Fermentation

25 pages, 9899 KB

Open AccessArticle

Production of Bioactive Metabolites in Streptomyces coelicolor Cultivated in the Presence of Citrus Seeds

by Loredana Abbate, Sara Amata, Teresa Faddetta, Carla Rizzo, Francesco Mercati, Giuseppe Gallo and Antonio Palumbo Piccionello

Fermentation 2026, 12(7), 321; https://doi.org/10.3390/fermentation12070321 (registering DOI) - 4 Jul 2026

Abstract

Plant–microbe interactions can modulate the production of bioactive compounds involved in plant growth-promoting activity. This study investigates the metabolic reprogramming of the actinomycete model strain Streptomyces coelicolor M145 during co-cultivation with Citrus aurantium and Citrus limon seeds, used as defined plant-derived chemical inputs, [...] Read more.

Plant–microbe interactions can modulate the production of bioactive compounds involved in plant growth-promoting activity. This study investigates the metabolic reprogramming of the actinomycete model strain Streptomyces coelicolor M145 during co-cultivation with Citrus aurantium and Citrus limon seeds, used as defined plant-derived chemical inputs, under contrasting nutritional conditions with or without L-tryptophan (Trp) supplementation. Untargeted metabolome profiling revealed medium- and Citrus seed-dependent metabolic shifts in co-cultures compared with corresponding Citrus seed and S. coelicolor single cultures used as controls. Under R2YE production conditions, co-cultivation with C. limon resulted in 27 extracellular metabolites, compared with 11 detected in the TSB vegetative medium; similar trends were observed for C. aurantium. Multivariate analyses confirmed that growth medium, Citrus species, and Trp significantly shaped S. coelicolor extracellular metabolic profiles, mainly in quantitative terms. Production conditions, particularly with Trp supplementation, promoted metabolites associated with antimicrobial activity and iron acquisition, whereas vegetative conditions promoted primary metabolism and biotransformation of Citrus-derived compounds. Spent medium bioassays on Solanum lycopersicum showed that these metabolic differences were correlated with distinct biological responses. Overall, these findings demonstrate that defined plant-derived inputs modulate S. coelicolor specialized metabolism in a context-dependent manner, generating metabolomic signatures associated with differential plant growth responses compared to single cultures. Full article

(This article belongs to the Special Issue Novel and Old Insights for Biotechnological Exploitation of Actinomycetota Strain Fermentations)

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36 pages, 4152 KB

Open AccessReview

Precision Fermentation of Low- and Non-Alcoholic Beer Using Non-Saccharomyces Yeast: A Framework for Process and Sensory Control

by Nora Haring, Milan Chňapek and Blažena Drábová

Fermentation 2026, 12(7), 320; https://doi.org/10.3390/fermentation12070320 (registering DOI) - 4 Jul 2026

Abstract

The production of low- and non-alcoholic beer remains a major technological challenge due to the need to restrict ethanol formation while maintaining acceptable sensory quality and fermentation-derived complexity. Conventional approaches, including physical dealcoholization and arrested fermentation, often result in flavor imbalance, reduced aroma [...] Read more.

The production of low- and non-alcoholic beer remains a major technological challenge due to the need to restrict ethanol formation while maintaining acceptable sensory quality and fermentation-derived complexity. Conventional approaches, including physical dealcoholization and arrested fermentation, often result in flavor imbalance, reduced aroma intensity, diminished mouthfeel, and persistent wort-like off-flavors. In this context, non-Saccharomyces yeasts have emerged as promising biological tools due to their species- and strain-dependent carbohydrate utilization, aroma production potential, and intrinsic metabolic constraints. This review provides a structured and mechanistically informed synthesis of current knowledge regarding the application of non-Saccharomyces yeasts in low- and non-alcoholic beer production, with emphasis on metabolic regulation, fermentation process control, and sensory implications. Particular attention is given to sugar transport limitations, glycolytic regulation, carbon redistribution, redox balance, and the role of controllable process variables, including wort fermentability, pitching rate, oxygen availability, and temperature. The available evidence indicates that fermentation outcomes depend strongly on interactions between strain-specific metabolic traits and process design. Collectively, this review proposes a brewery-oriented precision fermentation framework in which strain-specific physiological constraints are deliberately aligned with controllable process variables to support rational strain selection, more predictable ethanol control, and targeted sensory optimization in low- and non-alcoholic beer production. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry, 2nd Edition)

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19 pages, 633 KB

Open AccessArticle

Development of Yogurt Products Containing Plant-Derived Ingredients and Saccharomyces cerevisiae Biomass Enriched with Curcumin and Ergosterol

by Natalya Naumenko, Irina Kalinina, Rinat Fatkullin, Anastasia Antonova, Saveliy Grachev, Vladislav Leonov and Aleksandr Demidkin

Fermentation 2026, 12(7), 319; https://doi.org/10.3390/fermentation12070319 - 3 Jul 2026

Abstract

The development of functional yogurt products enriched with plant-derived ingredients and biologically active compounds represents a promising strategy to improve the nutritional, probiotic, and antioxidant properties of fermented dairy foods. The aim of this study was to evaluate how plant-derived ingredients (whole-meal flour [...] Read more.

