Fermentation

16 pages, 1239 KB

Open AccessArticle

Producing Chlorella vulgaris in Ricotta Cheese Whey Substrate

by Nahuel Casá, Paola Alvarez, Ricardo Mateucci, Maximiliano Argumedo Moix and Marina de Escalada Pla

Fermentation 2025, 11(12), 705; https://doi.org/10.3390/fermentation11120705 - 18 Dec 2025

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Abstract

Ricotta cheese whey (RCW) is a by-product with nutritional potential, but its use in the human diet is limited due to its high salinity. Chlorella vulgaris can use RCW as a substrate to enhance biomass productivity. The aim of this work was to [...] Read more.

Ricotta cheese whey (RCW) is a by-product with nutritional potential, but its use in the human diet is limited due to its high salinity. Chlorella vulgaris can use RCW as a substrate to enhance biomass productivity. The aim of this work was to evaluate different conditions for C. vulgaris growth in RCW, during scaling-up analysis. After preliminary assays to select growth conditions, two systems were prepared as follows: 500 mL Erlenmeyer flasks (control-system) and a 3 L Bioreactor. Microfiltrated RCW was used as a substrate for C. vulgaris LPMA39 production. Biomass was measured and productivity at 96 h, cell growth kinetics behaviour, biomass biochemical characterisation, and the efficiency of nutrient removal were determined. Both systems presented the same biomass concentration at 96 h (2.2–2.8 g·L⁻¹) and productivity (0.021–0.027 g·L⁻¹·h⁻¹). Nevertheless, 11 h lag-period for cell adaptation to the 3 L Bioreactor was required; thereafter, cells grew faster (µ_max: 0.32 ± 0.08 h⁻¹) than control-system. Finally, slight but significantly lower C_max: 2.14 ± 0.08 was obtained when comparing it to control-system. Lipids, proteins, and pigment contents decreased by the scaling-up; meanwhile, higher reduction in chemical oxygen demand (COD), total phosphorus, and total nitrogen were recorded in the 3 L Bioreactor. Identifying the operating conditions that improve C. vulgaris performance in non-diluted RCW remains a challenge from a sustainability standpoint. Full article

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

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20 pages, 2373 KB

Open AccessArticle

Isolation, Characterisation and Vitamin B12 Production Optimization of P. freudenreichii from Turkish Traditional Kars Gravyer

by Akif Emre Kavak, Zerya Beyza Alimoğlu, Akın Özdemir and Enes Dertli

Fermentation 2025, 11(12), 704; https://doi.org/10.3390/fermentation11120704 - 18 Dec 2025

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Abstract

In this study, nine different Propionibacterium freudenreichii strains were isolated from Kars Gravyer produced by traditional methods in Turkey and identified by sequencing the 16S–23S intergenic region using species-specific primers. The isolated strains were examined in vitro for the presence of the β-galactosidase [...] Read more.

In this study, nine different Propionibacterium freudenreichii strains were isolated from Kars Gravyer produced by traditional methods in Turkey and identified by sequencing the 16S–23S intergenic region using species-specific primers. The isolated strains were examined in vitro for the presence of the β-galactosidase enzyme, autoaggregation ability, sensitivity against eight selected antibiotics and survivability under harsh conditions in order to determine their potential probiotic properties. After probiotic potentials were evaluated, an experimental design was made to optimize the production of vitamin B12 in a 3 L glass bioreactor P. freudenreichii NUV774. While all strains showed similar resistance (92–98%) to gastric juice (0.3% pepsin, pH 3.0), they showed resistance to intestinal fluid (0.1% pancreatin, 0.3% bile salt, pH 8.0) between 60% and 92%. It was determined that the viability after 3 and 6 h of incubation in 0.5% and 1% bile salt differed between strains. All isolates exhibited resistance to ciprofloxacin, ampicillin, and trimethoprim–sulphamethoxazole; however, most were sensitive to ofloxacin. Overall, P. freudenreichii strains showed resistance to the gastrointestinal tract, tolerance to pH 3.0, and high tolerance to bile salts. As a result of optimization, maximum vitamin B12 production was found to be 156.8 mg/L. The optimum operating conditions were calculated as temperature = 36.9 °C, aeration = 2.430 vvm, and agitation = 159.120 rpm. Hence, P. freudenreichii, as future probiotic strain candidates, will offer an alternative source to Lactobacillus, Bifidobacterium and some Bacillus spp. In addition, this study denoted that the alteration of the production of active vitamin B12 by P. freudenreichii occurs in a strain-dependent manner. Full article

(This article belongs to the Special Issue Microbial Metabolism Focusing on Bioactive Molecules)

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18 pages, 2462 KB

Open AccessArticle

Fe/Mn-Modified Biochar Facilitates Functional Microbial Enrichment for Efficient Glucose–Xylose Co-Fermentation and Biohydrogen Production

by Jianing Fan, Jiwen Wu, Ji Zhao, Hongsheng Hao, Yange Yu, Guangli Cao and Nanqi Ren

Fermentation 2025, 11(12), 703; https://doi.org/10.3390/fermentation11120703 - 18 Dec 2025

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Abstract

Biohydrogen production can be derived from low-value lignocellulosic biomass; however, in many biohydrogen producing systems, xylose is utilized less efficiently than glucose, which limits overall substrate conversion. To address this issue, Fe/Mn-modified biochar was employed to enhance dark fermentation of glucose–xylose mixed sugars, [...] Read more.

Biohydrogen production can be derived from low-value lignocellulosic biomass; however, in many biohydrogen producing systems, xylose is utilized less efficiently than glucose, which limits overall substrate conversion. To address this issue, Fe/Mn-modified biochar was employed to enhance dark fermentation of glucose–xylose mixed sugars, and its performance was compared with other inoculum treatments. The biochar addition achieved a hydrogen yield of 2.57 ± 0.10 mol-H₂/mol-sugar, representing 14.6% enhancement over untreated controls, while enabling complete substrate utilization across varying xylose proportions. Biochar supplementation also reduced the lag phase by 24.4% and increased hydrogen productivity by 47.3% in mixed-sugar cultivation. Integrated analyses of the experimental data revealed the dual role of Fe/Mn-modified biochar in constructing conductive extracellular polymeric substance networks and directing metabolic flux toward high-yield butyrate pathways. This work establishes Fe/Mn-biochar as a multifunctional microbial engineering tool that alleviates carbon catabolite repression and promotes the enrichment of hydrogen-producing bacteria (HPB), thereby providing a practical and effective strategy for enhanced biohydrogen production from lignocellulosic biomass. Full article

(This article belongs to the Section Industrial Fermentation)

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20 pages, 5398 KB

Open AccessArticle

Bioaugmentation Versus pH Adjustment in High-Load Food Waste Anaerobic Digestion: Divergent Microbial Responses and Methanogenesis Regulation

by Chenyu Piao, Zhe Wang, Keqian Zhao, Mengfei Du and Ke Wang

Fermentation 2025, 11(12), 702; https://doi.org/10.3390/fermentation11120702 - 18 Dec 2025

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Abstract

High organic loading is known to destabilize anaerobic digestion (AD). This study compared bioaugmentation and pH adjustment under increasing organic loading rate (OLR: 2.0, 4.0 and 6.0 gVS L⁻¹ d⁻¹), focusing on the responses of microbial structure, metabolic pathways, and [...] Read more.

