generated through mixed fermentation pathways, while the addition of OMW > 55% inhibited microbial activity and reduced hydrogen production. The highest hydrogen yield (38 NmL/gVS), accompanied by 27.6%, Volatile Solids (VS) reduction and the highest Volatile Fatty Acids (VFAs) concentration (6.1 g/L). The same substrate mixture resulted in the highest accumulation of acetic and butyric acid in the acidified effluent, indicating the dominance of hydrogen-producing metabolic routes. The data suggest that co-fermentation of the selected residues not only enhances hydrogen production but also creates more stable operational conditions -including improved pH regulation, increased carbohydrate conversion, and greater VFAs accumulation- making the process more robust and viable for practical application. Full article

(This article belongs to the Special Issue Women’s Special Issue Series: Fermentation)

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25 pages, 7736 KB

Open AccessArticle

Valorization of the Non-Medicinal Parts of Polygonatum sibiricum and Gentiana scabra Bunge from Liaoning via Solid-State Co-Fermentation: Synergistic Antibacterial Enhancement

by Chenchen Fang, Jiaqing Wang, Shuang Ma, Wenzhong Huang, Xingjiang Liu, Mengcan He, Fengchen He and Junfan Fu

Fermentation 2025, 11(11), 643; https://doi.org/10.3390/fermentation11110643 - 14 Nov 2025

Cited by 1 | Viewed by 612

Abstract

The non-medicinal parts of Polygonatum sibiricum (P. sibiricum) and Gentiana scabra (G. scabra) are abundant but underutilized in Liaoning Province, China, creating an environmental burden. Solid-state fermentation (SSF) offers a strategy to enhance their bioactivity, yet triple microbial co-fermentation remains underexplored. [...] Read more.

The non-medicinal parts of Polygonatum sibiricum (P. sibiricum) and Gentiana scabra (G. scabra) are abundant but underutilized in Liaoning Province, China, creating an environmental burden. Solid-state fermentation (SSF) offers a strategy to enhance their bioactivity, yet triple microbial co-fermentation remains underexplored. This study applied a triple microbiota—featuring Aspergillus niger (A. niger), Bacillus subtilis (B. subtilis), and Saccharomyces cerevisiae (S. cerevisiae)—to ferment the stems and leaves of both plants. Antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) was assessed via the Kirby–Bauer test, while Liquid Chromatography–Tandem Mass Spectrometry (LC–MS/MS)-based non-targeted metabolomics identified differential metabolites and enriched pathways. Co-fermentation significantly increased the inhibition zones to 17.4 ± 0.8 mm for E. coli and 17.7 ± 0.3 mm for S. aureus, a 1.8-fold improvement over the unfermented controls (p < 0.001). Among the 2976 metabolites detected, 1236 were differentially expressed, with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighting activation of aminoacyl-tRNA biosynthesis, ABC transporter, and phenylalanine–tyrosine–tryptophan pathways. Differential abundance analysis indicated that the aminoacyl-tRNA pathway (DA score > 0.9) is critical for antimicrobial peptide synthesis. Phenylalanine derivatives, including 4-hydroxybenzaldehyde, which increased over 430-fold (Log₂ FC = 8.78), contributed to membrane-disruptive antibacterial effects. Mechanistically, A. niger hydrolyzes cellulose to release precursors, B. subtilis synthesizes antimicrobial peptides, and S. cerevisiae enhances metabolite solubility and excretion, collectively boosting antibacterial activity by 80%, suggesting a potent synergistic interaction among the triple microbiota. This cascade mechanism provides a scalable approach for valorizing approximately 55 million tons of traditional Chinese medicine (TCM) waste annually. Full article

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18 pages, 2090 KB

Open AccessArticle

Efficient Production of L-Threonine by E. coli Using High-Throughput Screening and Multi-Enzyme Complex Engineering

by Chuanzhuang Guo, Nan Li, Lu Yang, Jianbin Wang, Junlin Li, Piwu Li, Junqing Wang and Ruiming Wang

Fermentation 2025, 11(11), 642; https://doi.org/10.3390/fermentation11110642 - 12 Nov 2025

Viewed by 686

Abstract

To enhance the L-threonine synthesis level in Escherichia coli, this study constructed screening markers rich in L-threonine rare codons. By replacing all the threonine codons in the protein sequences with a high proportion of threonine with L-threonine rare codons and linking them [...] Read more.

To enhance the L-threonine synthesis level in Escherichia coli, this study constructed screening markers rich in L-threonine rare codons. By replacing all the threonine codons in the protein sequences with a high proportion of threonine with L-threonine rare codons and linking them to the fluorescent proteins with the same replacement, high-throughput screening of L-threonine production mutant strains was achieved. To address the metabolic imbalance caused by overexpression of a single enzyme, an artificial multi-enzyme complex system was constructed based on the principle of cellulosome self-assembly. By co-locating ThrC-DocA and ThrB-CohA, the substrate transfer path was shortened, achieving a 31.7% increase in L-threonine production. Furthermore, combined with multi-copy chromosomal integration technology via CRISPR-associated transposase (MUCICAT) technology, the thrC-docA-thrB-cohA gene cluster was integrated into the genome of the high-yield strains obtained through screening, eliminating the plasmid-dependent metabolic burden and significantly enhancing genetic stability. The modular assembly of metabolic pathways by using cellulosome elements provides a new paradigm for the optimization of complex pathways and lays a theoretical and technical foundation for the efficient production of L-threonine. Full article

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14 pages, 3083 KB

Open AccessArticle

Lacticaseibacillus Biosurfactant Production from Cacao Pod Husk Enzymatic Hydrolysates

by María Angélica Angarita-Rangel, Laura Plazas-Tovar, Edgar Ricardo Oviedo-Ocaña and Viviana Sanchez-Torres

Fermentation 2025, 11(11), 641; https://doi.org/10.3390/fermentation11110641 - 12 Nov 2025

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Abstract

During cocoa processing, approximately ten times more cacao pod husk (CPH) waste is generated than cacao beans. Due to its high lignocellulosic content, CPH is an alternative feedstock for the production of fermentable sugars and bioproducts. In this study, CPH enzymatic hydrolysates were [...] Read more.