The development of functional yogurt products enriched with plant-derived ingredients and biologically active compounds represents a promising strategy to improve the nutritional, probiotic, and antioxidant properties of fermented dairy foods. The aim of this study was to evaluate how plant-derived ingredients (whole-meal flour from sprouted wheat grain and a protein-rich functional ingredient derived from hemp press cake), used individually or in combination with curcumin- or ergosterol-enriched Saccharomyces cerevisiae biomass, influence the physicochemical, structural-mechanical, probiotic, antioxidant, and sensory characteristics of yogurt products. Two forms of yeast biomass were used as enrichment agents: one containing encapsulated curcumin and the other with a high ergosterol content. Milk mixtures were supplemented with yeast biomass containing 34.0 mg/g encapsulated curcumin or 10.55 mg/g ergosterol. Additionally, whole-meal flour from sprouted wheat grain or the hemp-derived protein ingredient was incorporated into the yogurt products at concentrations of 2–3%. These ingredients were tested both individually and in combination to identify optimal formulations that would confer novel properties to the final products. Based on the conducted studies, it was found that the addition of enriched yeast biomass and the protein ingredient resulted in a denser and more uniform structure in the yogurt products compared to those of the control. The titratable acidity of the experimental formulations ranged from 80.2 to 91.8 °T, while pH values ranged from 3.79 to 4.04. Compared with the control sample, these changes indicate enhanced lactic acid fermentation activity. The number of probiotic microorganisms in the experimental samples reached 1.6 × 10⁷–6.4 × 10⁷ MPN/g, exceeding those of the control by an order of magnitude. The type of plant ingredient used significantly determined the technological properties of the finished product. Compared with the control sample, yogurt products supplemented with the hemp press cake-derived protein ingredient exhibited higher protein content (33–34% on a dry matter basis), increased viscosity (2.5–2.6 Pa·s), and reduced syneresis (values of 16.1 mL). The whole-meal flour from sprouted wheat grain exhibited a more pronounced stimulating effect on the growth of probiotic microflora. Enrichment of yogurt products with yeast biomass also increased antioxidant activity: the AOA (DPPH) value increased to 69–84% compared to ~62% in the control. Biotesting using Paramecium caudatum, a sensitive protozoan model widely used for rapid assessment of biological compatibility, toxicity, and the relative biological value of food systems, demonstrated a statistically significant increase (p < 0.05) in protozoan growth to 104–106% compared with the control sample, suggesting the absence of toxic effects and the potential bioavailability of yogurt matrix components. This data confirm the potential of using enriched yeast biomass in combination with plant ingredients for creating probiotic yogurt products with improved structural and functional properties. Full article

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

28 pages, 15168 KB

Open AccessArticle

Enhanced Antifungal Activity of Bacillus velezensis R22 Against Botrytis cinerea Through Medium and Process Optimization

by Nadya Armenova, Lidia Tsigoriyna, Penka Petrova, Maria Gerginova, Ekaterina Krumova, Alexander Arsov, Lyudmila Velkova, Pavlina Dolashka and Kaloyan Petrov

Fermentation 2026, 12(7), 318; https://doi.org/10.3390/fermentation12070318 - 2 Jul 2026

Abstract

Botrytis cinerea, the causal agent of gray mold disease, is a major phytopathogen responsible for substantial losses in horticultural crops. In this study, cultivation conditions for Bacillus velezensis R22 were optimized to maximize overall antifungal activity against B. cinerea. A Plackett–Burman [...] Read more.

Botrytis cinerea, the causal agent of gray mold disease, is a major phytopathogen responsible for substantial losses in horticultural crops. In this study, cultivation conditions for Bacillus velezensis R22 were optimized to maximize overall antifungal activity against B. cinerea. A Plackett–Burman design was used to identify medium components affecting antifungal activity in flask cultures, followed by response surface methodology based on a central composite design (CCD) to optimize sucrose concentration, temperature, and agitation speed in a stirred bioreactor. Maximum antifungal activity was obtained at 17.45 g/L initial sucrose, 31.8 °C, and 293 rpm. The biological relevance of the optimized culture was confirmed in a tomato infection model, in which gray mold severity was reduced by 85.3% relative to the untreated control and by 59.9% relative to the non-optimized R22 culture. The same CCD approach was subsequently applied to determine cultivation conditions that maximize the concentration of R22 viable cells. The optimal parameters for 24-h growth (35.46 g/L sucrose, 36.5 °C, and 454 rpm) differed markedly from those identified for maximal antifungal activity. When evaluated on uninfected tomato plants, cultures produced under conditions favoring higher cell density showed enhanced plant growth-promoting activity compared to the non-optimized culture. Mass spectrometric analysis of lipopeptide extracts revealed that the enhanced antifungal activity was accompanied by an increased abundance of long-chain homologs across all major lipopeptide families, particularly surfactins. Thus, our results indicate that maximizing overall antifungal activity may be of greater practical significance than optimization of the individual fungicidal agent. Full article

(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis, 3rd Edition)

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20 pages, 2841 KB

Open AccessArticle

Enhancing the GABA Content and Sleep-Promoting Potential of the Baihe Dihuang Decoction Through Lactic Acid Bacteria Fermentation

by Yining Zhou, Jinqiu Luo, Xianping Li, Junying Zhao, Baoyu Yang, Quansheng Zhu, Weicang Qiao, Lu Liu and Lijun Chen

Fermentation 2026, 12(7), 317; https://doi.org/10.3390/fermentation12070317 - 1 Jul 2026

Abstract

γ-aminobutyric acid (GABA) is crucial in neural inhibition and sleep regulation. This study screened lactic acid bacteria isolated from breast milk and infant fecal samples for their GABA-producing ability; their acid tolerance, bile salt resistance, and growth performance were evaluated. Based on TLC-HPLC [...] Read more.