High organic loading is known to destabilize anaerobic digestion (AD). This study compared bioaugmentation and pH adjustment under increasing organic loading rate (OLR: 2.0, 4.0 and 6.0 gVS L⁻¹ d⁻¹), focusing on the responses of microbial structure, metabolic pathways, and energy metabolism. Results demonstrated that bioaugmentation maintained stable methane production of 400.54 ± 10.08 and 374.15 ± 24.32 mL·g-VS⁻¹ at 4.0 and 6.0 gVS L⁻¹ d⁻¹, respectively, whereas control and pH-adjusted reactors failed at 4.0 gVS L⁻¹ d⁻¹. The acidified system restored methane yield from 86.30 to 382.13 mL·g-VS⁻¹ after bioaugmentation, whereas pH adjustment and feeding cessation were ineffective, failing to produce methane within 25 days. Microbial analysis showed bioaugmentation enriched Methanosarcina, enhanced hydrogenotrophic/methylotrophic methanogenesis, and strengthened syntrophy with syntrophic propionate-oxidizing bacteria (SPOB), reducing volatile fatty acid accumulation via reinforced syntrophic propionate/butyrate oxidation. Upregulation of osmoregulatory (nha, kdp, proP) and energy metabolism genes (eha, mvh, hdr) maintained osmotic balance and energy supply under high load. In contrast, pH adjustment downregulated SPOB and propionate oxidation genes, causing persistent acid inhibition. This study elucidated the distinct regulatory effects of bioaugmentation and pH adjustment on high-load AD systems, providing actionable strategies for both maintaining operational stability in high-load reactors and recovering methanogenesis in acid-inhibited systems. Full article

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

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15 pages, 915 KB

Open AccessArticle

Silymarin in the Diet of Dairy Cows and Its Impacts on Liver Health, Ruminal Fermentation, Productive Performance, and Milk Quality

by Pablo Vinicius Novakoski, Luisa Nora, Guilherme Luiz Deolindo, Gilnei Bruno da Silva, Daiane Manica, Margarete Dulce Bagatini and Aleksandro Schafer da Silva

Fermentation 2025, 11(12), 701; https://doi.org/10.3390/fermentation11120701 - 18 Dec 2025

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Abstract

The search for natural alternatives that improve the productive efficiency and metabolic state of dairy cows has driven the use of phytogenic compounds such as silymarin, a flavonolignan extracted from Silybum marianum L. Gaertn with recognized antioxidant, anti-inflammatory, and hepatoprotective properties. This study [...] Read more.

The search for natural alternatives that improve the productive efficiency and metabolic state of dairy cows has driven the use of phytogenic compounds such as silymarin, a flavonolignan extracted from Silybum marianum L. Gaertn with recognized antioxidant, anti-inflammatory, and hepatoprotective properties. This study evaluated the effects of silymarin supplementation on the productive performance; milk composition; and ruminal, hematological, biochemical, and oxidative parameters of lactating Jersey cows kept in a confined system with robotic milking. Twelve cows (230 ± 30 days in lactation; 22 ± 3.5 kg/day of milk) were distributed in a crossover design, receiving a control diet (GCON) or a diet supplemented with 5 g/cow/day of silymarin (GSIL) for 28 days in each stage. Silymarin intake did not alter dry matter intake, feed efficiency, or average milk production (p > 0.05), but it increased milk fat content (4.27 × 4.02%; p = 0.05) and, consequently, milk production corrected for 4% fat (24.4 × 23.2 kg/day; p = 0.05). In the rumen environment, cows in the GSIL group showed higher concentrations of acetic acid (57.4 × 48.4 nmol/L), and total short-chain fatty acids (100.2 × 89.4 nmol/L; p = 0.01). Regarding the biochemical profile, silymarin reduced gamma-glutamyltransferase and aspartate aminotransferase activities, as well as haptoglobin levels, indicating a hepatoprotective effect, combined with a lower inflammatory response in the liver. Oxidative status was improved by decreased levels of TBARS (lipid peroxidation) and reactive oxygen species, as well as myeloperoxidase activity in the serum of cows fed silymarin (p ≤ 0.05), but there was no difference between groups for superoxide dismutase activity and glutathione levels. The inclusion of silymarin in the diet of lactating Jersey cows improved the antioxidant and hepatic profile, increased milk fat content, and favored ruminal fermentation, suggesting metabolic and productive benefits in confined systems with high physiological demands. Full article

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

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20 pages, 2429 KB

Open AccessReview

Epipolythiodioxopiperazines: From Chemical Architectures to Biological Activities and Ecological Significance—A Comprehensive Review

by Qingqing Zhang, Mingyang Jia, Hongyi Li, Tingting Shi, Ying Xu, Taili Zhao, Lixin Zhang, Peipei Zhao and Xuekui Xia

Fermentation 2025, 11(12), 700; https://doi.org/10.3390/fermentation11120700 - 17 Dec 2025

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Abstract

Epipolythiodioxopiperazines (ETPs), characterized by a diketopiperazine (DKP) core bridged by disulfide or polysulfide bonds, exhibit exceptional structural diversity and functional adaptability. This review comprehensively explores their multifaceted properties, covering chemical structural characteristics, therapeutic application potential, and ecological functional value. Structural diversity arises from [...] Read more.

Epipolythiodioxopiperazines (ETPs), characterized by a diketopiperazine (DKP) core bridged by disulfide or polysulfide bonds, exhibit exceptional structural diversity and functional adaptability. This review comprehensively explores their multifaceted properties, covering chemical structural characteristics, therapeutic application potential, and ecological functional value. Structural diversity arises from variations in the core DKP scaffold, sulfur bridge connectivity patterns, and additional modifications. Biosynthesis involves initial DKP assembly, enzyme-catalyzed sulfur incorporation and oxidation to form the signature sulfur bridge of ETPs, diversification by tailoring enzymes, and distinct regulatory mechanisms. ETPs possess diverse biological activities, including cytotoxicity, antitumor activity, antimicrobial properties, and immunomodulatory functions. From an ecological standpoint, ETPs mediate fungal–host interactions and influence competition and symbiosis within fungal communities. Furthermore, this review also addresses the current challenges and outlines future research directions. In summary, as a class of significant compounds spanning the fields of chemistry, biology, medicine, and ecology, ETPs deserve focused attention for their research value and application prospects. Full article

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

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16 pages, 3996 KB

Open AccessArticle

FTIR Spectroscopy, a New Approach to Evaluating Caseinolytic Activity of Probiotic Lactic Acid Bacteria During Goat Milk Fermentation and Storage

by Juan José Carol Paz, Ana Yanina Bustos and Ana Estela Ledesma

Fermentation 2025, 11(12), 699; https://doi.org/10.3390/fermentation11120699 - 17 Dec 2025

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Abstract

Goat milk can be a vehicle for beneficial microorganisms, such as probiotic lactic acid bacteria (LAB). During lactic fermentation, the hydrolysis of milk proteins can improve their nutritional properties and sensory attributes and even have beneficial health effects. The objective of this study [...] Read more.