During cocoa processing, approximately ten times more cacao pod husk (CPH) waste is generated than cacao beans. Due to its high lignocellulosic content, CPH is an alternative feedstock for the production of fermentable sugars and bioproducts. In this study, CPH enzymatic hydrolysates were used as a carbon source to produce Lacticaseibacillus biosurfactants. CPH was subjected to alkaline pretreatment followed by enzymatic hydrolysis using the commercial enzyme cocktail Cellic Ctec2. The resulting hydrolysates were used to formulate culture media for growing Lacticaseibacillus rhamnosus and Lacticaseibacillus casei. Cell growth and the activity of extracellular and cell-bound biosurfactants were evaluated. The highest glucose concentration in the hydrolysates (11.45 g/L) was achieved using 15% (w/v) solids loading of alkaline-pretreated CPH and an enzymatic load of 20 FPU/g CPH over 3 h. The maximum emulsification index (E24) was 60%, observed with the extracellular biosurfactant from L. rhamnosus cultured in CPH-based medium without supplementation. L. casei extracellular biosurfactants were effective at inhibiting Pseudomonas aeruginosa PA14 biofilm formation (39–45%) in CPH-based media supplemented with peptone, yeast extract, and both nutrients. These findings highlight the potential of CPH enzymatic hydrolysates as a sustainable carbon source for biosurfactant production with emulsification and antibiofilm activity, contributing to the valorization of cocoa agro-industrial waste. 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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19 pages, 3219 KB

Open AccessArticle

Improving Carbon Fixation and Acetate Production from Syngas Fermentation: On-Demand Versus Continuous Feeding

by Marta Pacheco, Tiago P. Silva, Carla Silva and Patrícia Moura

Fermentation 2025, 11(11), 640; https://doi.org/10.3390/fermentation11110640 - 12 Nov 2025

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Abstract

Syngas fermentation is a promising carbon capture and utilization (CCU) technology for producing carboxylic acids while transforming low-cost waste gas into high-value products. This study evaluates the two bioreactor feeding strategies for synthesis gas (syngas) fermentation by Eubacterium callanderi (formerly Butyribacterium methylotrophicum) [...] Read more.

Syngas fermentation is a promising carbon capture and utilization (CCU) technology for producing carboxylic acids while transforming low-cost waste gas into high-value products. This study evaluates the two bioreactor feeding strategies for synthesis gas (syngas) fermentation by Eubacterium callanderi (formerly Butyribacterium methylotrophicum) strain Marburg—on-demand feeding (ODF) and continuous feeding (CF)—with a synthetic syngas mixture of 23 vol% CO₂, 29 vol% CO, 32 vol% H₂, and 16 vol% CH₄, mimicking the syngas from lignocellulosic gasification. The ODF assay achieved a maximum syngas consumption rate of 112 mL/h, yielding 24.1 g/L acids, namely 22.9 g/L acetate and 1.3 g/L butyrate. CF of syngas at 223 mL/h required more gas (62.9 L) to produce 22.7 g/L total acids, from which 19.0 g/L acetate and 3.7 g/L butyrate were achieved. The CF-specific production rate (g_product/g_{dry_cell_weight}/hour) reached 0.5 g/g_DCW/h (acetate) and 0.17 g/g_DCW/h (butyrate), outperforming ODF with 0.3 and 0.02 g/g_DCW/h, respectively. ODF minimized gas wastage and enabled CH₄ accumulation inside the bioreactor up to approximately 78 vol%, while CF led to CO₂ accumulation, indicating a need for more efficient CO₂ utilization strategies, such as sequential fermentations. This work highlights the critical impact of the two feeding options studied with regard to scaling up the carbon-efficient production of carboxylic acids, and indicates that both strategies can have potential applications. ODF is ideal for increasing carbon fixation and achieving, simultaneously, gas cleaning, while CF fermentations are better suited to maximizing the acid production rate. Full article

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

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18 pages, 1168 KB

Open AccessArticle

Combined Effects of Cold Pre-Fermentative Maceration and the Use of Non-Saccharomyces Yeasts (L. thermotolerans and T. delbrueckii) on the Composition of Cayetana Blanca Wines Produced in a Semi-Arid Climate

by Fernando Sánchez-Suárez and Rafael A. Peinado

Fermentation 2025, 11(11), 639; https://doi.org/10.3390/fermentation11110639 - 11 Nov 2025

Viewed by 590

Abstract

Climate change poses a major challenge for wine production in semi-arid regions, where grape ripening frequently leads to excessive sugar accumulation and reduced acidity. This study evaluated the combined effect of cold pre-fermentative maceration (PM) and the use of non-Saccharomyces yeasts ( [...] Read more.