γ-aminobutyric acid (GABA) is crucial in neural inhibition and sleep regulation. This study screened lactic acid bacteria isolated from breast milk and infant fecal samples for their GABA-producing ability; their acid tolerance, bile salt resistance, and growth performance were evaluated. Based on TLC-HPLC analysis, Lactobacillus gasseri F002, Lactiplantibacillus plantarum R7, and Lacticaseibacillus rhamnosus B2-1 were identified as promising GABA-producing strains. L. gasseri F002 was selected for liquid-state fermentation of the Baihe Dihuang decoction. During fermentation, L. gasseri F002 utilized carbohydrates in the decoction matrix, increased GABA accumulation, with a peak of 0.063 mg/mL at 24 h, and reduced total saponin content, suggesting that lactic acid bacterial fermentation induced compositional shifts of major functional constituents in the Baihe Dihuang decoction. The sleep-promoting effect of the fermented decoction was assessed using a caffeine-induced zebrafish insomnia model. The fermented Baihe Dihuang decoction significantly prolonged sleep bout duration, while reducing wakefulness and total locomotor activity. Moreover, correlative changes altered sleep-related molecular and biochemical indicators in the zebrafish model. Correlative changes in the expression of gabra1, htr1aa, drd2a, dbh, and th, as well as in GABA, melatonin (MT), and monoamine oxidase (MAO) levels, suggest a potential association with the observed sleep-improving phenotypes. Therefore, fermentation with GABA-producing lactic acid bacteria may enhance the sleep-promoting potential of the Baihe Dihuang decoction and provide preliminary experimental support for the development of fermented medicinal–food homologous products aimed at improving sleep. Full article

(This article belongs to the Special Issue The Roles of Lactic Acid Bacteria in Food Fermentation)

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15 pages, 808 KB

Open AccessArticle

Analytical Solutions for Fungal Growth and Penicillin Production Dynamics with Simultaneous Product Hydrolysis in Batch Bioprocesses

by Samuel C. Oliveira and Helenice O. Florentino

Fermentation 2026, 12(7), 316; https://doi.org/10.3390/fermentation12070316 - 1 Jul 2026

Abstract

Few mathematical models describing the dynamics of cell growth, production formation and substrate consumption in batch and fed-batch bioprocesses have analytical solutions. In this study, analytical solutions for a mathematical model of a batch bioprocess of penicillin production based on the Logistic law [...] Read more.

Few mathematical models describing the dynamics of cell growth, production formation and substrate consumption in batch and fed-batch bioprocesses have analytical solutions. In this study, analytical solutions for a mathematical model of a batch bioprocess of penicillin production based on the Logistic law for cell growth and on the Luedeking–Piret equation for antibiotic formation are obtained using classical methods of solving ordinary differential equations. The analytical solutions were validated by substitution into the differential equations themselves, as well as by comparison with numerical solutions obtained through the fourth-order Runge–Kutta–Gill integration method, using typical fungus inoculum concentrations (X₀ = 0.25; 0.75% DW) and kinetic parameters (μ_m = 0.5 h⁻¹, X_m = 3.7% DW, β = 0.02 U/(mL·h·% DW) and k_h = 0.027 h⁻¹). The novelty in relation to the few studies published on the subject, which deal with the production of different metabolites, including other antibiotics, is that in the present study, the hydrolysis of penicillin is considered simultaneously with its production in the description of the dynamics of product formation. The main finding demonstrates that the hydrolysis reaction acts as a stabilizing factor, resulting in a system with two equilibrium points: an unstable point with no penicillin production, and a stable point in which a certain amount of antibiotic is produced. Full article

(This article belongs to the Special Issue Fungi for Bioprocesses: Food, Biofuel, Biocompounds and Wastewater Treatment)

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14 pages, 1511 KB

Open AccessArticle

Nitrogen Availability Influences Biomass Composition in Yarrowia lipolytica Grown on Acetate

by Renfeng He, Wei Liu, Xiaotong Shao, Zejiang Zhu, Keke Sun, Yuwan Liu, Huifeng Jiang and Dingyu Liu

Fermentation 2026, 12(7), 315; https://doi.org/10.3390/fermentation12070315 - 30 Jun 2026

Abstract

Microbial protein production from acetate represents a promising route for sustainable protein supply, yet its efficiency is constrained by limited understanding of carbon–nitrogen metabolic coordination. In this study, nitrogen availability was systematically varied to investigate its role in regulating biomass composition and protein [...] Read more.

Microbial protein production from acetate represents a promising route for sustainable protein supply, yet its efficiency is constrained by limited understanding of carbon–nitrogen metabolic coordination. In this study, nitrogen availability was systematically varied to investigate its role in regulating biomass composition and protein biosynthesis in Yarrowia lipolytica. Nitrogen limitation markedly reduced cell growth and protein accumulation (19.56% of dry cell weight) while increasing lipid content (up to 34.16%), indicating a altered protein and lipid accumulation under different nitrogen conditions. Transcriptomic analysis revealed a global downregulation of anabolic pathways under nitrogen limitation, accompanied by a shift in nitrogen assimilation from the glutamate dehydrogenase (GDH) pathway to the glutamine synthetase/glutamate synthase (GS–GOGAT) pathway, as well as significant upregulation of genes related to ammonium and amino acid transport. Guided by these findings, metabolic engineering of key nitrogen assimilation pathways was performed. Strains harboring additional copies of GDH and GS expression cassettes showed increased protein content from 48.52% to 55.77% and improved amino acid composition, whereas strains with an additional copy of the GOGAT gene exhibited reduced growth and protein accumulation. These results demonstrate that nitrogen availability regulates biomass composition through coordinated control of nitrogen transport and assimilation, and that balanced upregulation of GDH and GS genes is an effective strategy to improve microbial protein production from acetate, supporting the development of efficient fermentation processes using low-cost carbon sources. Full article

