Fermentation

16 pages, 2343 KB

Open AccessArticle

One-Step Activation, Purification, and Immobilization of Bovine Chymosin via Adsorption on Magnetic Particles

by Paulina G. Gonçalves, Paz García-García, Honoria S. Chipaca-Domingos, Gloria Fernandez-Lorente, Miguel Ladero and Benevides C. Pessela

Fermentation 2026, 12(1), 66; https://doi.org/10.3390/fermentation12010066 - 22 Jan 2026

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Abstract

Chymosin is an aspartyl protease widely used in the food industry for milk coagulation during cheesemaking. Although recombinant production has replaced natural extraction from rennet, current heterologous expression systems still face significant challenges, including low solubility, costly purification steps, and enzyme instability after [...] Read more.

Chymosin is an aspartyl protease widely used in the food industry for milk coagulation during cheesemaking. Although recombinant production has replaced natural extraction from rennet, current heterologous expression systems still face significant challenges, including low solubility, costly purification steps, and enzyme instability after activation. To address these limitations, we sought to develop a more efficient and economical production strategy for bovine chymosin by cloning its codon-optimized prochymosin A gene into Escherichia coli using the pBAD/His vector under the control of the L-arabinose-inducible PBAD promoter. Overexpression of the recombinant gene resulted in the formation of inclusion bodies, which were solubilized with NaOH and refolded by dilution and pH adjustment with glycine. The folded prochymosin was then activated by acidification. To simplify the downstream process and improve enzyme recovery, different immobilization strategies were explored to combine activation, purification, and immobilization in a single step. While polymeric agarose-based supports showed low immobilization efficiency (<20%) due to pore clogging, magnetic nanoparticles completely overcame these limitations, achieving nearly 100% immobilization yield and retaining about 85% of enzymatic activity. This integrated magnetic-based approach provides a cost-effective and scalable alternative for the production and stabilization of active chymosin. Full article

(This article belongs to the Special Issue Systems Metabolic Engineering for the Production of Value-Added Compounds)

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23 pages, 1598 KB

Open AccessArticle

Gluten-Free Steamed Bread Formulated with Rice–Amaranth Flours via Sourdough Fermentation

by Ricardo H. Hernández-Figueroa, Beatriz Mejía-Garibay, Enrique Palou, Aurelio López-Malo and Emma Mani-López

Fermentation 2026, 12(1), 65; https://doi.org/10.3390/fermentation12010065 - 21 Jan 2026

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Abstract

The aims of this study were to evaluate the impact of probiotics (added as a starter sourdough and microcapsules) on gluten-free (GF) rice–amaranth steamed bread (SB) regarding physicochemical characteristics, sensory attributes, probiotic viability, and volatile organic compounds (VOCs). Also, probiotic viability, pH, total [...] Read more.

The aims of this study were to evaluate the impact of probiotics (added as a starter sourdough and microcapsules) on gluten-free (GF) rice–amaranth steamed bread (SB) regarding physicochemical characteristics, sensory attributes, probiotic viability, and volatile organic compounds (VOCs). Also, probiotic viability, pH, total titratable acidity (TTA), moisture content, water activity, and texture were determined for 10 days of storage. GF-SB based on rice and amaranth was formulated and cooked at 90 ± 2 °C for 40 min. Three types of GF-SB were studied: control, with 30% sourdough fermented using Lactiplantibacillus plantarum NRRL B-4496 (GF-P), and with sourdough and encapsulated Limosilactobacillus reuteri DSM 17938 (GF-PC). The encapsulation yield was 94.9%. The viability of both probiotics was drastically reduced after steamed cooking, with losses ranging from 6 to 8 log₁₀ CFU/g. Sourdough decreased the pH (from 6.04 to 5.48–5.71) and hardness (control 46 N, sourdough ~25 N) while increasing lactic and acetic acids, moisture content (control 38%, sourdough ~46%), and water activity. Sourdough and probiotic capsules did not affect volume (~1.24 cm³/g), width-to-height ratio (~2.4), color, or sensory attributes. The VOCs revealed higher relative abundances of certain yeast-derived higher alcohols and oxidation-related carbonyl-trapping derivatives in control GF-SB, whereas bread with sourdough showed higher levels of long-chain hydrocarbons and esters, such as heptacosane and decanoic acid decyl ester. During the storage, Lpb. plantarum increased to ~3 log₁₀ CFU/g and Lim. reuteri remained steady. pH and TTA (0.03–0.04%) remained constant during storage. After 10 days of storage, hardness increased significantly (p < 0.05) in all GF-SB, doubling the initial values. Moisture content remained constant, while water activity decreased in GF-P (Δ = 0.025) and the control (Δ = 0.015). The use of sourdough in GF-SB improved texture, moisture content, and VOCs without modifying physical and sensory properties. Full article

(This article belongs to the Special Issue Innovations in Gluten Free (GF) Bread Production Through Fortification with Functional Supplements)

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16 pages, 1288 KB

Open AccessArticle

Genome Mining of Acinetobacter nosocomialis J2 Using Artificial Intelligence Reveals a Highly Efficient Acid Phosphatase for Phosphate Solubilisation

by Kaixu Chen, Huiling Huang, Xiao Yu, Jing Zhang, Chunming Zhou, Zhong Yao, Zheng Xu, Yang Liu and Yang Sun

Fermentation 2026, 12(1), 64; https://doi.org/10.3390/fermentation12010064 - 21 Jan 2026

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Abstract

Excessive application of chemical fertilisers has led to soil phosphorus immobilisation and aquatic eutrophication, making the development of highly efficient acid/neutral phosphatases crucial for sustainable phosphorus utilisation. In this study, we systematically investigated strain J2, which was isolated from phosphate-contaminated soil in Laoshan, [...] Read more.

Excessive application of chemical fertilisers has led to soil phosphorus immobilisation and aquatic eutrophication, making the development of highly efficient acid/neutral phosphatases crucial for sustainable phosphorus utilisation. In this study, we systematically investigated strain J2, which was isolated from phosphate-contaminated soil in Laoshan, Nanjing, China. 16S rRNA gene sequence analysis identified this strain as Acinetobacter nosocomialis J2, with 99.78% sequence similarity. Whole-genome sequencing generated a 3.83 Mb genome with a GC content of 38.59%, revealing multiple phospho-metabolism-related enzyme genes, including phospholipase C and α/β-hydrolases. A large language model–based protein representation learning strategy was employed to mine acid/neutral phosphatase genes from the genome, in which the model learned contextual and functional features from known phosphatase sequences and was used to identify semantically similar genes within the J2 genome. This approach predicted nine phosphatase candidate sequences, including AnACPase, a putative acid/neutral phosphatase. Biochemical characterisation showed that AnACPase exhibits optimal activity at pH 6.0 and 50 °C, with a K_m value of 0.2454 mmol/L for the p-NPP substrate, indicating high substrate affinity. Mn²⁺ and Ni²⁺ significantly enhanced enzyme activity, whereas Cu²⁺ and Zn²⁺ strongly inhibited it. Soil remediation experiments further validated the application potential of AnACPase, which solubilised 171.56 mg/kg of phosphate within seven days. Overall, this study highlights the advantages of deep learning-assisted genome mining for functional enzyme discovery and provides a novel technological pathway for the bioremediation of phosphorus-polluted soils. Full article

(This article belongs to the Special Issue Innovations in Microbial Enzyme Production: From AI-Driven Design to Industrial Bioprocessing)

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18 pages, 2848 KB

Open AccessArticle

Enhanced Squalene Production by Thraustochytrium sp. RT2316-16 by Polyphenols from Barley Bagasse

by Paris Paredes, Javiera Iturra and Carolina Shene

Fermentation 2026, 12(1), 63; https://doi.org/10.3390/fermentation12010063 - 21 Jan 2026

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Abstract

Squalene, a hydrocarbon with several industrial applications, is obtained from plants, animals, and microorganisms. Oleaginous thraustochytrids are also potential sources of squalene. In eukaryotes, squalene, an intermediary in the sterol/cholesterol pathway, accumulates when the activity of squalene epoxidase or an Alternative SQualene Epoxidase [...] Read more.