Goat milk can be a vehicle for beneficial microorganisms, such as probiotic lactic acid bacteria (LAB). During lactic fermentation, the hydrolysis of milk proteins can improve their nutritional properties and sensory attributes and even have beneficial health effects. The objective of this study was to evaluate the caseinolytic activity of LAB strains with probiotic potential and to monitor the changes induced by fermentation and during storage in milk components using Fourier transform infrared (FTIR) spectroscopy. First, the proteolytic activity of 36 LAB strains isolated from dairy products was qualitatively assessed. Then, 17 strains with probiotic potential and moderate to high proteolytic activity were selected for further analysis. Casein proteolysis was found to be strain-dependent, with a decrease in total protein concentration ranging from 28% to 87% and an increase in amino acids ranging from 29% to 88%. Furthermore, a notable difference was observed in the amide bands in the FTIR spectra between the beginning and end of incubation, showing a decrease in the intensities of the bands attributed to proteins. In fermented goat milk, LAB growth resulted in a final count between 0.62 and 2.6 log CFU/mL, a 0.29 to 2.0 drop in pH, and lactic acid production between 0.20 and 1 g/L. FTIR spectra revealed time-dependent modifications in amide I and II bands accompanied by a marked reduction in carbohydrate content and an increase in lactic acid signal. After 21 days of storage, the viability of the strains, pH, and lactic acid in the fermented milks were not substantially modified. These results highlight the potential of lactic fermentation with strains selected for their probiotic potential as an approach to producing value-added goat milk products, as well as the usefulness of FTIR spectroscopy for characterizing complex systems such as goat milk. Full article

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

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17 pages, 676 KB

Open AccessArticle

Bioyogurt Enriched with Provitamin A Carotenoids and Fiber: Bioactive Properties and Stability

by Camila Bernal-Castro, Ángel David Camargo-Herrera, Carolina Gutiérrez-Cortés and Consuelo Díaz-Moreno

Fermentation 2025, 11(12), 698; https://doi.org/10.3390/fermentation11120698 - 16 Dec 2025

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Abstract

Recent research has focused on yogurts supplemented with plant-derived and apiculture ingredients to enhance functional properties. This study evaluates the symbiotic potential of provitamin A carotenoids, dietary fiber, and oligosaccharides from carrots, mangoes, and honeydew honey in probiotic-enriched bioyogurt. Formulations were assessed during [...] Read more.

Recent research has focused on yogurts supplemented with plant-derived and apiculture ingredients to enhance functional properties. This study evaluates the symbiotic potential of provitamin A carotenoids, dietary fiber, and oligosaccharides from carrots, mangoes, and honeydew honey in probiotic-enriched bioyogurt. Formulations were assessed during fermentation (45 °C ± 1 °C for 5 h) and refrigerated storage (4 °C ± 1 °C for 21 days). Probiotic and starter culture viability was determined using pour-plate counts on MRS agar. Physicochemical parameters including pH, titratable acidity, total soluble solids, water-holding capacity, and antioxidant metrics (total phenolics and carotenoids) were analyzed. After 21 days of storage, the probiotic culture (VEGE 092) reached 10.26 log CFU/mL and the starter culture (YOFLEX) achieved 8.66 log CFU/mL, maintaining therapeutic thresholds. Total carotenoid content increased significantly (p < 0.05) from 2.15 to 3.96 µg β-carotene/g, indicating synergistic interactions between lactic acid bacteria and plant-derived bioactive compounds. These findings demonstrate that combining plant-derived carotenoids, prebiotic fibers, and honeydew oligosaccharides effectively maintains probiotic viability and enhances antioxidant stability throughout fermentation and refrigerated storage, supporting the development of functional dairy products with improved nutritional profiles. Full article

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

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18 pages, 7100 KB

Open AccessArticle

Intraspecific Diversity of Saccharomyces cerevisiae Associated with Traditional Fermented Beverages in Chiapas, Mexico

by Maritza Tawas-Penagos, Ruth Percino-Daniel, José Alberto Narváez-Zapata, René Quezada-Romero, Anne Christine Gschaedler-Mathis and Alma Gabriela Verdugo-Valdez

Fermentation 2025, 11(12), 697; https://doi.org/10.3390/fermentation11120697 - 16 Dec 2025

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Abstract

Traditional fermented beverages from Chiapas, Mexico, represent an important source of microbial diversity, particularly of Saccharomyces cerevisiae. In native strains isolated from traditional fermented beverages, Saccharomyces cerevisiae has been observed to display distinct morphological and physiological traits; therefore, the aim of this [...] Read more.

Traditional fermented beverages from Chiapas, Mexico, represent an important source of microbial diversity, particularly of Saccharomyces cerevisiae. In native strains isolated from traditional fermented beverages, Saccharomyces cerevisiae has been observed to display distinct morphological and physiological traits; therefore, the aim of this study was to evaluate the population growth and the tolerance of twenty isolates to different stress factors such as temperature, osmotic pressure, and high ethanol concentrations, as well as the genetic variability through interdelta analysis, and to determine whether these physiological and molecular characteristics are associated with the type of beverage and the locality of origin. Differences were observed in tolerance to various factors, including high ethanol concentrations and elevated temperatures, as well as in the production of volatile compounds, with Taberna and Mezcal isolates showing notable performance. These isolates were able to withstand temperatures ranging from 43 to 45 °C and ethanol concentrations of up to 17% in Mezcal and Pox isolates, and 15% in Taberna isolates. High concentrations of isoamyl acetate and higher alcohols such as isoamyl alcohol were detected. In addition, the genetic variability of the isolates was evaluated, and its relationship with the type of beverage and the geographical origin of production was explored, including isolates obtained from Taberna, Mezcal, Pox, and Chicha de Chilacayote. Intraspecific variability was assessed through a retrotransposon-based analysis of the interdelta region using different primer combinations (δ1-δ2, δ12-δ21, and δ12-δ2). The generated banding patterns were analyzed using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), which enabled the identification of molecular variability patterns among the isolates. Furthermore, a UPGMA analysis was performed using physiological and compound production data, revealing a relationship between these characteristics and the geographical origin of the isolates. The results revealed a high degree of intraspecific variability, which was associated with both the type of beverage and the locality of origin of the isolates. Full article

(This article belongs to the Special Issue Yeasts as Microbial Cell Factories: Diversity, Biotechnology Potential and Applications)

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14 pages, 895 KB

Open AccessArticle

Adding Digestive Enzymes to Anaerobic Co-Digestion of Cattle Manure and Industrial Corn Grain Waste

by Laís Medeiros Cintra, Roberta Passini, Luana Alves Akamine, Kedinna Dias de Sousa, Frank Freire Capuchinho, Sérgio Botelho de Oliveira and Silvia Robles Reis Duarte

Fermentation 2025, 11(12), 696; https://doi.org/10.3390/fermentation11120696 - 16 Dec 2025

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Abstract

Brazil is one of the world’s largest producers of grains and cattle, activities that generate a large amount of organic waste, which has high potential for biogas and methane production. Cattle manure (CM) and industrial waste from corn processing are substrates with significant [...] Read more.