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

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21 pages, 893 KB

Open AccessArticle

Antimicrobial Activity and Probiotic Potential of Lactic Acid Bacteria Isolated from São Jorge Cheese

by Susana C. Ribeiro, Sofia P. M. Silva, Vanessa Corvelo Pires and Célia C. G. Silva

Fermentation 2026, 12(7), 314; https://doi.org/10.3390/fermentation12070314 - 30 Jun 2026

Abstract

Six lactic acid bacteria isolated from São Jorge PDO cheese were characterised for technological, safety, antimicrobial, and probiotic properties. All isolates fermented a broad range of carbohydrates and lacked lipolytic activity, while SJC115 and SJC119 showed proteolysis. Safety profiling (γ-haemolysis, no DNase or [...] Read more.

Six lactic acid bacteria isolated from São Jorge PDO cheese were characterised for technological, safety, antimicrobial, and probiotic properties. All isolates fermented a broad range of carbohydrates and lacked lipolytic activity, while SJC115 and SJC119 showed proteolysis. Safety profiling (γ-haemolysis, no DNase or gelatinase activity, and generally favourable antibiotic susceptibility) is promising, but tetracycline resistance warrants caution and genomic confirmation. L. paracasei and L. brevis isolates inhibited a wide range of foodborne pathogens (Listeria monocytogenes, Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Bacillus spp.) and spoilage fungi (Penicillium and Aspergillus spp.). Notably, two isolates (SJC117 and SJC120) exhibited antibacterial activity in neutralized cell-free supernatants, indicating putative bacteriocin-like inhibitory substances (BLIS). The isolates survived intestinal conditions above the probiotic threshold, yet only SJC117 and SJC120 tolerated gastric acidity (pH 2.5, 1 h) with >5 log CFU/mL. Despite low hydrophobicity, strains showed good autoaggregation and pathogen coaggregation. All isolates produced exopolysaccharides (EPS) and angiotensin-converting enzyme (ACE) inhibitory peptides, whereas some exhibited moderate conjugated linoleic acid (CLA) production and glutamate decarboxylase (GAD) activity. L. paracasei SJC117 stood out by combining BLIS/antifungal activity, superior gastric tolerance, and an exceptional bioactive profile, making it a promising candidate for biopreservation and functional food applications that warrants further in vivo validation to confirm its efficacy and safety. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria in Functional Foods: From Microbiology to Health Benefits)

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20 pages, 1299 KB

Open AccessArticle

Harnessing the Microbial Terroir of High-Altitude Wine Valleys: Autochthonous Yeast Co-Inoculation for Base Wine Production of Torrontés Sanjuanino

by Diego Bernardo Petrignani, Yolanda Paola Maturano, Valeria Benegas, Leandro Ruiz, Simon Tornello, María José Valera, Francisco Carrau and Maria Victoria Mestre Furlani

Fermentation 2026, 12(7), 313; https://doi.org/10.3390/fermentation12070313 - 30 Jun 2026

Abstract

Sparkling wines are produced through a second fermentation of a base wine, whose composition strongly determines the final product quality. Yeast selection for primary fermentation is therefore crucial, as it influences both fermentation performance and sensory attributes. In this study, 156 yeasts were [...] Read more.

Sparkling wines are produced through a second fermentation of a base wine, whose composition strongly determines the final product quality. Yeast selection for primary fermentation is therefore crucial, as it influences both fermentation performance and sensory attributes. In this study, 156 yeasts were isolated from spontaneous fermentations of Vitis vinifera cv. Torrontés sanjuanino from Paraje de Hilario (1550 m.a.s.l., San Juan, Argentina), aiming to select autochthonous strains with oenological potential for sparkling base wine production. Isolates were phenotypically characterized and molecularly identified by sequencing the D1/D2 domain of the 26S rDNA. A total of 44 Saccharomyces cerevisiae and 60 non-conventional yeasts, mainly Hanseniaspora uvarum, were identified. Based on relevant oenological traits, two S. cerevisiae (M138M, F172M) and two H. uvarum (Mi14M, C135MJ) strains were selected. Laboratory and pilot-scale co-inoculation trials showed that the Mi14M/M138M (50:50) combination exhibited stable fermentation kinetics, low acetic acid production (0.44 g/L), high glycerol levels (7.1 g/L), and suitable pH (3.08) and ethanol content (11.2% v/v). Despite higher residual sugars than the control, no technological issues were observed. These findings support co-inoculation of autochthonous strains of S. cerevisiae and H. uvarum as a promising strategy to enhance wine quality and reinforce regional identity in sparkling base wines. Full article

(This article belongs to the Special Issue Biotechnology in Winemaking, 2nd Edition)

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20 pages, 2527 KB

Open AccessArticle

Comparative Evaluation of RSM and ANN Models on Prediction of Cellulase Production by Bacillus paralicheniformis Using Plumeria alba in Submerged Fermentation

by Javaria Bakhtawar, Muhammad Zubair Ali, Tri Handanyani Kurniati, Iram Hafiz, Muhammad Irfan and Emmanuel Atta-Obeng

Fermentation 2026, 12(7), 312; https://doi.org/10.3390/fermentation12070312 - 30 Jun 2026

Abstract

This study reports cellulase production by Bacillus paralicheniformis using Plumeria alba leaf powder under submerged fermentation with a focus on systematic bioprocess optimization. Physical parameters were first optimized using a one-factor-at-a-time (OFAT) approach, followed by optimization of yeast extract, MgSO₄ and (NH [...] Read more.