Squalene, a hydrocarbon with several industrial applications, is obtained from plants, animals, and microorganisms. Oleaginous thraustochytrids are also potential sources of squalene. In eukaryotes, squalene, an intermediary in the sterol/cholesterol pathway, accumulates when the activity of squalene epoxidase or an Alternative SQualene Epoxidase (AltSQE) is inhibited. The objective of this study was to evaluate the polyphenols extracted from barley bagasse for enhancement of the squalene content in Thraustochytrium sp. RT2316-16. In the media supplemented with terbinafine, an antifungal compound known as an inhibitor of squalene epoxidase, or the polyphenols from barley bagasse 72 h after inoculation, the squalene concentration was 308.7 ± 0.8 and 286.5 ± 0.1 mg L⁻¹ after 168 h, respectively, whereas in the control medium, it was 85.6 ± 0.2 mg L⁻¹. The final concentrations of the lipid-free biomass (4.5 ± 0.1 g L⁻¹) and total lipids (2.5 ± 0.3 g L⁻¹) were not affected by the polyphenols from barley bagasse; on the contrary, the concentration of total lipids in the terbinafine treatment was 30% lower than in the control. In RT2316-16, the gene coding for AltSQE, which is not found in all thraustochytrids, was upregulated under the control treatment, whereas its relative expression was not affected by terbinafine. The squalene accumulation in RT2316-16 in response to the treatment with polyphenols and the antifungal agent makes this strain a promising source of the triterpenoid. Full article

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

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22 pages, 1002 KB

Open AccessArticle

Effect of Fermentation on Phytochemical, Antioxidant, Functional, and Pasting Properties of Selected Legume Flours

by Janet Adeyinka Adebo

Fermentation 2026, 12(1), 62; https://doi.org/10.3390/fermentation12010062 - 21 Jan 2026

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Abstract

This study investigated the effect of fermentation time (24 and 48 h) on the pH, titratable acidity (TTA), phytochemicals, antioxidants, phenolic compounds, colour, functional, pasting, and thermal properties of flours from selected legumes (mung beans, haricot beans, butter beans, and black beans). The [...] Read more.

This study investigated the effect of fermentation time (24 and 48 h) on the pH, titratable acidity (TTA), phytochemicals, antioxidants, phenolic compounds, colour, functional, pasting, and thermal properties of flours from selected legumes (mung beans, haricot beans, butter beans, and black beans). The pH dropped significantly (p ≤ 0.05) after 48 h (6.61–4.91) of fermentation, with a corresponding increase in TTA, which ranged from 0.3 to 1.28 g lactic acid/100 g sample. Colour analysis showed that fermentation caused a decrease in L* values (2.97–23.86% reduction), with the highest reduction observed in black bean flour (23.86% at 24 h), along with an increase in the browning index. The total phenolic content increased significantly (p ≤ 0.05) in all the samples, with the most pronounced increase observed in mung bean 24 h (6.85 mg GAE/g). Similarly, the values for total flavonoid increased from 2.26 to 6.48 mg QE/g, and antioxidant activities such as DPPH ranged from 45.04 to 74.51%, FRAP from 1.65 to 8.03 Mm TE/g, and ABTS from 60.86 to 90.01%. Ultra-high performance liquid chromatography–photodiode array quantification of the targeted phenolic compounds showed a significant increase, with the highest notable increase for trans-ferulic acid in mung bean (330% after 48 h). Water absorption capacity generally showed an increase, whereas bulk density ranged from 0.55 to 0.91 g/cm³ and decreased in all legumes. There were differences in the pasting properties of the selected legumes. The peak time of unfermented butter bean was 33.08 min and remained constant at 33.15 min at 24 and 48 h of fermentation. Thermal analysis indicated the alteration of gelatinization parameters, with a decrease in peak temperature, whereas higher gelatinization enthalpy was observed. Findings from this study show that fermentation with the starter cultures can significantly improve the bioactive compound and functional properties of legume flours and thus act as potential ingredients in functional food development. Full article

(This article belongs to the Special Issue Fermented Cereals and Legumes: Innovation for the Development and Characterization of Functional Foods)

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14 pages, 9871 KB

Open AccessArticle

Sugar and Ethanol Conversion of Recovered Whole and Degermed Corn Kernel Fibers Pretreated with Sodium Carbonate

by Valerie García-Negrón and David B. Johnston

Fermentation 2026, 12(1), 61; https://doi.org/10.3390/fermentation12010061 - 21 Jan 2026

Viewed by 377

Abstract

Corn fermentation in biorefineries produces residual biomass and by-products, particularly corn kernel fiber and outgassed carbon dioxide (CO₂), that have value-added potential for improving sugar and bioethanol conversions. Recovered corn kernel fiber contains lignocellulosic components which can be made accessible by [...] Read more.

Corn fermentation in biorefineries produces residual biomass and by-products, particularly corn kernel fiber and outgassed carbon dioxide (CO₂), that have value-added potential for improving sugar and bioethanol conversions. Recovered corn kernel fiber contains lignocellulosic components which can be made accessible by pretreating the biomass with an alkaline sodium carbonate solution made with captured CO₂ and then used as supplemental biomass in corn ethanol production. In this work, different ratios of whole and degermed corn kernel fibers are pretreated and mixed with corn to be evaluated as beneficial ingredients in bioethanol co-fermentation. Sugar yields from enzymatic hydrolysis demonstrate the pretreatment promotes saccharification reaching over 70% total sugar conversion for the whole corn fibers. During co-fermentation, 10 and 20% corn solid loadings significantly increased ethanol yields while additional corn fiber loadings increased sugar yields. Conversion rates and yields were similar between the whole and degermed corn fibers supporting how a single recovery design can benefit multiple corn streams. Full article

(This article belongs to the Collection Bioconversion of Lignocellulosic Materials to Value-Added Products)

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21 pages, 7012 KB

Open AccessArticle

Effects of Different Electric-Field Intensities on Nitrogen Transformation and Bacterial Community Structure During Biochar Aerobic Composting

by Xiaoyun Lian, Lingling Chen, Hongmei Zhang, Deguo Kong, Ling Zhou, Weiguo Xu, Dongping Gao, Kunquan Li and Minghang Cheng

Fermentation 2026, 12(1), 60; https://doi.org/10.3390/fermentation12010060 - 20 Jan 2026

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Abstract

In this study, the effects of electric-field intensity on N transformation during aerobic composting of biochar/pig manure were investigated. Four experimental groups were established under different applied voltages: 0 V (Group CK); 2 V (Group L); 4 V (Group M); and 5 V [...] Read more.

In this study, the effects of electric-field intensity on N transformation during aerobic composting of biochar/pig manure were investigated. Four experimental groups were established under different applied voltages: 0 V (Group CK); 2 V (Group L); 4 V (Group M); and 5 V (Group H). The physicochemical properties of compost, as well as the nitrogen content and its existing forms in the compost, were systematically analyzed. The underlying mechanisms were further explored from the microscopic perspective by analyzing the pore structure of biochar and the microbial diversity in compost. The results showed that the total nitrogen content in compost increased by 5.66–20.87% with the application of the electric field. Cumulative NH₃ emissions decreased by 37.43%, 31.35%, and 40.95% in groups L, M, and H, respectively, while the NO₂ content decreased by 40.73%, 87.93%, and 94.44%, respectively, reducing the N losses during composting. The electric field significantly promoted the migration of nutrients from the compost to the surface of cotton stalk biochar. It also enhanced the microporous structure and adsorption capacity of cotton stalk biochar, thereby facilitating interfacial deposition and N immobilization. The amplification and sequencing of 16S rRNA gene further revealed that Ruminofilibacter, norank_f_MWH-CFBk5, and HN-HF0106 were the key bacterial genera affecting the gas emissions during aerobic composting. Among them, Ruminofilibacter and HN-HF0106 promoted the emission of N₂O, while norank_f_MWH-CFBk5 and Planktosalinus reduced NH₃ emission. This finding indicates that the electric field regulated N transformation and promoted N retention in compost by inhibiting the reproduction of denitrifying bacteria and increasing the abundance of nitrifying and nitrogen-fixing bacteria. This study confirms that electric field and biochar synergistically affect the nitrogen immobilization and waste resource utilization by optimizing the metabolic pathways of microorganisms and the structural characteristics of biochar. Full article

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26 pages, 1496 KB

Open AccessArticle

Novel Double-Layer Microencapsulated Phytosynbiotic Derived from Probiotics and Tiliacora triandra Extract for Application in Broiler Production

by Manatsanun Nopparatmaitree, Noraphat Hwanhlem, Watchrapong Mitsuwan, Atichat Thongnum, Payungsuk Intawicha, Juan J. Loor and Tossaporn Incharoen

Fermentation 2026, 12(1), 59; https://doi.org/10.3390/fermentation12010059 - 19 Jan 2026

Viewed by 518

Abstract

The global shift toward antibiotic-free poultry production has created an urgent need for sustainable feed additives that promote gut health and productivity. This study aimed to develop and evaluate a novel double-layered microencapsulated phytosynbiotic (DMP) comprising Tiliacora triandra extract, probiotics, and cereal by-products [...] Read more.