Brazil is one of the world’s largest producers of grains and cattle, activities that generate a large amount of organic waste, which has high potential for biogas and methane production. Cattle manure (CM) and industrial waste from corn processing are substrates with significant potential for biogas and methane generation, particularly through the process of anaerobic co-digestion (AcoD). This study aimed to assess the biogas and methane yield, as well as the stability of the AcoD process involving CM and corn grain residues (CG) derived from a grain processing agroindustry, in conjunction with the application of an enzyme complex. The experiment was conducted in plug-flow biodigesters, with a total volume of 28 L, under a semi-continuous feeding regime (OLR = 0.84 g vs. L d⁻¹) at ambient temperature. The findings indicated increases in daily biogas and methane production for AcoD, without the addition of enzymes, of 52.1% and 44.4%, respectively, in comparison to CM mono-digestion. The incorporation of the enzyme complex did not yield beneficial effects, irrespective of the substrate composition. The utilization of enzymes in semi-continuous biodigesters to enhance methane yields necessitates further investigation to achieve favorable outcomes and validate its efficiency. Full article

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

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27 pages, 778 KB

Open AccessReview

Yeast-Derived Biomolecules as Green Nanoplatforms for Sustainable Lignocellulosic Biorefineries

by Fabio P. Sanchez Vera, Naiara J. Clerici, Gabriela A. Lourenço, Sara B. Santa Rita, Kiara A. Garcia Bustos, Eduardo Florez Martinez, Guilherme O. Silva, Paulo R. Franco Marcelino, Julio César dos Santos and Silvio S. da Silva

Fermentation 2025, 11(12), 695; https://doi.org/10.3390/fermentation11120695 - 16 Dec 2025

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Abstract

Yeast-derived biomolecules are redefining the boundaries of green nanotechnology. Biosurfactants, exopolysaccharides, enzymes, pigments, proteins, and organic acids—when sourced from carbohydrate-rich lignocellulosic hydrolysates—offer a molecular toolbox capable of directing, stabilizing, and functionalizing nanoparticles (NPs) with unprecedented precision. Beyond their structural diversity and intrinsic biocompatibility, [...] Read more.

Yeast-derived biomolecules are redefining the boundaries of green nanotechnology. Biosurfactants, exopolysaccharides, enzymes, pigments, proteins, and organic acids—when sourced from carbohydrate-rich lignocellulosic hydrolysates—offer a molecular toolbox capable of directing, stabilizing, and functionalizing nanoparticles (NPs) with unprecedented precision. Beyond their structural diversity and intrinsic biocompatibility, these biomolecules anchor a paradigm shift: the convergence of biorefineries with nanotechnology to deliver multifunctional materials for the circular bioeconomy. This review explores: (i) the expanding portfolio of metallic and metal oxide NPs synthesized through yeast biomolecules; (ii) molecular-level mechanisms of reduction, capping, and surface tailoring that dictate NP morphology, stability, and reactivity; (iii) synergistic roles in intensifying lignocellulosic processes—from enhanced hydrolysis to catalytic upgrading; and (iv) frontier applications spanning antimicrobial coatings, regenerative packaging, precision agriculture, and environmental remediation. We highlight structure–function relationships, where amphiphilicity, charge distribution, and redox activity govern resilience under saline, acidic, and thermally harsh industrial matrices. Yet, critical bottlenecks remain: inconsistent yields, limited comparative studies, downstream recovery hurdles, and the absence of comprehensive life-cycle and toxicological evaluations. To bridge this gap, we propose a translational roadmap coupling standardized characterization with real hydrolysate testing, molecular libraries linking biomolecule chemistry to NP performance, and integrated techno-economic and environmental assessments. By aligning yeast biotechnology with nanoscience, we argue that yeast-biomolecule-driven nanoplatforms are not merely sustainable alternatives but transformative solutions for next-generation lignocellulosic biorefineries. Full article

(This article belongs to the Special Issue Yeast Biotechnology in Valorization of Waste and By-Products)

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14 pages, 1643 KB

Open AccessArticle

Use of Pichia manshurica as a Starter Culture for Spontaneous Cocoa Fermentation in Southern Bahia, Brazil

by Adriana Barros de Cerqueira e Silva, Eric de Lima Silva Marques, Rachel Passos Rezende, Cristiano Santana, Angelina Moreira Freitas, Maria Clara Bessa Souza, Carine Martins dos Santos, Adriana Cristina Reis Ferreira, Marianna Ramos Soares, Alberto Montejo Díaz, Ádanny Maia da Cruz Santos, Luan Melo Andrade, Louise Pereira Ramos, Carla Cristina Romano, João Carlos Teixeira Dias and Sérgio Eduardo Soares

Fermentation 2025, 11(12), 694; https://doi.org/10.3390/fermentation11120694 - 16 Dec 2025

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Abstract

To improve cocoa fermentation and the quality of its final products, microbial cultures with potential as starters were investigated. Yeasts were considered a promising option due to their adaptability to biotechnological processes and ease of laboratory manipulation. From 185 strains previously isolated from [...] Read more.

To improve cocoa fermentation and the quality of its final products, microbial cultures with potential as starters were investigated. Yeasts were considered a promising option due to their adaptability to biotechnological processes and ease of laboratory manipulation. From 185 strains previously isolated from spontaneous cocoa fermentation, those producing protease, amylase, and cellulase were identified. Strain CII87b (Pichia manshurica) exhibited the most favorable results and was evaluated for cytotoxicity using the MTT assay, showing no adverse effects. This culture was subsequently inoculated into freshly harvested cocoa almonds during the secondary (winter) harvest. The inoculum accelerated and increased the average fermentation temperature from 25 to 50 °C, reduced internal mold incidence, decreased defect rates, increased total fermentation, and resulted in a more desirable pH compared to the control. These findings demonstrate that the use of P. manshurica CII87b as a starter culture in winter harvests can improve fermentation efficiency and product quality, offering a biotechnological tool with potential benefits for cocoa producers and the chocolate industry. Full article

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

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12 pages, 307 KB

Open AccessArticle

Evaluation of Plant Essential Oils as Natural Alternatives to Monensin in In Vitro Ruminal Fermentation

by Amelia Barbosa Lima, Kemmily Lima de Almeida, Bruna Eduarda Teixeira de Lima, Khalid Haddi, Ludmila Couto Gomes Passetti, Gustavo Leão Rosado and Cláudia Braga Pereira Bento

Fermentation 2025, 11(12), 693; https://doi.org/10.3390/fermentation11120693 - 14 Dec 2025

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Abstract

Extensive growth promoter use in livestock production has raised concerns about their role in selective pressure on resistant microorganisms, driving interest in natural alternatives such as essential oils (EOs). This study aimed to evaluate the effects of tea tree, holy wood, and citronella [...] Read more.