This study reports cellulase production by Bacillus paralicheniformis using Plumeria alba leaf powder under submerged fermentation with a focus on systematic bioprocess optimization. Physical parameters were first optimized using a one-factor-at-a-time (OFAT) approach, followed by optimization of yeast extract, MgSO₄ and (NH₄)₂SO₄ via a central composite design (CCD) and response surface methodology (RSM). An artificial neural network (ANN) with a 5:3:1 network trained by the Levenberg–Marquardt algorithm further improved prediction of carboxylmethylcellulase (CMCase) and filter paper cellulase (FPase) activities. This study is the first to exploit Plumeria alba leaf powder as an untapped, low-cost lignocellulosic substrate for cellulase production by B. paralicheniformis and uniquely benchmarks RSM against ANN-based modeling to identify superior predictive frameworks for bioprocess optimization. Under optimized conditions (24 h, 4% w/v substrate, 1% v/v inoculum), the maximum FPase and CMCase activities reached 60.53 IU/mL/min and 332.10 IU/mL/min respectively. Partial characterization showed optimum FPase and CMCase activities at 50 °C and 70 °C, respectively, at pH 7.5. Enzymes also showed activation by NaCl and some select solvents while tolerating a broad range of metal ions. The enzymatic hydrolysis of P. alba biomass released 59.42 mg/mL total reducing sugars after 8hr, confirming efficient saccharification from a low-cost feedstock. The ANN model (R² = 97.59% for CMCase; 85.95% for FPase) outperformed RSM (R² = 85.95% and 78.25%, respectively), while radial basis function optimization reached 99.99%. These findings highlight B. paralicheniforms cellulase as a promising biocatalyst for biorefinery applications and demonstrate the value of integrating RSM and ANN for process optimization. Full article

(This article belongs to the Special Issue From Waste to Value: Microbial Fermentation for the Sustainable Valorization of Agri-Food Residues)

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23 pages, 863 KB

Open AccessReview

Untargeted Metabolomics in Fermented Food Systems

by Clarisse M. Lopes and Luis F. Guido

Fermentation 2026, 12(7), 311; https://doi.org/10.3390/fermentation12070311 - 30 Jun 2026

Abstract

Fermented foods are chemically complex systems in which substrate composition, microbial community dynamics, and physicochemical conditions interact to generate thousands of metabolites across diverse chemical classes. Conventional targeted analytical approaches quantify predefined compounds with high precision but operate within a restricted chemical space, [...] Read more.

Fermented foods are chemically complex systems in which substrate composition, microbial community dynamics, and physicochemical conditions interact to generate thousands of metabolites across diverse chemical classes. Conventional targeted analytical approaches quantify predefined compounds with high precision but operate within a restricted chemical space, systematically excluding emergent features central to product identity, safety, and sensory character. Untargeted metabolomics addresses this limitation by capturing global chemical fingerprints of fermented matrices, enabling discovery-driven investigation across a broad fraction of the metabolome. This review examines the application of untargeted metabolomics across key research areas in fermented food science, including fermentation monitoring, microbial interactions, flavour development, process optimisation, post-fermentation stability, and safety assessment. Across these domains, untargeted approaches reveal system-level metabolic relationships beyond the reach of targeted analyses, while also presenting interpretive challenges. A central limitation is the annotation bottleneck: despite high feature detection rates, only a small fraction of signals are structurally identified, constraining mechanistic interpretation and cross-study comparability. Additional challenges in data processing, statistical validation, and interlaboratory reproducibility further limit data interpretation. Addressing these constraints through improved spectral libraries, standardised workflows, and integration with complementary omics is essential for advancing untargeted metabolomics towards robust knowledge generation in fermented food systems. Full article

(This article belongs to the Special Issue Microbial Fermentation Technology: A Biological Engine Driving Innovation in the Food Industry)

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16 pages, 2305 KB

Open AccessArticle

Effects of Increasing Corn Grain Inclusion and Reducing Hay Proportion on Growth Performance, Methane Emissions, Rumen Fermentation, and Microbial Diversity in Winter-Housed Yaks

by Qunying Zhang, Hongmei Sun, Qi Wang, Lianbin Cao, Shujie Liu, Yanfen Cheng and Lizhuang Hao

Fermentation 2026, 12(7), 310; https://doi.org/10.3390/fermentation12070310 - 29 Jun 2026

Abstract

The expansion of ruminant production has increased methane (CH₄) emissions, highlighting the need for nutritional strategies that improve productivity while mitigating environmental impacts. Yaks, generally considered low CH₄ producers, are increasingly raised under intensive winter-housed systems on the Qinghai–Xizang Plateau, [...] Read more.

The expansion of ruminant production has increased methane (CH₄) emissions, highlighting the need for nutritional strategies that improve productivity while mitigating environmental impacts. Yaks, generally considered low CH₄ producers, are increasingly raised under intensive winter-housed systems on the Qinghai–Xizang Plateau, highlighting the need to assess how dietary concentrate-to-forage (C:F) ratios affect both CH₄ emissions and growth performance. This study investigated the effects of three dietary C:F ratios [L-C (48:52), M-C (60:40), H-C (72:28)] on growth performance, ruminal fermentation, microbial diversity (n = 6 per group) and CH₄ emission (n = 3 per group) in winter-housed yaks. The results indicated that average daily gain (ADG) was significantly higher in M-C and H-C, while the feed-to-gain ratio (F/G) was significantly lower in M-C and H-C than in L-C (p < 0.05). Total CH₄ production (g/day) did not differ among treatments (p > 0.05), while CH₄ yield per unit body weight gain (CH₄/BWG) was significantly reduced in M-C and H-C (p < 0.05). The protozoal count was significantly lower in H-C, and the proportions of isobutyrate and isovalerate were significantly higher in H-C and M-C compared with L-C (p < 0.05). 16S rRNA gene sequencing revealed that increasing the C:F ratio reduced the relative abundance of the archaeal genus Methanobrevibacter, while Thermogymnomonas exhibited a significant increase (p < 0.05). Collectively, these findings indicate that increasing the C:F ratio in winter-housed yaks improves growth efficiency and lowers CH₄/kg BWG, with the M-C group showing the most favorable balance between productivity and environmental sustainability. Full article