The global shift toward antibiotic-free poultry production has created an urgent need for sustainable feed additives that promote gut health and productivity. This study aimed to develop and evaluate a novel double-layered microencapsulated phytosynbiotic (DMP) comprising Tiliacora triandra extract, probiotics, and cereal by-products using lyophilization. In Experiment 1, we investigated the effects of cell wall materials (corn, defatted rice bran, and wheat bran) and different particle sizes (0.6 and 1.0 mm) on the physicochemical characteristics and probiotic encapsulation efficiency. Results revealed that wheat bran, particularly at the smaller particle size of 0.6 mm, enhanced probiotic viability, probiotic stability under simulated gastrointestinal and thermal conditions, and nutrient retention. Compared with other materials, wheat bran also provided superior powder flowability, lower density, and favorable color attributes. In Experiment 2, we assessed the influence of probiotic strains (P. acidilactici, Lactiplantibacillus plantarum TISTR 926, and Streptococcus thermophilus TISTR 894) on functional properties of the DMP. All strains exhibited high encapsulation efficiency and stability during gastrointestinal simulation, thermal exposure, and storage. However, P. acidilactici had superior fermentation kinetics and produced greater levels of beneficial short-chain fatty acids, especially acetic and butyric acids. Antibacterial activity was strain-dependent, with notable inhibitory effects against Gram-positive pathogens, primarily through bacteriostatic mechanisms. Overall, these findings confirm that the developed DMP formulations effectively stabilize probiotics and bioactive phytochemicals, offering a promising strategy for enhancing gut health and performance in antibiotic-free broiler production systems. Full article

(This article belongs to the Special Issue Fermentation Technology for Animals in Thailand: From Feed to Metabolites)

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5 pages, 142 KB

Open AccessEditorial

Application of Fermentation Technology in Animal Nutrition: 2nd Edition

by Siran Wang, Lin Sun, Lei Chen and Jie Bai

Fermentation 2026, 12(1), 58; https://doi.org/10.3390/fermentation12010058 - 19 Jan 2026

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Abstract

Fermentation technology has long been applied in animal nutrition worldwide, with its application primarily focused on animal feed [...] Full article

(This article belongs to the Special Issue Application of Fermentation Technology in Animal Nutrition: 2nd Edition)

18 pages, 1211 KB

Open AccessArticle

Modulation of Alcohol Content in Wines Using Mixed Cultures

by María Belén Listur, Valentina Martín, Laura Fariña, Eduardo Boido, Eduardo Dellacassa, Francisco Carrau and Karina Medina

Fermentation 2026, 12(1), 57; https://doi.org/10.3390/fermentation12010057 - 19 Jan 2026

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Abstract

Reducing the alcohol content of wines has received increasing attention, and various strategies have been proposed for this aim. In this study, non-Saccharomyces yeasts isolated from Uruguayan vineyards were screened to identify strains with low ethanol production for use in mixed cultures. [...] Read more.

Reducing the alcohol content of wines has received increasing attention, and various strategies have been proposed for this aim. In this study, non-Saccharomyces yeasts isolated from Uruguayan vineyards were screened to identify strains with low ethanol production for use in mixed cultures. Twenty-six strains belonging to six species were evaluated, considering key oenological parameters such as ethanol and glycerol production, glucose and fructose consumption, and absence of organoleptic defects. Based on these criteria, three strains from two genera were selected: Starmerella bacillaris (Sb1 and Sb2) and Metschnikowia fructicola (Mf2). In pure cultures, Starmerella bacillaris showed high sugar consumption along with high glycerol production. Subsequently, co-inoculation and sequential inoculation conditions were tested by combining the selected strains with commercial Saccharomyces cerevisiae (Sc). With Mf2 + Sc sequential inoculation, high sugar consumption, increased glycerol production, and a significant reduction in ethanol were observed compared to the control. For Starmerella bacillaris, only Sb1 achieved consistent alcohol reductions in sequential strategies. With co-inoculation, both strains reduced ethanol by 0.2–1% v/v, although only Sb1 showed complete sugar depletion. Overall, the results demonstrate a marked dependence of fermentation behavior on the strain and highlight the importance of studying biocompatibility and inoculation strategy in mixed cultures. Full article

(This article belongs to the Special Issue Applications of Microbial Biodiversity in Wine Fermentation)

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21 pages, 7411 KB

Open AccessArticle

Potential of Conversion of Cassava Processing Residues by Yeasts to Produce Value-Added Bioproducts

by Andreia Massamby, Johanna Blomqvist, Su-lin L. Leong, Yashaswini Nagaraj, Bettina Müller, Volkmar Passoth, Lucas Tivana, Custódia Macuamule and Mats Sandgren

Fermentation 2026, 12(1), 56; https://doi.org/10.3390/fermentation12010056 - 19 Jan 2026

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Abstract

Cassava is a major starch crop in Africa, generating substantial amounts of solid (peels and fibres) and liquid (process press water) residues that remain underutilised, particularly in smallholder and semi-industrial processing units. In Mozambique, where cassava is a staple and processed primarily by [...] Read more.

Cassava is a major starch crop in Africa, generating substantial amounts of solid (peels and fibres) and liquid (process press water) residues that remain underutilised, particularly in smallholder and semi-industrial processing units. In Mozambique, where cassava is a staple and processed primarily by local farmer associations, these residues—readily available and low-cost feedstocks—have significant potential for value-added applications. This study evaluated the potential of enzymatically hydrolysed cassava residues—peel and fibre hydrolysates—as substrates for independent yeast fermentations targeting microbial lipid and ethanol production. Rhodotorula toruloides CBS 14 efficiently converted sugars from both hydrolysates, producing up to 17.14 g L⁻¹ of cell dry weight (CDW) and 35% intracellular lipid content from the peel hydrolysate, and 16.5 g L⁻¹ CDW with 50% lipids from the fibre hydrolysate. Supplementation with ammonium sulphate accelerated sugar utilisation and reduced fermentation time but did not significantly increase the biomass or lipid yields. Saccharomyces cerevisiae J672 fermented the available sugars anaerobically, achieving ethanol yields of 0.45 ± 0.03 g g⁻¹ glucose from peels and 0.37 ± 0.06 g g⁻¹ glucose from fibres. These findings highlight the regional relevance of valorising cassava processing residues in Mozambique and demonstrate a dual-product valorisation strategy, whereby the same feedstocks are converted into either microbial lipids or ethanol through independent fermentations. This approach supports the sustainable, low-cost utilisation of agro-industrial residues, contributing to circular bioeconomy principles and enhancing the environmental and economic value of local cassava value chains. Full article

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12 pages, 1231 KB

Open AccessArticle

Hydroponically Sprouted Grains: Effects on In Situ Ruminal Nutrient Degradation, Fractional Disappearance Rate, and Effective Ruminal Degradation

by Gerald K. Salas-Solis, Ana Carolina S. Vicente, Jose A. Arce-Cordero, Martha U. Siregar, Mikayla L. Johnson, James R. Vinyard, Richard R. Lobo, Efstathios Sarmikasoglou and Antonio P. Faciola

Fermentation 2026, 12(1), 55; https://doi.org/10.3390/fermentation12010055 - 18 Jan 2026

Cited by 1 | Viewed by 460

Abstract

This study aimed to evaluate in situ ruminal nutrient degradation, fractional disappearance rate, and effective ruminal degradation of hydroponically sprouted barley, wheat, and triticale. Two ruminally canulated lactating cows were used in a complete randomized block design with four treatments and nine incubation [...] Read more.