Climate change poses a major challenge for wine production in semi-arid regions, where grape ripening frequently leads to excessive sugar accumulation and reduced acidity. This study evaluated the combined effect of cold pre-fermentative maceration (PM) and the use of non-Saccharomyces yeasts (Lachancea thermotolerans and Torulaspora delbrueckii) on the composition and sensory properties of Cayetana Blanca wines. Pre-fermentative maceration increased titratable acidity by 0.5 g/L and yeast-assimilable nitrogen by 28 mg/L, creating more favorable conditions for the metabolic activity of non-Saccharomyces species. Wines fermented with L. thermotolerans—especially in sequential inoculation with S. cerevisiae after PM—showed the highest acidity and lactic acid content (2 g/L), together with 1% v/v lower ethanol and 1 g/L higher glycerol than the control. These wines were perceived as fresher and better balanced, despite a moderate decrease in fruity esters such as ethyl hexanoate, ethyl octanoate, and isoamyl acetate. Cluster analysis confirmed that non-Saccharomyces fermentations developed distinct compositional profiles only when combined with PM. Overall, the PM + L. thermotolerans + S. cerevisiae treatment achieved the most favorable balance between acidity, ethanol, and sensory freshness. This approach provides a sustainable and readily applicable method to enhance acidity and freshness in white wines from warm-climate regions. Full article

(This article belongs to the Special Issue The Role of Non-Saccharomyces Yeasts in Crafting Alcoholic Drinks)

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18 pages, 2515 KB

Open AccessArticle

The Use of Electric-Field Can Effectively Reduce Greenhouse Gas Emissions and Promote Carbon Conversion in Compost

by Xiaoyun Lian, Lingling Chen, Hongmei Zhang, Deguo Kong, Ling Zhou and Weiguo Xu

Fermentation 2025, 11(11), 638; https://doi.org/10.3390/fermentation11110638 - 9 Nov 2025

Viewed by 604

Abstract

This study focused on the effect of electric field intensity on carbon transformation in aerobic composting of biochar–pig manure. Four treatment groups were set up with voltages of 0 V (CK group), 2 V (L group), 4 V (M group), and 5 V [...] Read more.

This study focused on the effect of electric field intensity on carbon transformation in aerobic composting of biochar–pig manure. Four treatment groups were set up with voltages of 0 V (CK group), 2 V (L group), 4 V (M group), and 5 V (H group). The physicochemical properties and carbon forms of the compost were characterized, and how they influence composting was investigated by observing the changes in the functional groups of the compost and the interactions between microorganisms and environmental factors. The results showed that the electric field treatment groups entered the thermophilic phase 2–3 d earlier than the CK group, and the duration of this phase was extended by 3–5 d. The seed germination indices were 95.2%, 106%, 110%, and 121% for the CK, L, M, and H treatment groups, respectively. The DOC content decreased by 11.7%, 11.4%, 16%, and 16.5%. The degradation rates of hemicellulose were 38.6%, 41.1%, 42.7%, and 42.8%, respectively. Those of cellulose were 46.8%, 47.7%, 51.8%, and 54.5%, respectively. Those of lignin were 37.2%, 40.8%, 47.9%, and 53.3%, respectively. Compared to the CK group, the cumulative emissions of CO₂ and CH₄ in the L, M, and H groups were reduced by 13.8–25% and 47.86–75.76%, respectively, resulting in lower carbon losses. Fourier transform infrared spectroscopy indicated that applying an external electric field induces changes in the functional groups of humic acid, the formation of aromatic functional groups, and the optimization of the maturation process. Compared to the CK group, applying an electric field (L/M/H groups) optimized the microbial communities (especially the Bacteroidota, Chloroflexi, and Acidobacteriota abundances), enriched Proteobacteria and Myxococcota, and regulated the moisture content and C/N ratio. These changes in the electric field treatment groups significantly improved the degradation efficiency of cellulose, lignin, and hemicellulose and reduced greenhouse gas emissions. Full article

(This article belongs to the Section Industrial Fermentation)

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15 pages, 591 KB

Open AccessArticle

Development of Smoothies Fermented with Kombucha Microorganisms: Sensory Characteristics, Functional Properties, and Microbiological Aspects

by Lorene Simioni Yassin, Camila Gomes Sheleidres, Thaís Estéfane Fischer, Acácio Antonio Ferreira Zielinski, Paulo Ricardo Los, Luiz Gustavo Lacerda, Aline Alberti and Alessandro Nogueira

Fermentation 2025, 11(11), 637; https://doi.org/10.3390/fermentation11110637 - 8 Nov 2025

Viewed by 806

Abstract

Smoothies and kombucha are beverages appreciated by contemporary consumers due to their appealing flavor, convenience, and perceived health benefits. This study aimed to develop fruit- and white tea-based smoothies with high sensory and functional quality, and to evaluate the effects of fermentation with [...] Read more.

Smoothies and kombucha are beverages appreciated by contemporary consumers due to their appealing flavor, convenience, and perceived health benefits. This study aimed to develop fruit- and white tea-based smoothies with high sensory and functional quality, and to evaluate the effects of fermentation with kombucha microorganisms. The smoothie base (70%) was composed of 60% strawberry pulp and 40% cryoconcentrated apple juice. Ten formulations were designed using a centroid simplex approach and subjected to sensory analysis. The two most accepted by consumers (E5: 15% blackberry pulp and 15% white tea; E10: 5% blackberry pulp and 5% acerola pulp, and 20% white tea) were fermented for 10, 15, and 20 h. The formulations were evaluated through sensory analysis. Fermentation led to significant (p < 0.05) reductions in glucose, fructose, and caffeine contents, while significantly (p < 0.05) increasing acidity, total phenolic content, ascorbic acid levels, and color intensity. Moreover, the fermented smoothie exhibited higher α-glucosidase inhibitory potential. One fermented smoothie (E5 fermented for 15 h) showed desirable sensory and functional properties. Therefore, this study demonstrates the successful development of smoothies, fermented or non-fermented with kombucha microorganisms, characterized by strong functional attributes and high sensory acceptance. Full article

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

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17 pages, 4907 KB

Open AccessArticle

Contribution of Debaryomyces hansenii to Microbial, Lipidome, and Flavor Properties of Sichuan Bacon

by Song Wang, Kaidi Hu, Wanshu Pan, Ling You, Yong Yang and Shuliang Liu

Fermentation 2025, 11(11), 636; https://doi.org/10.3390/fermentation11110636 - 7 Nov 2025

Viewed by 582

Abstract

Debaryomyces hansenii has the potential to enhance the flavor profile of traditional fermented meat products. This study investigates the impact of the D. hansenii LY090 strain on the microbial community, lipidome, flavor profiles, and sensory properties of Sichuan bacon. Inoculation with LY090 significantly [...] Read more.