(This article belongs to the Special Issue Feed Efficiency and Rumen Fermentation)

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43 pages, 1150 KB

Open AccessReview

Potential and Challenges of Microalgae in Wastewater Treatment for Bioregenerative Life Support Systems During Long-Term Space Missions

by Yana Ilieva, Maya Margaritova Zaharieva, Alexander Kroumov and Hristo Najdenski

Fermentation 2026, 12(7), 309; https://doi.org/10.3390/fermentation12070309 - 29 Jun 2026

Abstract

The engineering, resource, and financial constraints in space and spacecraft so far have not allowed the incorporation of biological components into a closed-loop bioregenerative life support system (BLSS), despite decades of research. The expected increase in deep-space exploration and planetary bases with limited [...] Read more.

The engineering, resource, and financial constraints in space and spacecraft so far have not allowed the incorporation of biological components into a closed-loop bioregenerative life support system (BLSS), despite decades of research. The expected increase in deep-space exploration and planetary bases with limited access to Earth-based resources necessitates the development of self-sustaining hybrid BLSS technology. The created physicochemical systems, together with photosynthetic organisms and bacteria, aim to revitalize the air, produce food, and recycle nutrients and water in mutually beneficial mini-ecosystems. While plants are best in the function of food production and bacteria in waste recycling, the incorporation of microalgae would add immense benefits in optimizing the life support system (LSS) and increasing the degree of closure. Microalgal photobioreactors (PBRs) could perform wastewater treatment (WWT), removing the nitrogen (N) and phosphorus (P) in the human-derived wastewater (WW), and couple it with converting carbon dioxide (CO₂) from the cabin to oxygen (O₂) and food production. As microalgal WWT on Earth is an emerging field with engineering hurdles, power, mass, volume, microgravity fluid dynamics, and other constraints have also prevented their operations in space. However, in space vehicles, there is no need for large upscaling of a laboratory prototype system, and the WW effluent is easier to predict, facilitating microalgal extraplanetary use in comparison to Earth treatment plants. These factors, combined with the qualities of microalgae such as surface-to-volume efficiency, fast growth rate, high yield, and tolerability to WW, etc., have led to many preliminary testbeds, prototypes, and ground demonstrations from space agencies, space centers, and academia, which show promising results. Microalgal participation in space WWT is beyond current operational practice; however, PBRs are on the space agenda, and the scientific community is elaborating the technologies that would allow their successful implementation. Full article

(This article belongs to the Special Issue Cyanobacteria and Eukaryotic Microalgae (2nd Edition))

16 pages, 1205 KB

Open AccessArticle

Intake of Live Microorganisms in Adults and Its Impact on Microbiota and Health Parameters

by Eva Gómez-Pérez, Aida Zapico, Silvia Arboleya, Nuria Salazar, Clara G. de los Reyes-Gavilán, Sonia González and Miguel Gueimonde

Fermentation 2026, 12(7), 308; https://doi.org/10.3390/fermentation12070308 - 29 Jun 2026

Abstract

The intake of live microorganisms (LMOs) may contribute to modulating gut microbial ecology with an impact on health. In this study, we examined the intake of LMOs in adults and its association with gut microbiota composition, intestinal short-chain fatty acids (SCFAs), and health-related [...] Read more.

The intake of live microorganisms (LMOs) may contribute to modulating gut microbial ecology with an impact on health. In this study, we examined the intake of LMOs in adults and its association with gut microbiota composition, intestinal short-chain fatty acids (SCFAs), and health-related biochemical parameters. A total of 151 adults were analyzed across three age groups (18–50, 51–65, and 66–95 years). Dietary intake was assessed using a food frequency questionnaire (FFQ), and LMOs consumption was estimated with a previously developed database. The levels of some relevant intestinal microbial groups were measured using Quantitative Polymerase Chain Reaction (qPCR), SCFAs were determined using gas chromatography, and biochemical markers were assessed through standardized laboratory methods. LMOs intake was significantly higher in the two older age groups compared with younger adults, with yogurt identified as the primary dietary source of LMOs across all ages. In the middle-aged group, bacterial LMOs intake independently predicted higher abundances of Akkermansia and Bacteroides-related taxa, while fungal LMOs were positively associated with butyric acid levels. In the older age group, bacterial LMOs intake was directly associated with branched-chain fatty acids (BCFAs) while fungal LMOs intake was directly associated with circulating cholesterol and inversely with malondialdehyde (MDA). Overall, the findings suggest that LMOs consumption, mainly bacteria intake from fermented dairy products, increases with age and is linked to age-specific changes in gut microbiota, microbial metabolites, and biochemical health parameters. Full article

(This article belongs to the Special Issue Novel Insights into Fermented Dairy Products and Their Health Relevance)

39 pages, 6788 KB

Open AccessReview

Ester Formation and Aroma Modulation by Non-Saccharomyces Yeasts in Wine Fermentation: A Scoping Review

by Narjara de Medeiros Ribeiro, Esther Pedroso Theisen, Yuri Duarte Porto, Maressa Caldeira Morzelle and Juliana Aparecida Correia Bento

Fermentation 2026, 12(7), 307; https://doi.org/10.3390/fermentation12070307 - 29 Jun 2026

Abstract

This scoping review maps and synthesizes scientific evidence on the use of non-Saccharomyces yeasts in wine fermentation, focusing on their contribution to ester formation and aroma modulation. The review followed the Joanna Briggs Institute (JBI) methodology and the PRISMA-ScR guidelines. A total [...] Read more.