This study aimed to evaluate in situ ruminal nutrient degradation, fractional disappearance rate, and effective ruminal degradation of hydroponically sprouted barley, wheat, and triticale. Two ruminally canulated lactating cows were used in a complete randomized block design with four treatments and nine incubation times (0, 2, 4, 8, 12, 24, 48, 72, and 240 h). Treatments were corn silage (control), and sprouted barley, triticale, and wheat. Quadruplicate samples (5 g each) were placed in Dacron bags and incubated in the rumen. Then, bags were rinsed and spun, dried (48 h × 55 °C; 3 h × 105 °C), and weighed to determine residual dry matter (DM). Data were analyzed using mixed models (MIXED, SAS 9.4) with treatment, time, and their interaction as fixed effects, and cow and replicate (cow) as random effects. Denominator degrees of freedom were adjusted using the Kenward–Roger method, and means were separated by Tukey–Kramer. Significance was declared at p ≤ 0.05 and tendencies at 0.05 < p ≤ 0.10. Sprouted triticale and wheat treatments had a greater rapidly soluble fraction for DM (p < 0.01), the greatest fractional disappearance rate for DM (p < 0.01) and neutral detergent fiber (NDF; p < 0.01), and greater effective ruminal degradability (ERD) for DM (p < 0.01) and crude protein (CP; p < 0.01). Sprouted wheat also had the greatest ERD for NDF (p < 0.01). In contrast, sprouted barley had the lowest rapidly soluble fractions for DM (p < 0.01), NDF (p < 0.01), and CP (p < 0.01), lower fractional disappearance rate for DM (p < 0.01) and NDF (p < 0.01) than sprouted triticale and wheat, and the lowest ERD for DM (p < 0.01) and CP (p < 0.01). Overall, sprouted triticale and wheat had greater in situ ruminal nutrient degradation, effective ruminal degradation, and nutrient degradation kinetics, indicating their potential for inclusion in dairy cattle diets to improve nutrient degradability. Full article

(This article belongs to the Special Issue Ruminal Fermentation: 2nd Edition)

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37 pages, 2650 KB

Open AccessReview

Considerations of Bacterial Robustness and Stability to Improve Bioprocess Design

by Pauline Pijpstra, Stéphane E. Guillouet, Petra Heidinger, Robert Kourist and Nathalie Gorret

Fermentation 2026, 12(1), 54; https://doi.org/10.3390/fermentation12010054 - 16 Jan 2026

Viewed by 863

Abstract

Harnessing nature’s ingenuity with microorganisms for industrial production is an attractive solution to today’s climate concerns. Nature’s innate diversity allows the production of many value-added chemicals and can be expanded on through genetic engineering. Although the use of microbial cell factories (MCFs) has [...] Read more.

Harnessing nature’s ingenuity with microorganisms for industrial production is an attractive solution to today’s climate concerns. Nature’s innate diversity allows the production of many value-added chemicals and can be expanded on through genetic engineering. Although the use of microbial cell factories (MCFs) has been extremely successful at lab scale, the numbers of successful bioprocesses remain limited. High cell densities and long cultivation times lead to reductions in productivity over the course of the cultivation through the effects of genetic and expression instability of the strain. This instability leads to population diversification. In this review, we explore the roots of genetic instability in microorganisms, focusing on prokaryotic bioprocesses, and how organisms cope with this instability. We spotlight single-cell detection methods capable of monitoring populations within the bioprocess both in- and on-line. We also examine different approaches to minimizing population diversification, both through strain development and bioprocess engineering. With this review, we highlight the fact that population-averaged metrics overlook the single-cell stresses driving genetic and functional instability, leading to an overestimation of microbial bioprocess robustness. High-throughput single-cell monitoring in industry-like conditions remains essential to identify and select truly stable microbial cell factories and bioprocesses. Full article

(This article belongs to the Special Issue Scale-Up Challenges in Microbial Fermentation)

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17 pages, 3143 KB

Open AccessArticle

High Cell Density Fermentation Strategy for High-Level Soluble Expression of Glucagon-like Peptide-1 Analogue in Escherichia coli

by Sushmita R. Kumar, Esha Shukla and Gaurav Pandey

Fermentation 2026, 12(1), 53; https://doi.org/10.3390/fermentation12010053 - 16 Jan 2026

Viewed by 709

Abstract

Glucagon-like peptide-1 (GLP-1) is an incretin hormone and therapeutic agent for Type II diabetes mellitus. However, recombinant production in E. coli yields insufficient quantities, increasing manufacturing costs and limiting patient access. Improving yield and productivity is crucial to make GLP-1 treatments more affordable. [...] Read more.

Glucagon-like peptide-1 (GLP-1) is an incretin hormone and therapeutic agent for Type II diabetes mellitus. However, recombinant production in E. coli yields insufficient quantities, increasing manufacturing costs and limiting patient access. Improving yield and productivity is crucial to make GLP-1 treatments more affordable. An optimized bioprocess was developed to enhance the yield of recombinant GLP-1 (rGLP-1) analogues. Expression constructs encoding monomeric and concatemeric GLP-1 fused to GST were designed. Batch fermentations of these clones at varying pre-induction specific growth rates guided the fed-batch strategy for yield enhancement. The specific yield of monomer construct exhibited higher yields than the concatemer. Process optimization achieved a specific yield (Yp/x) of 116.7 mg/g, a dry cell weight of 88.9 g/L, and a volumetric yield of 10.3 g/L. The specific productivity of soluble rGLP-1 reached 0.4 g/L/h. Purification via affinity chromatography and enterokinase cleavage yielded authentic GLP-1 peptide confirmed by Western blot and mass spectrometry. The developed high-yield fermentation process significantly enhances rGLP-1 productivity in E. coli, potentially reducing upstream production costs by 20–30% and enabling wider accessibility to affordable GLP-1 therapies. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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14 pages, 1056 KB

Open AccessArticle

Kinetics of Lactic Acid, Acetic Acid and Ethanol Production During Submerged Cultivation of a Forest Litter-Based Biofertilizer

by Sophie Nafil, Lucie Miché, Loris Cagnacci, Martine Martinez and Pierre Christen

Fermentation 2026, 12(1), 52; https://doi.org/10.3390/fermentation12010052 - 16 Jan 2026

Viewed by 408

Abstract

Fermented forest litter (FFL) is a biofertilizer obtained by anaerobic fermentation of forest litter combined with agricultural by-products. Its production involves an initial one-month solid-state fermentation of oak litter mixed with whey, molasses and wheat bran, followed by a one-week submerged fermentation-called the [...] Read more.

Fermented forest litter (FFL) is a biofertilizer obtained by anaerobic fermentation of forest litter combined with agricultural by-products. Its production involves an initial one-month solid-state fermentation of oak litter mixed with whey, molasses and wheat bran, followed by a one-week submerged fermentation-called the “activation” phase-during which the solid FFL is fermented with sugarcane molasses diluted in water. This study aimed to evaluate the effects storage duration (6, 18 and 30 months), and temperature (ambient and 29 °C) on the activation phase. For this purpose, pH, sugar consumption and metabolite production dynamics were monitored. Under all experimental conditions, the pH dropped to values close to 3.5, sucrose was rapidly hydrolyzed, and glucose was preferentially consumed over fructose. Fructose was metabolized only after glucose was depleted, suggesting the involvement of fructophilic microorganisms. The time-course evolution of lactic acid (LA) concentration was adequately fitted by the Gompertz model (R² > 0.970). The highest LA_max concentration (6.30 g/L) and production rate (2.16 g/L·d) were obtained with FFL stored for 6 months. Acetic acid (AA) and ethanol were also detected reaching maxima values of 1.19 g/L and 0.96 g/L, respectively. Their profiles varied depending on the experimental conditions. Notably, the AA/LA ratio increased with the age of the FFL. Overall, sugar consumption and metabolite production were significantly slower at ambient temperature, than at 29 °C. These results contribute to a better understanding of the metabolic dynamics during FFL activation and highlight key parameters that should be considered to optimize future biofertilizer production processes. Full article

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

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16 pages, 4282 KB

Open AccessArticle

Expression Profiling of Recombinant Biofilm Surface Layer Protein A in Pichia pastoris Under Constant Dissolved Oxygen and Oxygen-Limited Fermentation

by Lan Yu, Lei Zhang, Junbo Zhou, Yixuan Li, Yuwei Guo and Rongkai Guo

Fermentation 2026, 12(1), 51; https://doi.org/10.3390/fermentation12010051 - 15 Jan 2026

Viewed by 433

Abstract

BslA (Biofilm surface layer protein A), a highly hydrophobic lipoprotein from Bacillus spp., self-assembles at fluid interfaces to form a crystalline film that reduces surface tension. In this study, we selected Pichia pastoris as a eukaryotic system for expressing recombinant BslA identified in [...] Read more.