Debaryomyces hansenii has the potential to enhance the flavor profile of traditional fermented meat products. This study investigates the impact of the D. hansenii LY090 strain on the microbial community, lipidome, flavor profiles, and sensory properties of Sichuan bacon. Inoculation with LY090 significantly inhibited the relative abundance of other yeasts, except for Debaryomyces, and altered bacterial community composition. The presence of LY090 led to a notable reduction (p < 0.05) in the levels of ceramide and phosphatidylcholine, resulting in an excessive inhibition of lipid degradation. This further affected the development of flavor and color in Sichuan bacon. However, the concentrations of aldehydes (249.80 μg/kg), ethyl 3-methylbutyrate (81.01 μg/kg), and acetoin (223.91 μg/kg) were all found to be abundant, and the bacon achieved the highest overall acceptance scores when inoculated with both LY090 and commercial starter culture FAST301. Correlation analysis indicated that the differential metabolites exhibited a stronger association with the yeast community, which plays a vital role in the flavor development of Sichuan bacon. These detailed investigations provide meaningful implications for D. hansenii LY090 implementation strategies in the Sichuan bacon industry. Full article

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

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29 pages, 15539 KB

Open AccessArticle

Multifunctional Performance of Bacterial Cellulose Membranes in Saline and Oily Emulsion Filtration

by Alexandre D’Lamare Maia de Medeiros, Cláudio José Galdino da Silva Junior, Yasmim de Farias Cavalcanti, Matheus Henrique Castanha Cavalcanti, Maryana Rogéria dos Santos, Ana Helena Mendonça Resende, Ivison Amaro da Silva, Julia Didier Pedrosa de Amorim, Andréa Fernanda de Santana Costa and Leonie Asfora Sarubbo

Fermentation 2025, 11(11), 635; https://doi.org/10.3390/fermentation11110635 - 7 Nov 2025

Viewed by 746

Abstract

The separation of oil-in-water emulsions from industrial wastewater remains a significant challenge, particularly under saline conditions. This study evaluated bacterial cellulose (BC) membranes from Komagataeibacter hansenii for filtering synthetic effluents with high oil content (ES1) and saline oil-in-water emulsions (ES2). FTIR confirmed the [...] Read more.

The separation of oil-in-water emulsions from industrial wastewater remains a significant challenge, particularly under saline conditions. This study evaluated bacterial cellulose (BC) membranes from Komagataeibacter hansenii for filtering synthetic effluents with high oil content (ES1) and saline oil-in-water emulsions (ES2). FTIR confirmed the incorporation of lipophilic compounds into the BC matrix. Crystallinity decreased from 78.8% to 40% following ES1 filtration, while a new peak at 2θ ≈ 31.8° appeared in ES2, indicating salt deposition. TGA revealed increased mass loss in the oil-saturated membrane (BCO), whereas the saline-exposed membrane (BCOS) exhibited higher thermal stability. SEM showed fiber compaction and localized deposition of oil and salt, corroborated by EDS, which identified Na, Cl, Ca, and elevated oxygen levels. Mechanical testing indicated that oil acted as a plasticizer, increasing the elongation at break of BCO, while salt crystallization enhanced BCOS stiffness. The membranes removed up to 98% of organic load (BOD and COD), 69% of oils and greases, and reduced turbidity and apparent color by 92%. Partial salt retention (~23%) and a significant decrease in dissolved oxygen were also observed. These results demonstrate the potential of BC membranes as an effective and sustainable solution for the treatment of complex oily and saline wastewater. Full article

(This article belongs to the Section Industrial Fermentation)

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14 pages, 2854 KB

Open AccessArticle

Enhanced Bioprocess Performance and β-Glucosidase Productivity of a Novel Komagataella phaffii Strain Generated by Intraspecific Crossing

by Edgar Velastegui, Johan Quezada, Belén Ponce, Cristóbal Adrián, Benjamin Offei, Kenneth H. Wolfe, Julio Berríos and Stephanie Braun-Galleani

Fermentation 2025, 11(11), 634; https://doi.org/10.3390/fermentation11110634 - 7 Nov 2025

Viewed by 709

Abstract

This research characterized a novel Komagataella phaffii strain generated through intraspecific crossing between a wild isolate and a laboratory strain. This segregant, called S467, expressed 2.2-fold more secreted recombinant β-glucosidase than its parental strains in microtiter scale, which suggested that S467 could be [...] Read more.