Extensive growth promoter use in livestock production has raised concerns about their role in selective pressure on resistant microorganisms, driving interest in natural alternatives such as essential oils (EOs). This study aimed to evaluate the effects of tea tree, holy wood, and citronella EOs on in vitro ruminal fermentation. The study follows a completely randomized design with the following five treatments: control, monensin (5 μM), tea tree EO (50 mg/L), holy wood EO (50 mg/L), and citronella EO (50 mg/L), each conducted in triplicate. Incubations were performed at 39 °C for 48 h in the rumen fluid collected from fistulated cattle fed a 20:80 forage-to-concentrate diet. Notably, EOs exhibited no significant effects on pH, microbial protein production, total volatile fatty acids, or in vitro dry matter digestibility (p > 0.05). Tea tree and holy wood EOs enhanced deamination activity, and all treatments increased ammonia concentration compared with that in the control. Monensin treatment increased acetate concentration and reduced in vitro neutral detergent fiber digestibility; holy wood EO exhibited a similar trend. Altogether, the findings of this study suggest that EOs can selectively modulate the ruminal microbiota, influencing nitrogen metabolism and fermentation patterns without impairing rumen stability. Full article

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

19 pages, 306 KB

Open AccessArticle

In Vitro and In Situ Evaluation of White Mulberry (Morus alba) Pomace and Leaf: Fermentation Kinetics, Digestibility, and Potential as Alternative Ruminant Feed Sources

by Zekeriya Safa İnanç and Huzur Derya Arik

Fermentation 2025, 11(12), 692; https://doi.org/10.3390/fermentation11120692 - 12 Dec 2025

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Abstract

Mulberry (Morus alba) by-products represent underutilized feed resources with potential for ruminant nutrition. This study evaluated the rumen fermentation kinetics and rumen digestibility of dried mulberry pomace (MP) and leaf (ML) to determine optimal inclusion strategies in dairy cattle diets. Mulberry [...] Read more.

Mulberry (Morus alba) by-products represent underutilized feed resources with potential for ruminant nutrition. This study evaluated the rumen fermentation kinetics and rumen digestibility of dried mulberry pomace (MP) and leaf (ML) to determine optimal inclusion strategies in dairy cattle diets. Mulberry pomace (MP) and mulberry leaf (ML) were sun-dried and incorporated at 50% substitution levels into total mixed rations (TMR) with varying concentrations (30%, 35%, 40%, 45%, and 50%) of neutral detergent fiber (NDF). This created ten treatment groups: 30NP through 50NP (pomace-supplemented, where the number represents basal TMR NDF%) and 30NL through 50NL (leaf-supplemented), plus control groups containing only MP or ML and five basal TMR controls (30N through 50N). Rumen fluid was collected from two non-lactating Holstein cows fitted with ruminal cannulas. Chemical analysis revealed that ML contained 19% crude protein and 27.4% NDF, while MP contained 14.9% crude protein and 35.8% NDF. The highest gas production was observed in the 45NP (43.20 mL) and 50NL (43.50 mL) groups. Results demonstrated that MP achieved optimal fermentation when combined with 40–45% NDF TMR (maximum total volatile fatty acid (VFA): 88.86 mmol/L in 40NP at 48 h), whereas ML performed best with 45% NDF TMR (45NL: 88.03 mmol/L total VFA), indicating these as the most promising treatment combinations for ruminant feeding systems pending in vivo validation. Acetate proportions were higher in ML groups (84–96%), while propionate ratios were elevated in MP groups. Both materials maintained optimal ruminal pH (6.2–6.8). In vitro NDF digestibility was significantly higher for ML, with differences increasing from 2.97% at 2 h to 16.44% at 240 h. In situ degradation of MP was nearly complete at 48 h, while ML reached maximum degradation at 24 h. These findings indicate the potential of MP and ML as valuable alternative feed sources for ruminants, particularly in TMRs containing 40–45% NDF. Full article

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

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12 pages, 2908 KB

Open AccessArticle

An Intelligent Strategy for Colony De-Replication Using Raman Spectroscopy and Hybrid Clustering

by Xinli Li, Mingyang Liu, Jiaqi Sun and Su Wang

Fermentation 2025, 11(12), 691; https://doi.org/10.3390/fermentation11120691 - 12 Dec 2025

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Abstract

Efficient de-redundant colony picking is essential to accelerating strain screening in fermentation microbiology. Conventional random picking is inefficient, exhibits high redundancy, and often misses low-abundance but valuable strains. To address this, we present a high-efficiency de-redundant selection strategy based on colony Raman spectroscopy [...] Read more.

Efficient de-redundant colony picking is essential to accelerating strain screening in fermentation microbiology. Conventional random picking is inefficient, exhibits high redundancy, and often misses low-abundance but valuable strains. To address this, we present a high-efficiency de-redundant selection strategy based on colony Raman spectroscopy and a hybrid clustering algorithm. We directly acquire colony Raman spectra and combine the complementary strengths of k-means and hierarchical clustering (HCA) to achieve both balanced global partitioning and sensitivity to low-abundance taxa. Systematic application on pure colonies and complex plate settings shows that, by picking only 12–26% of colonies, the method attains 80–100% species coverage. Relative to manual random picking and image-based feature selection, picking efficiency increased by 116.8% and 44.5%, respectively, substantially shortening the screening cycle and reducing workload. Overall, Raman-guided hybrid clustering substantially reduces redundant picking and improves detection of low-abundance strains. It provides practical support for efficient strain discovery, library construction, and process optimization. Full article

(This article belongs to the Section Fermentation Process Design)

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19 pages, 3721 KB

Open AccessArticle

Effect of Bulking Agent Particle Size on Garden Waste–Dairy Manure Composting: Relationship Between Microbial Community Dynamics and Physicochemical Factors

by Qian Liu, Zhike Liu, Shaohan Ma, Le Li, Qing Hao, Shiyu Liu, Mingyi Lu and Yanhua Li

Fermentation 2025, 11(12), 690; https://doi.org/10.3390/fermentation11120690 - 12 Dec 2025

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Abstract

Garden waste is a solid waste produced by plant littering or pruning. Improper disposal can easily pollute the environment. The addition of bulking agents (BAs) can improve the efficiency of organic waste composting. In this study, garden waste and dairy manure were used [...] Read more.

Garden waste is a solid waste produced by plant littering or pruning. Improper disposal can easily pollute the environment. The addition of bulking agents (BAs) can improve the efficiency of organic waste composting. In this study, garden waste and dairy manure were used as raw materials, and easily available and recyclable branches were used as bulking agents to realize the synergistic resource utilization of the two. Three treatments were set up in the experiment, and 10% crushed branches, 1 cm branches, and 3 cm branches were added to the raw materials, respectively. The results showed that compared with the control group (adding crushed branches), the addition of 1 cm branches and 3 cm branches increased the cellulose degradation rate by 13.16–13.33% and the hemicellulose degradation rate by 18.24–23.86%. The monitoring results of CO₂ release showed that the cumulative CO₂ release of the treatment groups with 1 cm and 3 cm branches was 78.56 L and 102.17 L, respectively, which was significantly higher than that of the crushed branches (67.24 L), indicating that the addition of 1 cm and 3 cm branches increased microbial activity and degradation efficiency. Microbial diversity analysis further showed that in the treatment group with 1 cm branches, the number of nodes in the co-occurrence network increased by 24.11% and 2.84%, respectively, compared with the crushed branches and 3 cm branches, and the number of edges increased by 44.25% and 19.72%, forming the most abundant and complex microbial community, which verified its promotion effect on the composting process from the microbial level. In summary, this study recommends the use of branches with a particle size of 1 cm as BAs for garden waste composting. Full article

(This article belongs to the Special Issue Resource Recovery and Microbial Transformation of Organic Solid Waste)

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20 pages, 2939 KB

Open AccessArticle

Caproate Production from Yellow Water Fermentation: The Decisive Roles of Electron Donors

by Kai Shen, Xing Chen, Jiasheng Shi, Xuedong Zhang, Yaya Sun, He Liu, Salma Tabassum and Hongbo Liu

Fermentation 2025, 11(12), 689; https://doi.org/10.3390/fermentation11120689 - 12 Dec 2025

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Abstract

Caproate is a valuable medium-chain fatty acid (MCFA) that is found to be extensively used in biofuel production, food preservation, and the pharmaceutical industries. Short-chain fatty acids (SCFAs) from waste streams can be upgraded sustainably through their biological synthesis via anaerobic chain elongation. [...] Read more.