BslA (Biofilm surface layer protein A), a highly hydrophobic lipoprotein from Bacillus spp., self-assembles at fluid interfaces to form a crystalline film that reduces surface tension. In this study, we selected Pichia pastoris as a eukaryotic system for expressing recombinant BslA identified in Bacillus paralicheniformis BL-1. The secretory expression of recombinant BslA in the P. pastoris GS115 strain under the AOX1 promoter was confirmed in shake-flask cultivation. Next, two fed-batch fermentation strategies, constant dissolved oxygen strategy (DO-stat) and oxygen-limited fed-batch (OLFB) strategy, in a 5 L scale, were compared. The DO-stat process led to late-stage cell death and product degradation, limiting yields. Switching to the OLFB process by removing the glycerol feeding phase mitigated this issue, allowing extended fermentation and increasing the final recombinant BslA concentration to 657 mg/L. This study establishes P. pastoris with an OLFB strategy as an effective system for secreting recombinant BslA protein, providing a basis for future industrial-scale production. Full article

(This article belongs to the Section Yeast)

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15 pages, 760 KB

Open AccessArticle

Combined Antimicrobial Effects of Lactiplantibacillus plantarum-Derived Biosurfactant and Supercritical CO₂-Extracted Rosmarinus officinalis Against Multidrug-Resistant Staphylococcus aureus

by Najla Haddaji, Nadia Leban, Wissal Rouihem, Ali Saud Almalg, Muna O. Alamoudi, Hatem Majdoub and Abdelkarim Mahdhi

Fermentation 2026, 12(1), 50; https://doi.org/10.3390/fermentation12010050 - 15 Jan 2026

Viewed by 496

Abstract

The global prevalence of antibiotic-resistant bacteria, such as Staphylococcus aureus, presents a substantial challenge to public health, necessitating the development of innovative therapeutic strategies to combat these infections. This study examined the synergistic effects of a biosurfactant (BS) derived from Lactiplantibacillus plantarum [...] Read more.

The global prevalence of antibiotic-resistant bacteria, such as Staphylococcus aureus, presents a substantial challenge to public health, necessitating the development of innovative therapeutic strategies to combat these infections. This study examined the synergistic effects of a biosurfactant (BS) derived from Lactiplantibacillus plantarum and a novel extract from Rosmarinus officinalis (RoME) obtained through supercritical CO₂ extraction against S. aureus sourced from the microbiology laboratory at King Salman Hospital in Ha’il, Saudi Arabia. Antibacterial efficacy was determined using minimum inhibitory concentration (MIC) assays, assessments of bacterial membrane damage, and qRT-PCR analysis of genes associated with antibiotic resistance. The findings revealed that the S. aureus strain exhibited resistance to multiple antibiotics with a resistance score of 0.44. RoME and BS demonstrated MICs of 0.125 mg/mL and 0.5 mg/mL, respectively. The assays indicated significant bacterial membrane damage and reduced expression of the norA, mdeA, and sel genes, which are implicated in resistance and virulence, respectively. The combination of BSs with plant extracts may provide innovative approaches for treating infections caused by multidrug-resistant bacteria, highlighting the potential of probiotic-derived BSs in combination with plant extracts. 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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17 pages, 1391 KB

Open AccessArticle

Effect of Sequential Inoculation with Metschnikowia pulcherrima and Saccharomyces cerevisiae on the Chemical Composition of American Pale Ale (APA) Beer

by Julian Karaulli, Nertil Xhaferaj, Bruno Testa, Rosaria Cozzolino, Cristina Matarazzo, Antonio de Nigris, Francesca Coppola, Mamica Ruci, Mariantonietta Succi, Renata Kongoli, Onejda Kyçyk, Fatbardha Lamçe, Ilir Lloha, Kapllan Sulaj and Massimo Iorizzo

Fermentation 2026, 12(1), 49; https://doi.org/10.3390/fermentation12010049 - 14 Jan 2026

Viewed by 541

Abstract

Recent studies have shown that the use of non-Saccharomyces yeasts, either alone or in co-fermentation with Saccharomyces cerevisiae, can enhance the development of specialty beers with distinctive compositional characteristics. This study aimed to evaluate the main compositional and sensory differences between [...] Read more.

Recent studies have shown that the use of non-Saccharomyces yeasts, either alone or in co-fermentation with Saccharomyces cerevisiae, can enhance the development of specialty beers with distinctive compositional characteristics. This study aimed to evaluate the main compositional and sensory differences between American Pale Ale (APA) beers produced using the commercial strain S. cerevisiae US-05 as a single starter (Test 1), and those produced through sequential inoculation with Metschnikowia pulcherrima 62 followed by S. cerevisiae US-05 (Test 2). Analyses focused on key chemical parameters and volatile compounds at the end of primary fermentation (F1) and after 20 days of refermentation at 20 °C (F2). After F1, Test 2 samples showed higher concentrations of glycerol and higher alcohols (isoamyl alcohol, benzeneethanol) and lower concentrations of esters (isoamyl acetate, ethyl hexanoate, ethyl octanoate) compared to Test 1. After F2, the differences in higher alcohol content became less significant, whereas ester concentrations, particularly ethyl acetate and ethyl octanoate, were significantly higher in Test 2. Sensory evaluation revealed that beers from Test 2 exhibited more pronounced floral and fruity notes and achieved higher overall scores in the panel assessment. These findings indicate that sequential inoculation with M. pulcherrima 62 followed by S. cerevisiae enhances both the chemical complexity and sensory appeal of APA beers, highlighting the strain’s potential as a valuable tool for developing specialty beers with unique aromatic profiles. Full article

(This article belongs to the Special Issue Microbiological Challenges in Malt and Beer Production)

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41 pages, 3378 KB

Open AccessReview

Current Trends of Cellulosic Ethanol Technology from the Perspective of Industrial Development

by Gabrielly Karla Silva Santos, Carlos Eduardo de Farias Silva, Brígida Maria Villar da Gama, Josimayra Almeida Medeiros, Mathieu Brulé, Albanise Enide da Silva, Renata Maria Rosas Garcia Almeida, Daniele Vital Vich, Rafail Isemin, Xianhua Guo and Ana Karla de Souza Abud

Fermentation 2026, 12(1), 48; https://doi.org/10.3390/fermentation12010048 - 14 Jan 2026

Viewed by 817

Abstract

Driven by the energy transition within the framework of the United Nations Framework Convention on Climate Change, second-generation (2G) ethanol stands out as a technical and sustainable alternative to fossil fuels. Although first-generation ethanol, produced from saccharine and starchy feedstocks, represents an advance [...] Read more.

Driven by the energy transition within the framework of the United Nations Framework Convention on Climate Change, second-generation (2G) ethanol stands out as a technical and sustainable alternative to fossil fuels. Although first-generation ethanol, produced from saccharine and starchy feedstocks, represents an advance in mitigating emissions, its expansion is limited by competition with areas destined for food production. In this context, 2G ethanol, obtained from residual lignocellulosic biomass, emerges as a strategic route for diversifying and expanding the renewable energy matrix. Thus, this work discusses the current state of 2G ethanol technology based on the gradual growth in production and the consolidation of this route over the last few years. Industrial second-generation ethanol plants operating around the world demonstrate the high potential of agricultural waste as a raw material, particularly corn straw in the United States, which offers a lower cost and significant yield in the production of this biofuel. Similarly, in Brazil, sugarcane by-products, especially bagasse and straw, are consolidating as the main sources for 2G ethanol, integrated into the biorefinery concept and the valorization of by-products obtained during the 2G ethanol production process. However, despite the wide availability of lignocellulosic biomass and its high productive potential, the consolidation of 2G ethanol is still conditioned by technical and economic challenges, especially the high costs associated with pretreatment stages and enzymatic cocktails, as well as the formation of inhibitory compounds that compromise the efficiency of the process. Genetic engineering plays a particularly important role in the development of microorganisms to produce more efficient enzymatic cocktails and to ferment hexoses and pentoses (C₆ and C₅ sugars) into ethanol. In this scenario, not only are technological limitations important but also public policies and tax incentives, combined with the integration of the biorefinery concept and the valorization of (by)products, which prove fundamental to reducing costs, increasing process efficiency, and ensuring the economic viability and sustainability of second-generation ethanol. Full article