This scoping review maps and synthesizes scientific evidence on the use of non-Saccharomyces yeasts in wine fermentation, focusing on their contribution to ester formation and aroma modulation. The review followed the Joanna Briggs Institute (JBI) methodology and the PRISMA-ScR guidelines. A total of 71 original articles published between 2000 and 2025 were included, and evidence mapping was combined with an exploratory textual analysis of abstracts using Iramuteq^® to characterize thematic trends, methodological approaches, and knowledge gaps. The textual analysis highlighted fermentation ecology, inoculation strategies, and aroma modulation as central themes, with ester formation emerging as a key topic. Torulaspora, Hanseniaspora, Lachancea, Metschnikowia, and Candida/Starmerella were the most frequently investigated genera, reflecting their potential to diversify wine sensory profiles beyond those typically associated with Saccharomyces cerevisiae fermentations. Non-Saccharomyces yeasts proved particularly relevant in the synthesis and modulation of ethyl and acetate esters linked to fruity and floral characteristics, especially in mixed fermentations. Key knowledge gaps include the limited transferability of laboratory-scale results to industrial conditions, insufficient understanding of interspecies interactions, and the need for stronger sensory validation of volatile compounds. These findings highlight the potential of non-Saccharomyces yeasts as tools for innovation, terroir expression, and enhanced sensory complexity in winemaking. Full article

(This article belongs to the Section Yeast)

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19 pages, 1127 KB

Open AccessArticle

The Usage of Fermented Milk By-Products in Cabbage Pickle Fermentation Through a Sustainable Food Production Approach

by Ayşe Janseli Denizkara, Gökhan Akarca, Azize Atik and İlker Atik

Fermentation 2026, 12(7), 306; https://doi.org/10.3390/fermentation12070306 - 28 Jun 2026

Abstract

This study examined the physicochemical, microbiological, textural, organic acid, colour, and sensory aspects of cabbage pickles made with fermented dairy by-products as a brine medium. Yoghurt whey, whey, kefir whey, and buttermilk were used as brine media and compared with vinegar. Brine samples [...] Read more.

This study examined the physicochemical, microbiological, textural, organic acid, colour, and sensory aspects of cabbage pickles made with fermented dairy by-products as a brine medium. Yoghurt whey, whey, kefir whey, and buttermilk were used as brine media and compared with vinegar. Brine samples showed substantial changes in pH, Brix, colour, and rheology (p < 0.05). Yoghurt whey-based samples had the lowest brine pH (2.87) and Brix (10.04%), while buttermilk samples had the highest pH (3.26) and Brix (10.83%). Vinegar-based brine showed higher a* and b* values, whereas yoghurt whey-based brine had the highest L*. Yoghurt whey-based samples had lower consistency and a lower viscosity index. Pickle samples made with different brine types showed significant differences in physicochemical, microbiological, textural, and organic acid properties (p < 0.05). Pickle samples made with vinegar had the lowest pH (2.99), while samples made with buttermilk had the highest (3.31). Vinegar-based pickles had the highest dry matter (5.27%) and drained weight (64.15%). Yoghurt whey-based samples had the highest counts of Lactobacillus spp. (6.38 log CFU/g) and Lactococcus/Streptococcus (6.81 log CFU/g), while vinegar-based samples had the highest counts of acetic acid bacteria and total aerobic mesophilic bacteria. However, kefir whey-based samples had the highest yeast count (5.72 log CFU/g). The textural analysis showed that yoghurt whey-based samples had the highest hardness (471.72 N) and springiness, whereas buttermilk-based samples had higher adhesiveness and cohesiveness. Whey-based samples had the highest gumminess and chewiness. Yoghurt whey-based samples had the highest levels of lactic acid (14,569.39 mg/L) and citric acid, whereas vinegar-based samples had the highest levels of acetic acid (63,795.64 mg/L) and propionic acid. Kefir whey-based samples had the highest butyric acid content. Yoghurt whey-based pickles were the most popular with panellists, followed by whey and vinegar-based pickles. Buttermilk-based samples scored lowest in sensory rating. Finally, fermented dairy by-products can be used as a functional brine medium for cabbage pickle. Yoghurt whey has shown promise in improving microbiological quality, textural characteristics, and sensory acceptability. Using dairy industry by-products in pickle making is an innovative way to produce sustainable food and add value to by-products. Full article

(This article belongs to the Special Issue Advances in Fermented Fruits and Vegetables—2nd Edition)

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13 pages, 278 KB

Open AccessArticle

Evaluating the Combined Effect of Lactococcus lactis, Bacillus subtilis and Saccharomyces cerevisiae in the Mixed Silage of Navel Orange Pomace and Rice Straw

by Siyu Lu, Vanajah Liyinthan, Gang Liao, Qinghua Qiu, Xianghui Zhao, Yanjiao Li and Kehui Ouyang

Fermentation 2026, 12(7), 305; https://doi.org/10.3390/fermentation12070305 - 27 Jun 2026

Abstract

A three-factor completely randomized design was used to evaluate the effects of Lactococcus lactis, Bacillus subtilis, and Saccharomyces cerevisiae on the fermentation quality and nutritional composition of mixed silage prepared from navel orange pomace and rice straw. The addition of L. [...] Read more.