Caproate is a valuable medium-chain fatty acid (MCFA) that is found to be extensively used in biofuel production, food preservation, and the pharmaceutical industries. Short-chain fatty acids (SCFAs) from waste streams can be upgraded sustainably through their biological synthesis via anaerobic chain elongation. However, caproate production is frequently limited in real-world systems due to low carbon conversion efficiency and a lack of electron donors. In this study, we developed a two-stage fermentation strategy employing yellow water—a high-strength organic wastewater from liquor manufacturing—as a novel substrate. During primary fermentation, Lactobacillus provided endogenous electron donors by converting the residual carbohydrates in the yellow water into lactic acid. Nano zero-valent iron (NZVI) was introduced to the secondary fermentation to enhance power reduction and electron flow, further promoting caproate biosynthesis. The caproate production increased significantly due to the synergistic action of lactic acid and NZVI, reaching a maximum concentration of 20.41 g·L⁻¹ and a conversion efficiency of 69.50%. This strategy enhances carbon recovery and electron transport kinetics while lowering dependency on expensive external donors like hydrogen or ethanol. Microbial community analysis using 16S rRNA sequencing revealed enrichment of chain-elongating bacteria such as Clostridium kluyveri. These findings demonstrate the feasibility of employing an integrated fermentation–electron management technique to valorize industrial yellow water into compounds with added value. This study offers a scalable and environmentally sound pathway for MCFA production from waste-derived resources. Full article

(This article belongs to the Special Issue Fermentation of Organic Waste for High-Value-Added Product Production—2nd Edition)

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16 pages, 2154 KB

Open AccessArticle

Low-Cost Production Process of Saccharomyces cerevisiae Yeast for Craft Beer Fermentation

by Jessica Rodríguez, Domenica Villavicencio, Alys Raza, Fernanda Hernández-Alomía, Carlos Bastidas-Caldes and María Alejandra Cruz

Fermentation 2025, 11(12), 688; https://doi.org/10.3390/fermentation11120688 - 12 Dec 2025

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Abstract

The production of craft beer depends on the quality and availability of yeast. However, many small breweries in developing countries face high costs due to their reliance on imported yeast strains. Developing efficient and low-cost propagation methods is therefore essential for sustainable production. [...] Read more.

The production of craft beer depends on the quality and availability of yeast. However, many small breweries in developing countries face high costs due to their reliance on imported yeast strains. Developing efficient and low-cost propagation methods is therefore essential for sustainable production. A lager-type Saccharomyces cerevisiae strain (SC-Lager2) was propagated using both synthetic and low-cost alternative media. The latter was formulated with malt extract as a carbon source and yeast extract obtained from brewery by-products as a nitrogen source. A Plackett–Burman design identified significant factors influencing growth (p < 0.05), and a full factorial design (2⁴) optimized conditions. Growth kinetics and biomass yield were validated at laboratory (2 L) and pilot (83 L) scales. Maltose, yeast extract, zinc sulfate, and agitation significantly affected cell density and viability (p < 0.05). Under optimized conditions, 100% viability, a maximum cell density of 1.4 × 10¹⁰ cells/mL, and a biomass yield of 10 g/L were achieved values that were statistically higher (p < 0.05) than those obtained with the synthetic medium. The maximum specific growth rate (μ_max) increased by 52%, while doubling time decreased by 39%. Overall, the use of agro-industrial by-products reduced medium costs by approximately 65% compared to conventional synthetic formulations. The proposed low-cost medium provides a scalable, economical, and sustainable solution for yeast propagation, reducing production costs while maintaining high cell viability and performance. This approach supports the autonomy and competitiveness of the craft beer sector in developing regions. Full article

(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)

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19 pages, 877 KB

Open AccessArticle

The Influence of Winemaking Processes on the Formation of Biogenic Amines in Wine

by Karolina Kostelnikova, Mojmir Baron, Michal Kumsta and Jiri Sochor

Fermentation 2025, 11(12), 687; https://doi.org/10.3390/fermentation11120687 - 11 Dec 2025

Viewed by 530

Abstract

This study investigated the influence of different winemaking processes, particularly fermentation type and must clarification, on the formation of biogenic amines (BA) in Sauvignon wine. The experiment investigated seven methods of vinification combining spontaneous and controlled alcoholic and malolactic fermentation. The concentrations of [...] Read more.

This study investigated the influence of different winemaking processes, particularly fermentation type and must clarification, on the formation of biogenic amines (BA) in Sauvignon wine. The experiment investigated seven methods of vinification combining spontaneous and controlled alcoholic and malolactic fermentation. The concentrations of six biogenic amines (histamine, tyramine, tryptamine, phenylethylamine, putrescine, and cadaverine) were determined using a HILIC-LC-MS/MS. Statistical evaluation confirmed the significant effect of alcoholic and malolactic fermentation, maturation stage, and must processing on the overall amine profile of the wine (p < 0.001). The total BA content in all the variants was low and well below values considered to pose a health risk. Histamine and tryptamine were only detected in trace amounts (<0.1 mg/L), whereas putrescine and tyramine exhibited the greatest variability. Higher concentrations were recorded in variants that underwent malolactic fermentation, particularly in combination with clarified must. In contrast, whole-mash fermentation produced the lowest BA concentrations, possibly due to factors associated with extended skin and seed contact. These findings indicate that the choice of fermentation strategy significantly affects the formation of biogenic amines in wine. Full article

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

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21 pages, 2080 KB

Open AccessArticle

Fermentation of Wheat Bread with Lactiplantibacillus plantarum: Study of Changes in Acrylamide and Microbiological Spoilage During Packaging at Different Temperatures

by Almas Zhanbolat, Ulbala Tungyshbayeva, Zhanat Iskakova, Maryna Mardar, Raushangul Uazhanova, Maxat Iztileuov, Sholpan Amanova, Bakhytkul Assenova, Raushan Izteliyeva, Sagynysh Aman and Farida Amutova

Fermentation 2025, 11(12), 686; https://doi.org/10.3390/fermentation11120686 - 10 Dec 2025

Viewed by 538

Abstract

The safety and shelf life of wheat bread depend not only on recipe formulation and fermentation but also on post-baking handling, particularly the packaging stage. This study focused on evaluating the effect of the temperature of the bread crumb at the moment of [...] Read more.