(This article belongs to the Special Issue Microbial Upcycling of Organic Waste to Biofuels and Biochemicals)

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14 pages, 923 KB

Open AccessArticle

Isolation, Identification and Spoilage Capability of Specific Spoilage Organisms on Silage During Aerobic Deterioration

by Xin-Yu Liang, Tao Shao, Hao-Peng Liu, Jun-Feng Li, Zhi-Hao Dong and Jie Zhao

Fermentation 2026, 12(1), 47; https://doi.org/10.3390/fermentation12010047 - 14 Jan 2026

Viewed by 413

Abstract

Silage is a core roughage resource for ruminant production, but aerobic deterioration caused by microorganisms severely reduces its nutritional value and increases microbial risk. This study aimed to isolate and identify specific spoilage organisms (SSOs) from Napier grass silages during aerobic deterioration and [...] Read more.

Silage is a core roughage resource for ruminant production, but aerobic deterioration caused by microorganisms severely reduces its nutritional value and increases microbial risk. This study aimed to isolate and identify specific spoilage organisms (SSOs) from Napier grass silages during aerobic deterioration and evaluate their spoilage capability. Based on morphological observation, physiological and biochemical tests, and ITS rDNA sequence analysis, four SSOs were obtained as Trichosporon asahii (TA32), Nakaseomyces glabratus (NG38), Candida tropicalis (CT39), and Pichia kudriavzevii (PK41) with high lactate-assimilating and spoilage capacity. All four strains were facultative anaerobic yeast and exhibited robust growth within the range of 25–40 °C and pH 3.5–6.5. To verify their spoilage capability, these purified strains were inoculated into Napier grass silage and exposed to air. Fermentation and chemical parameters were monitored at 0, 2, 5, and 9 days. Results showed that silages inoculated with PK41 or TA32 exhibited the lowest aerobic stability with most rapid increase in pH (p < 0.05), while the control (CON) remained the highest aerobic stability (p < 0.05). These results provide a theoretical basis for developing targeted preservation technologies to extend the shelf-life of silage. Full article

(This article belongs to the Special Issue Research Progress of Rumen Fermentation, 2nd Edition)

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11 pages, 406 KB

Open AccessArticle

Effect of Different Types of Propolis on the Quality Characteristics of Fermented Sucuk

by Zeyneb Sadıgzade, Recep Kara and Ali Sorucu

Fermentation 2026, 12(1), 46; https://doi.org/10.3390/fermentation12010046 - 13 Jan 2026

Viewed by 385

Abstract

Fermented sucuk is a fermented food product widely consumed and enjoyed by people in Türkiye. Spices and other additives are used in the production of fermented sucuk. Due to the increasing demand for natural and healthy food consumption, the need for natural additives [...] Read more.

Fermented sucuk is a fermented food product widely consumed and enjoyed by people in Türkiye. Spices and other additives are used in the production of fermented sucuk. Due to the increasing demand for natural and healthy food consumption, the need for natural additives is also growing. Propolis is naturally obtained from honeybee hives and consists of bioactive compounds with antimicrobial and antioxidant properties. Studies have been conducted on the addition of propolis to various meat and meat products, as well as other food products. However, no studies have been found on the addition of propolis to fermented sucuk. The aim was to investigate the effect of different types of propolis (red, green, brown) on the quality characteristics of fermented sucuks. Microbiological, physicochemical, textural and sensory analyses were performed on the sucuk samples produced. It was observed that propolis did not have an adverse effect on the analysis results of propolis-added sucuks. In particular, it was determined that the growth of pathogenic bacteria was inhibited in propolis-added sucuk, resulting in low TBARS values, and other analyses yielded results in line with these standards. Based on these findings, the addition of propolis has been shown to have a positive effect on the quality of fermented sucuk. Full article

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

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15 pages, 5093 KB

Open AccessArticle

Single-Cell Tracking of Brewing Yeast Dynamics in Baijiu Fermentation Using GFP-Labeled Engineered Saccharomyces cerevisiae FSC01

by Yeyu Huang, Jie Meng, Xinglin Han, Dan Huang, Ruiqi Luo and Deliang Wang

Fermentation 2026, 12(1), 45; https://doi.org/10.3390/fermentation12010045 - 13 Jan 2026

Viewed by 489

Abstract

In view of the technical bottleneck of microbial dynamic monitoring during the solid-state fermentation of traditional Baijiu, this study introduced green fluorescent protein (GFP) labeling technology into the dominant Saccharomyces cerevisiae of Jiang-flavored Baijiu to construct the chromosomal integration engineering strain named FSC01. [...] Read more.

In view of the technical bottleneck of microbial dynamic monitoring during the solid-state fermentation of traditional Baijiu, this study introduced green fluorescent protein (GFP) labeling technology into the dominant Saccharomyces cerevisiae of Jiang-flavored Baijiu to construct the chromosomal integration engineering strain named FSC01. By designing an integrated recombinant plasmid containing the GFP gene and the geneticmycin resistance gene, an engineered strain that stably expresses fluorescent proteins was obtained by electroconversion. Flow cytometry verification showed that FSC01 showed excellent linear responses in the pure microbial system (R² = 0.998) and the complex matrix of Baijiu jiupei (R² = 0.981), with a detection limit of 10² cells/mL, and the detection cycle was shortened to 10 min. Solid-state fermentation simulation experiments show that the inoculation volume of FSC01 of 10⁵ cells/kg can not only ensure the effective identification of fluorescence signals, but also does not significantly interfere with the growth and growth patterns of the original yeast (p > 0.05), which is highly consistent with the results of the traditional plate counting method. Dynamic monitoring shows that Saccharomyces cerevisiae during fermentation presents a typical succession pattern of “increase first and then decrease”, reaching a peak on the 7th day (1.2 × 10⁷ cells/g), which is positively correlated with the base alcohol yield rate (26.7%). Compared with metagenomic (72 h) and PMA-qPCR (4 h) methods, this technology breaks through the limitations of specificity and timeliness of live bacteria detection, and provides a single-cell-level dynamic analysis tool for the digitization of traditional brewing processes. In the future, it will be expanded to monitor key functional microorganisms such as lactic acid bacteria through a multi-color fluorescent labeling system, and optimized pretreatment to eliminate starch granule interference, and promote the in-depth application of synthetic biology technology in the traditional fermentation industry. Full article

(This article belongs to the Section Fermentation Process Design)

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17 pages, 1037 KB

Open AccessArticle

Sustainable Production of Bioactive Chitosan from Fermented Rice Bran and Husk via Solid-State Fermentation

by Helena L. Gouvea, Meritaine da Rocha, Eliezer Q. Oreste, Sergiane C. Barbosa, Larine Kupski and Ednei G. Primel

Fermentation 2026, 12(1), 44; https://doi.org/10.3390/fermentation12010044 - 12 Jan 2026

Viewed by 519

Abstract

Sustainable production of high-quality chitosan from agro-industrial by-products remains a challenge in biotechnology. This study aimed to improve chitosan production from fermented rice bran and rice husk using Rhizopus oryzae in solid-state fermentation (SSF), and evaluated the physicochemical and biological properties of the [...] Read more.