This research characterized a novel Komagataella phaffii strain generated through intraspecific crossing between a wild isolate and a laboratory strain. This segregant, called S467, expressed 2.2-fold more secreted recombinant β-glucosidase than its parental strains in microtiter scale, which suggested that S467 could be an attractive host for bioprocess optimization. S467 was grown alongside the laboratory strain CBS7435 expressing β-glucosidase (CBS_BGL9), as a control, in a 1.5 L bioreactor to determine kinetics parameters, and similar cell growth rate (0.12 h⁻¹) but higher recombinant protein activity, measured as enzymatic activity, was observed in S467. The effect of specific cell growth rate was studied using continuous cultures (chemostat) at different dilution rates, identifying conditions that provided up to a twofold increase in enzymatic activity in S467. RT-qPCR was conducted on key genes associated with the genetic background of S467, in order to clarify differences at the transcriptomic level that render S467 as a potential superior host for recombinant protein production. Overall, this study provides quantitative evidence of the positive effect of the natural isolate IRA1 allele for the generation of recombinant β-glucosidase and highlights the usability of natural genetic diversity in K. phaffii. Full article

(This article belongs to the Special Issue Yeast Fermentation, 2nd Edition)

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14 pages, 2597 KB

Open AccessArticle

Lactobacillus gasseri Decreases p-Cresol Levels in Serum and Cecum and Improves Skin Characteristics in Mice Fed with Tyrosine-Rich Diets

by Johan Hariwitonang, Yutaka Makizaki, Nao Fujiyama, Yuto Hirano, Seigo Iwama, Hitomi Iikawa, Yoshiki Tanaka, Hiroshi Ohno, Yoshihiro Tokudome, Munehiro Tanaka and Hiroshi Kitagaki

Fermentation 2025, 11(11), 633; https://doi.org/10.3390/fermentation11110633 - 6 Nov 2025

Viewed by 697

Abstract

Investigation of the influence of alive or dead dietary lactic acid bacteria, specifically Lactobacillus gasseri, on mice fed a tyrosine-rich diet was conducted in this study. Mice fed a tyrosine-rich diet exhibited increased p-cresol levels in the serum and cecum and [...] Read more.

Investigation of the influence of alive or dead dietary lactic acid bacteria, specifically Lactobacillus gasseri, on mice fed a tyrosine-rich diet was conducted in this study. Mice fed a tyrosine-rich diet exhibited increased p-cresol levels in the serum and cecum and deteriorated skin characteristics in terms of skin moisture and transepidermal water loss. These conditions were partially ameliorated by the intake of lactic acid bacteria. To gain insight into the mechanism, the intestinal microbiota of mice fed lactic acid bacteria was examined. The results revealed an increase in bacteria including genus Faecalibacterium and Lactobacillus in fecal samples from mice fed lactic acid bacteria. Muribaculaceae was most associated with the added group of alive or dead L. gasseri. These findings indicate that lactic acid bacteria inhibit the conversion of tyrosine to p-cresol in the colon, thereby ameliorating skin disorders. 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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25 pages, 1607 KB

Open AccessReview

Recent Developments in the Valorization of Sugarcane Bagasse Biomass via Integrated Pretreatment and Fermentation Strategies

by Mbuyu Germain Ntunka, Thobeka Pearl Makhathini, Siphesihle Mangena Khumalo, Joseph Kapuku Bwapwa and Marc Mulamba Tshibangu

Fermentation 2025, 11(11), 632; https://doi.org/10.3390/fermentation11110632 - 6 Nov 2025

Viewed by 1430

Abstract

The growing global demand for clean energy and sustainability has increased interest in lignocellulosic biomass as a viable alternative to conventional fossil fuels. Among the various biomass resources, sugarcane bagasse, an abundant agro-industrial by-product, has emerged as a promising feedstock to produce renewable [...] Read more.

The growing global demand for clean energy and sustainability has increased interest in lignocellulosic biomass as a viable alternative to conventional fossil fuels. Among the various biomass resources, sugarcane bagasse, an abundant agro-industrial by-product, has emerged as a promising feedstock to produce renewable fuels and value-added chemicals. Its high carbohydrate content offers significant potential for bioconversion. However, its complex and recalcitrant lignocellulosic matrix presents significant challenges that necessitate advanced pretreatment techniques to improve enzymatic digestibility and fermentation efficiency. This review consolidates recent developments in the valorization of sugarcane bagasse focusing on innovative pretreatment and fermentation strategies for sustainable bioethanol production. It emphasizes the synergistic benefits of integrating various pretreatment and fermentation methods to improve bioethanol yields, reduce processing costs and enhance overall process sustainability. This review further explores recent technological advancements, the impact of fermentation inhibitor, and emerging strategies to overcome these challenges through microbial strains and innovative fermentation methods. Additionally, it highlights the multi-faceted advantages of bagasse valorization, including waste minimization, renewable energy production and the promotion of sustainable agricultural practices. By evaluating the current state of research and outlining future perspectives, this paper serves as a comprehensive guide to advancing the valorization of sugarcane bagasse in the transition towards a low-carbon economy. The novelty of this review lies in its holistic integration of technological, economic, and policy perspectives, uniquely addressing the scalability of integrated pretreatment and fermentation processes for sugarcane bagasse, and outlining practical pathways for their translation from laboratory to sustainable industrial biorefineries within the circular bioeconomy framework. Full article

(This article belongs to the Special Issue Lignocellulosic Biomass in Biorefinery Processes)

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17 pages, 9188 KB

Open AccessArticle

Genomic and Transcriptomic Characterization of a High-Yield Docosahexaenoic Acid (DHA) Mutant Schizochytrium sp. HS01

by Huichang Zhong, Weifeng Liu and Yong Tao

Fermentation 2025, 11(11), 631; https://doi.org/10.3390/fermentation11110631 - 5 Nov 2025

Viewed by 723

Abstract

Docosahexaenoic acid (DHA), an omega-3 polyunsaturated fatty acid essential for human health, is primarily produced at scale using Schizochytrium sp. Mutagenesis-based strain improvement has increased DHA yields, but the genetic and metabolic mechanisms underlying high productivity remain poorly understood. Here, we conducted the [...] Read more.