A three-factor completely randomized design was used to evaluate the effects of Lactococcus lactis, Bacillus subtilis, and Saccharomyces cerevisiae on the fermentation quality and nutritional composition of mixed silage prepared from navel orange pomace and rice straw. The addition of L. lactis increased lactic acid content and Flieg’s score of the mixed silage. The addition of B. subtilis decreased the pH value and increased the lactic acid content of the mixed silage. The addition of S. cerevisiae decreased the lactic acid content and Flieg’s score of the mixed silage. However, the interaction between the three strains significantly affected many parameters of the mixed silage. With respect to fermentation quality (Flieg’s score), adding 0.3 g kg⁻¹ L. lactis and not adding S. cerevisiae achieved the best performance of the mixed silage. Under these conditions, increasing the level of B. subtilis resulted in a higher crude protein content of the mixed silage, whereas neutral detergent fiber and acid detergent fiber contents first decreased and then increased, and water-soluble carbohydrate content first increased and then decreased. Therefore, within the selected combination of adding 0.3 g kg⁻¹ L. lactis and not adding S. cerevisiae, the addition of 0.8 g kg⁻¹ B. subtilis gave the best nutritional quality. Full article

29 pages, 1580 KB

Open AccessReview

Advances in the Biosynthetic Production of Daunomycin: Genetic, Metabolic, and Process Engineering Strategies

by Alexandra Cristina Blaga, Irina Cârlescu, Ioan Mămăligă and Elena Niculina Drăgoi

Fermentation 2026, 12(7), 304; https://doi.org/10.3390/fermentation12070304 - 26 Jun 2026

Abstract

Daunomycin (daunorubicin) is one of the most clinically significant anthracyclines used in chemotherapy, and its efficient production remains a major objective for biotechnological researchers. Industrial manufacturing relies on the fermentation of Streptomyces peucetius and Streptomyces coeruleorubidus, which produce daunomycin as a secondary [...] Read more.

Daunomycin (daunorubicin) is one of the most clinically significant anthracyclines used in chemotherapy, and its efficient production remains a major objective for biotechnological researchers. Industrial manufacturing relies on the fermentation of Streptomyces peucetius and Streptomyces coeruleorubidus, which produce daunomycin as a secondary metabolite under controlled conditions. This review will focus on the methods to enhance the total efficiency of biotechnological production, from upstream biosynthesis to downstream processing. Given the complexity of the daunomycin biosynthetic pathway in Streptomyces spp., substantial progress has been made in strain improvement to increase yield, metabolic robustness, and process stability. Advances in classical mutagenesis, pathway engineering, regulatory network modulation, and precursor supply optimization, along with rational medium design and advanced process control, have led to substantial increases in product titers and productivity. At the same time, innovations in downstream processes, such as extraction, purification and process integration, have increased recovery efficiency, product quality, and economic feasibility. With improvements in the production process, novel drug delivery modalities have been developed (e.g., drug carriers based on erythrocytes, drug nanocarriers based on hyaluronic acid) with increased efficiency and lower systemic toxicity. These developments indicate an evolution from pathway-level engineering to industrial-scale manufacturing and clinical application, underlining the evolution of daunomycin research and biotechnological production. Full article

(This article belongs to the Special Issue Fermentation Processes and Product Development)

26 pages, 900 KB

Open AccessReview

Controlled Fermentation and Integrated Valorization of Coffee Cherry Pulp: Applications in Food, Bioactive, Biopolymers, and Animal Feed

by Kamon Yakul, Chayatip Insomphun, Phisit Seesuriyachan, Thanongsak Chaiyaso, Su Lwin Htike, Yuthana Phimolsiripol, Juan Manuel Castagnini and Churairat Moukamnerd

Fermentation 2026, 12(7), 303; https://doi.org/10.3390/fermentation12070303 - 26 Jun 2026

Abstract

Coffee cherry pulp (CCP; cascara), a major by-product of coffee processing, has gained increasing attention as a sustainable source of phenolic compounds, dietary fiber, and other bioactive constituents with applications in food, nutraceutical, feed, and biomaterial industries. However, its utilization remains limited by [...] Read more.

Coffee cherry pulp (CCP; cascara), a major by-product of coffee processing, has gained increasing attention as a sustainable source of phenolic compounds, dietary fiber, and other bioactive constituents with applications in food, nutraceutical, feed, and biomaterial industries. However, its utilization remains limited by compositional variability, anti-nutritional compounds, and inefficiencies in conventional processing. Controlled fermentation has emerged as a promising strategy to enhance the release, transformation, and bioavailability of CCP-derived bioactive through targeted microbial biotransformation and controlled bioprocessing. This review summarizes recent advances in enzymatic pretreatment, microbial fermentation, and metabolite-directed processing, with emphasis on their effects on phenolic transformation, antioxidant activity, and functional properties. The roles of selected lactic acid bacteria, yeasts, and microbial consortia in improving the nutritional, sensory, and biological characteristics of CCP-derived products are critically discussed. Potential applications of fermented CCP in functional foods and beverages, bioactive ingredients, biopolymers, and animal feed are also highlighted within the framework of an integrated circular bioeconomy. Finally, current challenges and future perspectives related to process scalability, metabolite control, regulatory approval, and AI-assisted bioprocess optimization are addressed. Full article

(This article belongs to the Special Issue Microbial Cell Factories for Value-Added Products from Agro-Industrial Residues)

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