Sustainable production of high-quality chitosan from agro-industrial by-products remains a challenge in biotechnology. This study aimed to improve chitosan production from fermented rice bran and rice husk using Rhizopus oryzae in solid-state fermentation (SSF), and evaluated the physicochemical and biological properties of the resulting biopolymer. A full factorial design (2³) was applied to assess key fermentation parameters, including moisture content, substrate composition, and nitrogen supplementation. Among the tested conditions, the highest chitosan yield was at 55% moisture, 50% rice husk, and 1.8 g/L urea. The obtained chitosan was characterized for degree of deacetylation (DD) using FTIR and NMR, and molecular weight (MW) by viscometry. Antimicrobial activity was tested against Gram-positive and Gram-negative bacteria, and antioxidant capacity was measured via DPPH and ABTS assays. The chitosan exhibited a high DD (86.4 ± 0.6%) and a MW of 59.65 kDa, values comparable to commercial standards. It showed strong antimicrobial activity, particularly against Gram-negative strains. Antioxidant assays confirmed concentration-dependent activity, reaching 94% DPPH inhibition at 5.00 mg mL⁻¹. Overall, the results demonstrate that agro-industrial residues can be effectively transformed into high-quality, bioactive chitosan, offering a sustainable and circular alternative to conventional production routes. Full article

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

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44 pages, 1670 KB

Open AccessReview

Synergistic Interactions Between Bacteria-Derived Metabolites and Emerging Technologies for Meat Preservation

by Carlos Alberto Guerra, André Fioravante Guerra and Marcelo Cristianini

Fermentation 2026, 12(1), 43; https://doi.org/10.3390/fermentation12010043 - 10 Jan 2026

Viewed by 769

Abstract

Considering the challenges associated with implementing emerging technologies and bacterial-derived antimicrobial metabolites at an industrial scale in the meat industry, this comprehensive review investigates the interactions between lactic acid bacteria-producing antimicrobial metabolites and emerging food preservation technologies applied to meat systems. By integrating [...] Read more.

Considering the challenges associated with implementing emerging technologies and bacterial-derived antimicrobial metabolites at an industrial scale in the meat industry, this comprehensive review investigates the interactions between lactic acid bacteria-producing antimicrobial metabolites and emerging food preservation technologies applied to meat systems. By integrating evidence from microbiology, food engineering, and molecular physiology, the review characterizes how metabolites-derived compounds exert inhibitory activity through pH modulation, membrane permeabilization, disruption of proton motive force, and interference with cell wall biosynthesis. These biochemical actions are evaluated in parallel with the mechanistic effects of high-pressure processing, pulsed electric fields, cold plasma, irradiation, pulsed light, ultrasound, ohmic heating and nanotechnology. Across the literature, consistent patterns of synergy emerge: many emerging technologies induce structural and metabolic vulnerabilities in microbial cells, thereby amplifying the efficacy of antimicrobial metabolites while enabling reductions in process intensity. The review consolidates these findings to elucidate multi-hurdle strategies capable of improving microbial safety, extending shelf life, and preserving the physicochemical integrity of meat products. Remaining challenges include optimizing combinational parameters, ensuring metabolite stability within complex matrices, and aligning integrated preservation strategies with regulatory and industrial constraints. Full article

(This article belongs to the Special Issue Microbial Fermentation: A Sustainable Approach to Food Production)

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33 pages, 415 KB

Open AccessReview

Cheese Whey Valorization via Microbial Fermentation (Lactic Acid Bacteria, Yeasts/Fungi, and Microalgae), Postbiotic Production, and Whey-Based Encapsulation Strategies

by Tlalli Uribe-Velázquez, Cesar E. Najar-Almanzor, Francisco R. Osuna-Orozco, Félix Arto-Paz, Cristian Valdés, Luis Eduardo Garcia-Amezquita, Danay Carrillo-Nieves and Tomás García-Cayuela

Fermentation 2026, 12(1), 42; https://doi.org/10.3390/fermentation12010042 - 9 Jan 2026

Cited by 1 | Viewed by 996

Abstract

Cheese whey, the major by-product of the dairy industry, poses an environmental challenge due to its high organic load but simultaneously represents a nutrient-dense matrix suitable for biotechnological valorization. This review synthesizes recent advances positioning whey as (i) a fermentation substrate for lactic [...] Read more.

Cheese whey, the major by-product of the dairy industry, poses an environmental challenge due to its high organic load but simultaneously represents a nutrient-dense matrix suitable for biotechnological valorization. This review synthesizes recent advances positioning whey as (i) a fermentation substrate for lactic acid bacteria, yeasts/fungi, and microalgae, enabling the production of functional biomass, organic acids, bioethanol, exopolysaccharides, enzymes, and wastewater bioremediation; (ii) a platform for postbiotic generation, supporting cell-free preparations with functional activities; and (iii) a food-grade encapsulating material, particularly through whey proteins (β-lactoglobulin, α-lactalbumin), which can form emulsions, gels, and films that protect biotics and bioactive compounds during processing, storage, and gastrointestinal transit. We analyze key operational variables (whey type and pretreatment, supplementation strategies, batch and continuous cultivation modes), encapsulation routes (spray drying, freeze-drying, and hybrid protein–polysaccharide systems), and performance trade-offs relevant to industrial scale-up. Finally, we outline future directions, including precision fermentation, mixed-culture processes with in situ lactase activity, microfluidics-enabled encapsulation, and life-cycle assessment, to integrate product yields with environmental performance. Collectively, these strategies reframe whey from a high-impact waste into a circular bioeconomy resource for the food, nutraceutical, and environmental sectors. Full article

(This article belongs to the Special Issue Exploring Fermentation Strategies for the Valorization of Food By-Products and Their Bioactive Potential)

16 pages, 1359 KB

Open AccessArticle

Theobroma bicolor (Pataxte) Fermentation: A Novel Source of Promising Probiotic Lactic Acid Bacteria

by María Fernanda Rosas-Ordaz, Beatriz Pérez-Armendáriz, María de Lourdes Meza-Jiménez, Laura Contreras-Mioni and Gabriel Abraham Cardoso-Ugarte

Fermentation 2026, 12(1), 41; https://doi.org/10.3390/fermentation12010041 - 9 Jan 2026

Viewed by 577

Abstract

This study reports the isolation, identification, and functional characterization of lactic acid bacteria (LAB) obtained from the endogenous fermentation of Theobroma bicolor (pataxte), an understudied Mesoamerican species with unexplored biotechnological potential. Five lactic acid bacteria strains were isolated and selected for comprehensive in [...] Read more.

This study reports the isolation, identification, and functional characterization of lactic acid bacteria (LAB) obtained from the endogenous fermentation of Theobroma bicolor (pataxte), an understudied Mesoamerican species with unexplored biotechnological potential. Five lactic acid bacteria strains were isolated and selected for comprehensive in vitro evaluation of their probiotic attributes. The assays included antimicrobial activity (disk diffusion and minimum inhibitory concentration), tolerance to simulated gastrointestinal conditions, and comparison of survival between non-encapsulated and bigel-encapsulated cells during digestion. All five isolates demonstrated notable antimicrobial activity against Escherichia coli ATCC 25922, Salmonella Enteritidis ATCC 13076, and Staphylococcus aureus ATCC 25923. Strain S1.B exhibited exceptional resistance to acidic pH (2.0) and bile salts, reaching 3.61 ± 0.00 log (CFU/mL) after gastrointestinal simulation. The strain was identified as Lactiplantibacillus pentosus via 16S rRNA gene sequencing, marking the first documented isolation of this species from pataxte fermentation. Bigel encapsulation markedly enhanced its survival, increasing viability to 5.08 ± 0.10 log (CFU/mL). These findings identify Lactiplantibacillus pentosus 124-2 as a potential probiotic candidate originating from pataxte fermentation and highlight bigel systems as powerful vehicles for bacterial protection. Collectively, this work expands the microbial biodiversity known in Theobroma fermentations and underscores their promise for future functional food applications. Full article

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

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42 pages, 8148 KB

Open AccessReview

Revitalizing Urban Rivers with Biotechnological Strategies for Sustainability and Carbon Capture

by Igor Carvalho Fontes Sampaio, Virgínia de Lourdes Carvalho dos Santos, Isabela Viana Lopes de Moura, Geisa Louise Moura Costa, Estela Sales Bueno de Oliveira, Jailton Azevedo and Paulo Fernando de Almeida

Fermentation 2026, 12(1), 40; https://doi.org/10.3390/fermentation12010040 - 9 Jan 2026

Viewed by 803

Abstract

Urban rivers are essential resources for human societies; however, their degradation poses serious public health, economic, and environmental risks. Conventional physical remediation methods can partially mitigate pollution by targeting specific contaminants, but they are often limited in scope, lack long-term sustainability, and fail [...] Read more.