The safety and shelf life of wheat bread depend not only on recipe formulation and fermentation but also on post-baking handling, particularly the packaging stage. This study focused on evaluating the effect of the temperature of the bread crumb at the moment of packaging (30, 40, and 45 °C) on acrylamide content and microbiological spoilage during storage. Wheat bread samples prepared with 5, 10, and 15% Lactiplantibacillus plantarum sourdough were compared to control bread without sourdough. The results revealed that packaging at elevated temperatures (40–45 °C) led to higher residual acrylamide levels and accelerated mold growth due to condensation and increased humidity inside polyethylene bags. In contrast, packaging at 30 °C significantly reduced acrylamide formation, limited microbial proliferation, and extended the shelf life of bread up to 7 days while maintaining acceptable sensory qualities. The combined effect of sourdough concentration and packaging temperature demonstrated that the optimal conditions for ensuring safety and extending shelf life are the use of 5–10% sourdough and packaging at 30 °C. These findings underline the critical role of sourdough content and packaging temperature in controlling chemical contaminants and microbiological spoilage in bread production. Full article

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

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18 pages, 4952 KB

Open AccessArticle

Defatted Soybean Meal-Based Koji Promotes Flavor Development in Deyang Baiwo Soy Sauce: A Comparative Multi-Omics Study

by Kai-Yao Chen, Na Zhang, Wen-Hu Liu, Cheng Wang, Yong-Qi Hu, Cai-Hong Shen, Li Zeng and Xu Ran

Fermentation 2025, 11(12), 685; https://doi.org/10.3390/fermentation11120685 - 10 Dec 2025

Viewed by 461

Abstract

Although the influence of raw material composition on soy sauce koji fermentation is well recognized, the differences in microbial succession and metabolic pathways between whole soybean koji (WSK) and defatted soybean–wheat bran koji (DSK) remain unclear. In this study, a multi-omics approach integrating [...] Read more.

Although the influence of raw material composition on soy sauce koji fermentation is well recognized, the differences in microbial succession and metabolic pathways between whole soybean koji (WSK) and defatted soybean–wheat bran koji (DSK) remain unclear. In this study, a multi-omics approach integrating absolute quantitative PCR and physicochemical analyses was employed to elucidate the mechanisms by which DSK enhances the quality of Deyang Baiwo soy sauce. Compared with WSK, DSK exhibited lower moisture content but higher total acidity, amino nitrogen, and reducing sugar levels, indicating its suitability for high-quality soy sauce production. Volatile analysis revealed greater accumulation of key aroma compounds such as 2-methoxy-4-vinylphenol and 4-vinylguaiacol in DSK, contributing characteristic smoky flavors. At the microbial community level, Aspergillus, Weissella, Enterobacter, and Bacillus were enriched in DSK, promoting the accumulation of flavor and aroma compounds in alignment with industrial koji production objectives. Metabolic pathway analysis indicated that Weissella in DSK was primarily responsible for lactic acid accumulation, whereas Aspergillus dominated early-stage substrate degradation and played a key role in the enrichment of 1-octen-3-ol in WSK. This study provides insights into the “substrate–microbiota–metabolite” regulatory network and offers a theoretical basis for optimizing the use of defatted soybean in traditional soy sauce fermentation. Full article

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

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21 pages, 4834 KB

Open AccessReview

Probiotic-Fermented Foods and Antimicrobial Stewardship: Mechanisms, Evidence, and Translational Pathways Against AMR

by Karina Teixeira Magalhães

Fermentation 2025, 11(12), 684; https://doi.org/10.3390/fermentation11120684 - 10 Dec 2025

Viewed by 594

Abstract

Antimicrobial resistance (AMR) remains a critical global challenge, requiring novel complementary strategies beyond antibiotic development. Probiotic-fermented foods (PFFs) offer an emerging, low-cost approach to mitigate AMR risk through ecological, molecular, and immunological mechanisms. This review integrates mechanistic insights, clinical evidence, and translational frameworks [...] Read more.

Antimicrobial resistance (AMR) remains a critical global challenge, requiring novel complementary strategies beyond antibiotic development. Probiotic-fermented foods (PFFs) offer an emerging, low-cost approach to mitigate AMR risk through ecological, molecular, and immunological mechanisms. This review integrates mechanistic insights, clinical evidence, and translational frameworks linking PFFs to antimicrobial stewardship. Key mechanisms include colonization resistance, nutrient and adhesion-site competition, production of antimicrobial metabolites, such as bacteriocins, hydrogen peroxide, and organic acids and Quorum-quenching-sensing activities that suppress pathogen virulence. Randomized clinical trials indicate that fermented diets and probiotic supplementation can improve microbiome diversity, reduce inflammatory cytokines, and decrease antibiotic-associated diarrhea, though direct AMR outcomes remain underexplored. Evidence from kefir, kombucha, and other microbial consortia suggests potential for in vivo pathogen suppression and reduced infection duration. However, safe translation requires standardized starter-culture genomics, resistome monitoring, and regulatory oversight under QPS/GRAS frameworks. Integrating PFF research with One Health surveillance systems, such as the WHO GLASS platform, will enable tracking of antimicrobial consumption and resistance outcomes. Collectively, these findings position PFFs as promising adjuncts for AMR mitigation, linking sustainable food biotechnology with microbiome-based health and global stewardship policies. Full article

(This article belongs to the Special Issue Feature Review Papers on Fermentation for Food and Beverages 2025)

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20 pages, 1589 KB

Open AccessArticle

Functional Fortification of Tibicos with Lemon Catnip (Nepeta cataria var. citriodora) Hydrolate: Fermentation Kinetics, Health-Promoting Potentials and Sensory Evaluation

by Ana Tomić, Olja Šovljanski, Milica Aćimović, Luka Tucakov, Anja Vučetić, Aleksandra Ranitović, Snežana Filip, Staniša Latinović, Jasna Čanadanović-Brunet and Dragoljub Cvetković

Fermentation 2025, 11(12), 683; https://doi.org/10.3390/fermentation11120683 - 9 Dec 2025

Viewed by 430

Abstract

The development of plant-based synbiotic beverages is gaining increasing attention as consumers seek sustainable, functional alternatives to dairy products. This preliminary study investigated the fortification of tibicos (water kefir) with lemon catnip (Nepeta cataria var. citriodora) hydrolate, an aromatic distillation byproduct [...] Read more.

The development of plant-based synbiotic beverages is gaining increasing attention as consumers seek sustainable, functional alternatives to dairy products. This preliminary study investigated the fortification of tibicos (water kefir) with lemon catnip (Nepeta cataria var. citriodora) hydrolate, an aromatic distillation byproduct rich in bioactive terpenoids. After 72 h-fermentation of tibicos, physicochemical, microbiological, health-promoting and sensory parameters were evaluated. Both control and fortified beverages exhibited typical fermentation kinetics, including a decrease in pH, reduction of soluble solids, and accumulation of organic acids. Lactic acid bacteria count remained stable, while yeast proliferation was slightly reduced in the hydrolate-fortified sample, consistent with the known yeast-sensitive nature of certain hydrolate-derived terpenoids. Importantly, hydrolate fortification significantly enhanced antioxidant capacity (DPPH: +34%; ABTS: +39%; RP: +38%). Enzyme-inhibitory activities also increased significantly in the hydrolate-fortified samples (α-Amylase and α-Glucosidase inhibition rates increased by 9% and 11%, respectively). ACE inhibition similarly increased from 32% to 44%, indicating an enhanced antihypertensive potential. HMG-CoA reductase inhibition increased from 31% to 42%, showing improved hypolipidemic activity. Sensory evaluation indicated improved sensory acceptability, imparting citrus–floral notes that balanced the acidic profile of tibicos. These findings highlight the potential of valorizing lemon catnip hydrolate as a functional fortifier in non-dairy synbiotic beverages. Full article

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

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22 pages, 1766 KB

Open AccessReview

Comprehensive Advances on Probiotic-Fermented Medicine and Food Homology

by Huijun Dong, Derui Bu, Yutong Cheng, Wen Gao and Fubo Han

Fermentation 2025, 11(12), 682; https://doi.org/10.3390/fermentation11120682 - 8 Dec 2025

Viewed by 869

Abstract

In China, the concept of Medicine and Food Homology (MFH) is deeply rooted in the ancient practices of Traditional Chinese Medicine (TCM). Nonetheless, challenges persist regarding the low levels of bioactive compounds and limited absorption efficiency associated with MFH, as well as the [...] Read more.