Docosahexaenoic acid (DHA), an omega-3 polyunsaturated fatty acid essential for human health, is primarily produced at scale using Schizochytrium sp. Mutagenesis-based strain improvement has increased DHA yields, but the genetic and metabolic mechanisms underlying high productivity remain poorly understood. Here, we conducted the comparative whole-genome sequencing and transcriptomic profiling of a high-DHA-yielding mutant strain (HS01) and its parental strain (GS00). The GS00 genome assembly spans 62.4 Mb and encodes 14,886 predicted genes. Functional annotation highlighted pathways involved in central metabolism, saturated fatty acid (SFA) synthesis, and polyunsaturated fatty acid (PUFA)/DHA biosynthesis. Comparative genomics identified 40 insertions/deletions and 396 single-nucleotide polymorphisms between HS01 and GS00, including mutations in the coding and regulatory regions of key metabolic genes. Transcriptomic analysis revealed extensive metabolic reprogramming in HS01, including the upregulation of glycolysis and tricarboxylic acid (TCA) cycle genes, along with a distinct fatty acid profile and the altered expression of fatty acid metabolism genes compared with GS00. Collectively, the integrated genomic and transcriptomic analyses not only pinpointed specific mutations potentially associated with the HS01 high-DHA phenotype but also revealed substantial transcriptional and metabolic remodeling, providing valuable insights into the mechanisms that drive enhanced DHA biosynthesis. 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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13 pages, 1162 KB

Open AccessArticle

Comparative Evaluation of Ionophores on the In Vitro Fermentation Dynamics of Wheat Silage Using a Gas Production System

by Ana Luiza de Freitas dos Santos, Mateus Henrique Signor, Gabrielly Chechi Giraldi, Isadora Zago, Rafael Vinicius Pansera Lago, Idacir Antonio Santin Junior, Viviane Dalla Rosa, Amanda Scussiato, Marcos Inácio Marcondes, Jacir Dal Magro, Pedro Del Bianco Benedeti and Ana Luiza Bachmann Schogor

Fermentation 2025, 11(11), 630; https://doi.org/10.3390/fermentation11110630 - 5 Nov 2025

Viewed by 658

Abstract

Wheat silage is an underexplored forage in ruminant nutrition that offers potential benefits due to its high crude protein content and capacity to mitigate methane emissions. However, little is known about its interaction with feed additives. This study evaluated the effects of monensin [...] Read more.

Wheat silage is an underexplored forage in ruminant nutrition that offers potential benefits due to its high crude protein content and capacity to mitigate methane emissions. However, little is known about its interaction with feed additives. This study evaluated the effects of monensin (25 ppm) and narasin (13 ppm) on the in vitro ruminal fermentation of wheat silage using a randomized complete block design with three treatments and seven replicates per incubation. Gas production was recorded over 48 h, and fermentation parameters, including pH, in vitro organic matter digestibility (IVOMD), metabolizable energy (ME), ammonia nitrogen (NH₃-N), and volatile fatty acid (VFA) profiles, were determined. Both ionophores maintained a higher ruminal pH compared to the control (p < 0.01) and reduced total gas production, ME, and IVOMD (p < 0.01), without significant differences between monensin and narasin. No effects were observed on total VFA production, acetate-to-propionate ratio, or ammonia concentration, although isobutyrate was reduced (p < 0.01). Fermentation kinetics revealed decreased gas production and digestion rates in the slowly degradable fraction, particularly with monensin. In conclusion, ionophores modulated fermentation but did not improve digestibility or energy availability, suggesting limited nutritional benefits when wheat silage is used as the sole forage source. Full article

(This article belongs to the Special Issue Research Progress of Rumen Fermentation)

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13 pages, 1844 KB

Open AccessArticle

Optimization of Fermentation Parameters and Medium Composition for Producing Prodiginines from Marine Bacterium Spartinivicinus ruber MCCC 1K03745^T

by Xiaosi Lin, Peiyun Wu, Yajue Huang and Congjie Dai

Fermentation 2025, 11(11), 629; https://doi.org/10.3390/fermentation11110629 - 4 Nov 2025

Viewed by 661

Abstract

Cycloheptylprodigiosin exhibits potent anticancer activity through a unique mechanism involving the induction of severe Golgi stress, a previously unrecognized cell death pathway. To increase the prodiginine production from the marine bacterium Spartinivicinus ruber MCCC 1K03745^T, we investigated key fermentation parameters, including [...] Read more.

Cycloheptylprodigiosin exhibits potent anticancer activity through a unique mechanism involving the induction of severe Golgi stress, a previously unrecognized cell death pathway. To increase the prodiginine production from the marine bacterium Spartinivicinus ruber MCCC 1K03745^T, we investigated key fermentation parameters, including incubation time and initial medium pH. The culture medium composition was then sequentially optimized by single-factor experiments, a full factorial design, and an orthogonal design. Our results showed that the optimal incubation time was 30 h post inoculation, while initial pH had no effect on prodiginine production within the range of pH 6.0 to 8.0. By orthogonal design, the optimal medium was determined as follows: peptone 11 g/L, yeast extract 1 g/L, soybean oil 5 mL/L and MgCl₂·6H₂O 3 g/L in seawater. Verification experiments showed that prodiginine concentration under the optimized conditions reached 14.64 mg/L, representing 2.62 times the concentration obtained in basal Marine Broth 2216. These findings provide a basis for the cost-effective production of prodiginines from S. ruber MCCC 1K03745^T for potential pharmaceutical applications. Full article

(This article belongs to the Section Fermentation Process Design)

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15 pages, 3784 KB

Open AccessArticle

Saturnispora diversa: A New Acid-Reducing Yeast in Co-Fermentation with Saccharomyces cerevisiae to Optimize Flavor Balance in Blueberry Wine

by Qian Wang, Huiyan Jiang, Liping Weng, Jing Qiu, Shuai Yue, Junbo Liu and Ligen Zou

Fermentation 2025, 11(11), 628; https://doi.org/10.3390/fermentation11110628 - 3 Nov 2025

Viewed by 774

Abstract

The high acidity of blueberry wine remains a critical factor limiting consumer acceptance. In this study, an acid-reducing yeast strain isolated from naturally fermented blueberry juice was co-fermented with Saccharomyces cerevisiae to evaluate its effects on physicochemical properties and the profile of volatile [...] Read more.