Urban rivers are essential resources for human societies; however, their degradation poses serious public health, economic, and environmental risks. Conventional physical remediation methods can partially mitigate pollution by targeting specific contaminants, but they are often limited in scope, lack long-term sustainability, and fail to restore ecological functions. In contrast, biotechnological approaches integrated with ecological engineering offer sustainable and nature-based solutions for river depollution, conservation, and revitalization. Although these strategies are supported by a solid theoretical framework and successful applications in other aquatic systems, their large-scale implementation in urban rivers has only recently begun to gain momentum. This review critically examines strategies for the revitalization of polluted urban rivers, progressing from conventional remediation techniques to advanced biotechnological interventions. It highlights real-world applications, evaluates their advantages and limitations, and discusses policy frameworks and management strategies required to promote the broader adoption of biotechnological solutions for sustainable urban river restoration. The goal is to demonstrate the transformative potential of integrated biotechnological, eco-engineering, and data-driven approaches—particularly microbial, phytoplankton-based, and biofilm systems—to reduce energy demand and carbon emissions in urban river restoration while highlighting the need for scalable designs, adaptive management, and supportive regulatory frameworks to enable their large-scale implementation. Full article

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

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24 pages, 1753 KB

Open AccessArticle

Valorization of Produced Water from Oilfields for Microbial Exopolysaccharide Synthesis in Stirred Tank Bioreactors

by Igor Carvalho Fontes Sampaio, Pamela Dias Rodrigues, Isabela Viana Lopes de Moura, Maíra dos Santos Silva, Luiz Fernando Widmer, Cristina M. Quintella, Elias Ramos-de-Souza and Paulo Fernando de Almeida

Fermentation 2026, 12(1), 39; https://doi.org/10.3390/fermentation12010039 - 8 Jan 2026

Viewed by 640

Abstract

The increasing volume of produced water (PW) generated by oil extraction activities has intensified the need for environmentally sustainable strategies that enable its reuse and valorization. Biotechnological approaches, particularly those involving the microbial production of value-added compounds, offer a promising route for transforming [...] Read more.

The increasing volume of produced water (PW) generated by oil extraction activities has intensified the need for environmentally sustainable strategies that enable its reuse and valorization. Biotechnological approaches, particularly those involving the microbial production of value-added compounds, offer a promising route for transforming PW from an industrial waste into a useful resource. In this context, bacterial exopolysaccharides (EPS) have gained attention due to their diverse functional properties and applicability in bioremediation, bioprocessing and petroleum-related operations. This study evaluated the potential of Lelliottia amnigena to synthesize EPS using oilfield PW as a component of the culture medium in stirred-tank bioreactors. Three conditions were assessed: a control using distilled water (dW), PW diluted to 25% (PW25%) and dialyzed PW (DPW). Batch experiments were conducted for 24 h, during which biomass growth, EPS accumulation and dissolved oxygen dynamics were monitored. Post-cultivation analyses included elemental and monosaccharide composition, scanning electron microscopy and rheological characterization of purified EPS solutions. EPS production varied among treatments, with dW and DPW yielding approximately 9.6 g L⁻¹, while PW25% achieved the highest productivity (17.55 g L⁻¹). The EPS samples contained fucose, glucose and mannose, with compositional differences reflecting the influence of PW-derived minerals. Despite reduced apparent viscosity under PW25% and DPW conditions, the EPS exhibited physicochemical properties suitable for biotechnological applications, including potential use in fucose recovery, drilling fluids and lubrication systems in the petroleum sector. The EPS also demonstrated substantial adsorption capacity, incorporating salts from PW and contributing to contaminant removal. This study demonstrates that PW can serve both as a substrate and as a source of functional inorganic constituents for microbial EPS synthesis, supporting an integrated approach to PW valorization. These findings reinforce the potential of EPS-based bioprocesses as sustainable green technologies that simultaneously promote waste mitigation and the production of high-value industrial bioproducts. Full article

(This article belongs to the Special Issue Wastewater and Industrial By-Products as Inputs for the Production of Microbial Exopolysaccharides and Surfactants)

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27 pages, 4143 KB

Open AccessArticle

The Effects of Trichilia claussenii Extract on the Efficacy of Entomopathogenic Fungi Produced by Submerged Fermentation

by Lissara Polano Ody, Leonardo Ramon de Mesquita Gomes, Gustavo Ugalde, Franciéle dos Santos Soares, Jerson Vanderlei Carús Guedes, Denise Tonato, Marcio Antonio Mazutti, Marcus Vinícius Tres and Giovani Leone Zabot

Fermentation 2026, 12(1), 38; https://doi.org/10.3390/fermentation12010038 - 8 Jan 2026

Viewed by 672

Abstract

The search for sustainable pest management alternatives has intensified due to the risks of chemical pesticides. Entomopathogenic fungi and plant extracts, rich in insecticidal secondary metabolites, are among the most promising approaches. Integrating these agents can enhance complementary mechanisms and reduce environmental impact. [...] Read more.

The search for sustainable pest management alternatives has intensified due to the risks of chemical pesticides. Entomopathogenic fungi and plant extracts, rich in insecticidal secondary metabolites, are among the most promising approaches. Integrating these agents can enhance complementary mechanisms and reduce environmental impact. This study evaluated the insecticidal potential of fungi produced by submerged fermentation (Beauveria bassiana, Metarhizium anisopliae, Trichoderma asperelloides, Isaria javanica, and Cordyceps fumosorosea) applied alone and combined with Trichilia claussenii extract against Euschistus heros and Spodoptera frugiperda. Fermentation showed good fungal adaptation and high sporulation, especially B. bassiana (8.33 × 10⁸ spores mL⁻¹) and T. asperelloides (9.42 × 10⁷ spores mL⁻¹). Adding the plant extract increased colony-forming units, notably for M. anisopliae (7.40 × 10⁷ CFU mL⁻¹) and B. bassiana (1.55 × 10⁸ CFU mL⁻¹). In bioassays, cell suspensions were more effective than isolated metabolites, reaching 97.8% mortality for E. heros and 91.5% for S. frugiperda with B. bassiana plus extract. These results indicate that combining entomopathogenic fungi with T. claussenii extract is a promising strategy for developing efficient and sustainable biopesticides, contributing directly to integrated pest management practices with reduced environmental impact. Full article

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Open AccessArticle

Bentonite as a Natural Additive to Enhance Fermentation Quality and Reduce Losses in Corn Silage

by Bruna dos Santos Souza, Juliana Silva de Oliveira, Alberto Jefferson da Silva Macêdo, João Paulo de Farias Ramos, Liliane Pereira Santana, Luana Milena Pinheiro Rodrigues, Paloma Gabriela Batista Gomes, Anderson Lopes Pereira, Evandro de Sousa da Silva and Edson Mauro Santos

Fermentation 2026, 12(1), 37; https://doi.org/10.3390/fermentation12010037 - 7 Jan 2026

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Abstract

This study evaluated the effects of different bentonite levels on the fermentation profile, losses, microbial populations, aerobic stability, and chemical composition of corn silage. A 5 × 3 factorial completely randomized design was used, with five bentonite inclusion levels (0, 20, 40, 60, [...] Read more.

This study evaluated the effects of different bentonite levels on the fermentation profile, losses, microbial populations, aerobic stability, and chemical composition of corn silage. A 5 × 3 factorial completely randomized design was used, with five bentonite inclusion levels (0, 20, 40, 60, and 80 g/kg) and three storage times (30, 90, and 180 days), with four repetitions. Significant additive × storage time interactions were detected for key parameters. After 180 days, pH increased to 4.20 at 80 g/kg bentonite, while lactic acid peaked at 54.02 g/kg DM with 60 g/kg at 90 days. Acetic acid reached 22.36 g/kg DM at 180 days, and lactic acid bacteria ranged from 3.42 to 7.43 log CFU/g. Yeast counts were lowest (≤0.57 log CFU/g) at 180 days with 20–60 g/kg bentonite. Dry matter rose to 311 g/kg with 60 g/kg bentonite, whereas soluble carbohydrates decreased from 123.9 to 68.2 g/kg DM. Aerobic stability markedly improved, reaching 142.06 h with 40 g/kg bentonite at 180 days, almost three times higher than the control. The inclusion of bentonite in corn silage at levels of 20–60 g/kg of fresh matter effectively enhances silage quality during 180 days of storage by improving fermentation characteristics, microbial stability, and aerobic stability. Full article

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

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Fermentation, Volume 12, Issue 1 (January 2026) – 66 articles

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