The high acidity of blueberry wine remains a critical factor limiting consumer acceptance. In this study, an acid-reducing yeast strain isolated from naturally fermented blueberry juice was co-fermented with Saccharomyces cerevisiae to evaluate its effects on physicochemical properties and the profile of volatile compounds, characterized using gas chromatography–mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). Results demonstrated that a yeast strain isolated from 484 candidate strains achieved a citric acid reduction rate of 92.04 ± 2.76% and was identified as Saturnispora diversa. This strain has been deposited in the China General Microbiological Culture Collection Center (CGMCC) with the accession number CGMCC No. 28902. Co-fermentation with Saccharomyces cerevisiae significantly reduced the acidity of blueberry wine, while exerting no significant impact on other physicochemical properties. The combined GC-MS and GC-IMS approach provided comprehensive volatile profiling, revealing that Saccharomyces cerevisiae fermentation preferentially enhanced ester biosynthesis, while the acid-reducing co-fermentation system optimized flavor balance. Collectively, the synergistic use of acid-reducing and Saccharomyces cerevisiae offers a promising production strategy for premium blueberry wine, effectively mitigating excessive acidity to improve palatability while preserving aroma integrity. Full article

(This article belongs to the Special Issue Science and Technology of Winemaking)

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24 pages, 1679 KB

Open AccessArticle

Integrated Biorefinery of Brewer’s Spent Grain for Second-Generation Ethanol, Mycoprotein, and Bioactive Vinasse Production

by Sara Saldarriaga-Hernandez, José García-Béjar, Anahid Esparza-Vasquez, Rosa Leonor González-Díaz, Eduardo Joel López-Torres, Julio César López-Velázquez, Lorena Amaya-Delgado, Tomás García-Cayuela, Hemant Choudhary, Blake A. Simmons and Danay Carrillo-Nieves

Fermentation 2025, 11(11), 627; https://doi.org/10.3390/fermentation11110627 - 3 Nov 2025

Viewed by 1178

Abstract

Brewer’s spent grain (BSG), the main lignocellulosic by-product of the beer industry, represents an abundant yet underutilized resource with high potential for valorization. This study presents an integrated biorefinery approach to convert BSG into second-generation (2G) ethanol, bioactive vinasse for plant growth promotion, [...] Read more.

Brewer’s spent grain (BSG), the main lignocellulosic by-product of the beer industry, represents an abundant yet underutilized resource with high potential for valorization. This study presents an integrated biorefinery approach to convert BSG into second-generation (2G) ethanol, bioactive vinasse for plant growth promotion, and fungal biomass as a potential mycoprotein source. The biomass was first subjected to biological delignification using the white-rot fungus Ganoderma lucidum, after which two valorization routes were explored: (i) evaluation of the fungal biomass as a mycoprotein candidate and (ii) alcoholic fermentation for ethanol production. For the latter, three pretreatment strategies were assessed (diluted sulfuric acid and two deep eutectic solvents (DESs) based on choline chloride combined with either glycerol or lactic acid) followed by a one-pot enzymatic saccharification and fermentation using Kluyveromyces marxianus SLP1. The highest ethanol yield on substrate (Y_P/S) was achieved with [Ch]Cl:lactic acid pretreatment (0.46 g/g, 89.32% of theoretical). Vinasse, recovered after distillation, was characterized for organic acid content and tested on Solanum lycopersicum seed germination, showing promising biostimulant activity. Overall, this work highlights the potential of BSG as a sustainable feedstock within circular economy models, enabling the production of multiple bio-based products from a single residue. Full article

(This article belongs to the Special Issue Biotechnological Strategies for Agro-Industrial Food Waste Management)

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12 pages, 349 KB

Open AccessArticle

Valorization of Artichoke Wastes via Ozonation Pretreatment and Enzyme Fibrolytic Supplementation: Effect on Nutritional Composition, Ruminal Fermentation and Degradability

by Khalil Abid

Fermentation 2025, 11(11), 626; https://doi.org/10.3390/fermentation11110626 - 2 Nov 2025

Viewed by 539

Abstract

The increasing demand for sustainable ruminant feeds has driven interest in the valorization of agro-industrial wastes. Artichoke wastes are attractive in the Mediterranean region due to their availability and richness in protein (CP) and fiber (NDF), but their high lignin (ADL) and tannin [...] Read more.

The increasing demand for sustainable ruminant feeds has driven interest in the valorization of agro-industrial wastes. Artichoke wastes are attractive in the Mediterranean region due to their availability and richness in protein (CP) and fiber (NDF), but their high lignin (ADL) and tannin contents limit their nutritional value. This experiment was conducted using a completely randomized design with four treatments—control, ozone (O₃), exogenous fibrolytic enzyme (EFE), and O₃ + EFE—tested over six runs, each including three replicates per treatment. The study evaluated the effects of ozone (O₃) and exogenous fibrolytic enzyme (EFE) treatments, applied alone or in combination, on artichoke waste chemical composition, ruminal fermentation, microbial populations, enzyme activity, and degradability. Ozone pretreatment significantly reduced fiber fractions (NDF −10%, ADF −7%), ADL (−16%), and condensed tannins (−64%), while increasing CP (+13%) and non-fibrous carbohydrates (NFC +38%). These modifications enhanced ruminal bacterial populations (+29%) and fibrolytic enzyme activities (xylanase +21%, endoglucanase +19%, exoglucanase +10%), resulting in higher dry matter degradability (DMD +11%), fiber degradability (NDFD +14%), total volatile fatty acids (VFAs +13%), and a lower acetate-to-propionate ratio. EFEs alone showed negligible effects; however, when applied after ozone, further improvements were observed in NFCs (+21%), bacterial populations (+21%), enzyme activities (xylanase +11%, endoglucanase +10%), DMD (+8%), NDFD (+7%), and VFAs (+6%) compared to ozone alone. These findings demonstrate that O₃ pretreatment facilitates the enzymatic hydrolysis of lignocellulosic structures and enhances the effectiveness of EFEs, offering a sustainable and eco-efficient strategy for the bioconversion of artichoke wastes into high-value feed for ruminants, contributing to resource efficiency and circular bioeconomy development in livestock systems. 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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17 pages, 802 KB

Open AccessArticle

Bio-Enhancement of Phenolic Content and Antioxidant Capacity of Coffee (Coffea arabica L.) Cherry Husks by Solid-State Fermentation with Trichoderma Fungi

by Punyawatt Pintathong, Narit Thaochan, Benjarat Suwannawong, Sarita Sangthong and Phanuphong Chaiwut

Fermentation 2025, 11(11), 625; https://doi.org/10.3390/fermentation11110625 - 1 Nov 2025

Viewed by 1007

Abstract

Fermentation possesses intriguing and promising potential as a bioprocess for enhancing and/or transforming bioactive compounds derived from agricultural processing by-products. This study aimed to enhance the phenolic compounds and antioxidant properties of coffee cherry husks through the sustainable methodology of solid-state fermentation (SSF) [...] Read more.

Fermentation possesses intriguing and promising potential as a bioprocess for enhancing and/or transforming bioactive compounds derived from agricultural processing by-products. This study aimed to enhance the phenolic compounds and antioxidant properties of coffee cherry husks through the sustainable methodology of solid-state fermentation (SSF) using various Trichoderma fungi, specifically Trichoderma asperellum CB-Pin-01 and two Trichoderma isolates (NTY211 and PSUT001). The coffee cherry husks underwent fermentation at a controlled temperature of 28 ± 1 °C over a duration of 7 days. Both fermented and unfermented extracts, prepared using different solvents (water, ethanol, and acetone), were systematically evaluated concerning total phenolic content (TPC), total flavonoid content (TFC), and antioxidant capacities measured via DPPH and ABTS radical scavenging assays, as well as ferric reducing antioxidant power (FRAP). The findings indicated that SSF involving Trichoderma fungi significantly augmented the phenolic content and antioxidant activities in comparison to the unfermented samples (p < 0.05). Notably, the acetonic extract obtained from fermentation with the isolate NTY211 exhibited the highest contents of phenolic (191.48 ± 3.94 mg GAE/g extract) and flavonoid (106.61 ± 3.09 mg QE/g extract). The identification of phenolic compounds by UHPLC-QqQ-MS/MS analysis revealed a predominant increase in chlorogenic acid and quercetin through SSF. Consequently, SSF utilizing Trichoderma fungi may represent a viable strategy for enhancing the value of coffee cherry husks, rendering them into bioactive ingredients with potential applications in the cosmetic and food industries. Full article

(This article belongs to the Special Issue Application and Research of Solid State Fermentation, 2nd Edition)

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In Vitro Digestibility Methodology Modification to Account for Horse Foregut Digestion Using Diets with Increased Soluble Carbohydrates and Protein

by Ryon W. Springer, Trinette N. Jones, Michaela R. Plowman, Nichole M. Cherry, Walter F. Owsley, Tryon A. Wickersham and James P. Muir

Fermentation 2025, 11(11), 624; https://doi.org/10.3390/fermentation11110624 - 1 Nov 2025

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Abstract

Ruminant in vitro methodologies use washing with neutral detergent solution (NDS) after incubation to mimic ruminant digestion, which is physiologically different compared to that of horses. Our objectives were to determine if washing feed samples with NDS before in vitro fermentation (PRE) would [...] Read more.

Ruminant in vitro methodologies use washing with neutral detergent solution (NDS) after incubation to mimic ruminant digestion, which is physiologically different compared to that of horses. Our objectives were to determine if washing feed samples with NDS before in vitro fermentation (PRE) would suppress fiber digestion versus a post-incubation wash (POST), and to compare in vitro digestibility of forage-based feed mixtures with added soluble carbohydrates (CARB), soluble protein (PROT), or soluble carbohydrates and soluble protein (C + P) to only-forage samples (CONT). Dried, ground feed mixtures sealed in ANKOM filter bags were placed in Daisy^II incubators for 48 h in a split–split-plot batch culture design. Digestibility was determined as in vitro neutral detergent fiber digestibility (IVNDFD), in vitro acid detergent fiber digestibility (IVADFD), in vitro hemicellulose digestibility (IVHD), and in vitro true digestibility (IVTD). The PRE treatment decreased IVHD for CARB versus POST (p = 0.007). Pooling all mixtures, PRE decreased IVTD (p = 0.001), IVADFD (p = 0.036), and IVHD (p = 0.001) and tended to decrease IVNDFD (p = 0.072). The CARB mixture increased IVTD versus all other mixtures (p < 0.001). Pre-washing with NDS suppressed in vitro fermentation by removing soluble carbohydrates. Without removal of soluble carbohydrates to mimic in vivo digestion, fiber digestibility is likely overestimated. Full article

(This article belongs to the Special Issue In Vitro Fermentation, Fourth Edition)

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Fermentation, Volume 11, Issue 11 (November 2025) – 51 articles

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