In China, the concept of Medicine and Food Homology (MFH) is deeply rooted in the ancient practices of Traditional Chinese Medicine (TCM). Nonetheless, challenges persist regarding the low levels of bioactive compounds and limited absorption efficiency associated with MFH, as well as the potential toxic side effects of certain MFH substances. Probiotic fermentation emerges as a promising strategy to address these issues, as it can effectively transform and enhance the active components of MFH through specific metabolic processes. This review provides a comprehensive analysis of the interactions between MFH and probiotics, the pharmacological benefits of probiotic-fermented MFH, the development of efficient probiotic fermentation systems, and the quality control measures necessary for MFH fermentation. Furthermore, the article discusses the challenges and future directions for MFH fermentation. The integration of artificial intelligence (AI) and synthetic biology techniques holds the potential to significantly enhance the efficiency and efficacy of probiotic-fermented MFH. In conclusion, this article offers an in-depth examination of the potential for probiotic-fermented MFH to contribute to the modernization of TCM. Full article

(This article belongs to the Section Probiotic Strains and Fermentation)

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17 pages, 456 KB

Open AccessArticle

Enhanced In Vitro System for Predicting Methane Emissions from Ruminant Feed

by Seongwon Seo and Mingyung Lee

Fermentation 2025, 11(12), 681; https://doi.org/10.3390/fermentation11120681 - 7 Dec 2025

Viewed by 516

Abstract

Mitigating enteric methane emissions through diet formulation remains a significant challenge in cattle nutrition. This study developed a system to evaluate the methane production potential of feeds, expressed as the effective ruminal methane production rate (eRMR, mL/g dry matter [DM]), using a discontinuous [...] Read more.

Mitigating enteric methane emissions through diet formulation remains a significant challenge in cattle nutrition. This study developed a system to evaluate the methane production potential of feeds, expressed as the effective ruminal methane production rate (eRMR, mL/g dry matter [DM]), using a discontinuous in vitro ruminal fermentation system using rumen fluid. Sixteen concentrate feeds and two forages were tested, with a reference diet (ryegrass straw:corn:corn gluten feed = 1:1:1) included in each batch to standardize conditions and account for associative effects among feeds. Test feeds were incubated with the reference diet in closed bottles under strictly anaerobic conditions. Methane and total gas production were measured at 2, 4, 6, and 24 h, and true dry matter digestibility was calculated after 6 and 24 h. For each batch, sample feed values were corrected and standardized using those of the reference diet. The eRMR value was calculated by integrating a differential equation with parameters incorporating ruminal digestion and passage dynamics. The test feed eRMR values ranged from 1.2 mL/g DM (soybean meal) to 56.7 mL/g DM (soybean hull), with the reference diet at 14.8 mL/g DM. Evaluation of feed eRMR using data from two in vivo studies demonstrated strong correlations between predicted diet-specific eRMR values and measured methane emissions from Hanwoo steers (r = 0.93 and 0.85). This system, incorporating rumen dynamics with a reduced sampling schedule, provides a precise and practical tool for predicting in vivo enteric methane production and optimizing diet formulations to mitigate methane emissions from cattle. Full article

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

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15 pages, 710 KB

Open AccessReview

Insights into the Feed Additive Inhibitor and Alternative Hydrogen Acceptor Interactions: A Future Direction for Enhanced Methanogenesis Inhibition in Ruminants

by Ibrahim Ahmad, Richard P. Rawnsley, John P. Bowman, Rohan Borojevic and Apeh A. Omede

Fermentation 2025, 11(12), 680; https://doi.org/10.3390/fermentation11120680 - 5 Dec 2025

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Abstract

Enteric methane (CH₄) emissions from ruminants contribute significantly to agricultural greenhouse gases. Anti-methanogenic feed additives (AMFA), such as Asparagopsis spp. and 3-nitrooxypropanol (3-NOP), reduce CH₄ emissions by inhibiting methanogenic enzymes. However, CH₄ inhibition often leads to dihydrogen (H₂ [...] Read more.

Enteric methane (CH₄) emissions from ruminants contribute significantly to agricultural greenhouse gases. Anti-methanogenic feed additives (AMFA), such as Asparagopsis spp. and 3-nitrooxypropanol (3-NOP), reduce CH₄ emissions by inhibiting methanogenic enzymes. However, CH₄ inhibition often leads to dihydrogen (H₂) accumulation, which can impact rumen fermentation and decrease dry matter intake (DMI). Recent studies suggest that co-supplementation of CH₄ inhibitors with alternative electron acceptors, such as phloroglucinol, fumaric acid, or acrylic acid, can redirect excess H₂ during methanogenesis inhibition into fermentation products nutritionally beneficial for the host. This review summarizes findings from rumen simulation experiments and in vivo trials that have investigated the effects of combining a CH₄ inhibitor with an alternative H₂ acceptor to achieve effective methanogenesis inhibition. These trials demonstrate variable outcomes depending on additive combinations, inclusion rates, and adaptation periods. The use of phloroglucinol in vivo consistently decreased H₂ emissions and altered fermentation patterns, promoting acetate production, compared with fumaric acid or acrylic acid as alternative electron acceptors. As a proof-of-concept, phloroglucinol shows promise as a co-supplement for reducing CH₄ and H₂ emissions while enhancing volatile fatty acid profiles in vivo. Optimizing microbial pathways for H₂ utilization through targeted co-supplementation and microbial adaptation could enhance the sustainability of CH₄ mitigation strategies using feed additive inhibitors in ruminants. Further research using multi-omics approaches is needed to elucidate the microbial mechanisms underlying the redirection of H₂ toward beneficial fermentation products during enteric methanogenesis inhibition. This knowledge will help guide the formulation of novel co-supplements designed to reduce CH₄ emissions and improve energy efficiency for sustainable livestock production. Full article

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15 pages, 7298 KB

Open AccessArticle

Candida utilis Biosurfactant from Licuri Oil: Influence of Culture Medium and Emulsion Stability in Food Applications

by Lívia Xavier de Araújo, Peterson Felipe Ferreira da Silva, Renata Raianny da Silva, Leonie Asfora Sarubbo, Jorge Luíz Silveira Sonego and Jenyffer Medeiros Campos Guerra

Fermentation 2025, 11(12), 679; https://doi.org/10.3390/fermentation11120679 - 5 Dec 2025

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Abstract

Biosurfactants (BSs) are natural, biodegradable compounds crucial for replacing synthetic emulsifiers in the food industry, provided their production costs can be reduced through the use of sustainable and low-cost substrates. This study evaluated the viability of licuri oil as a carbon source for [...] Read more.

Biosurfactants (BSs) are natural, biodegradable compounds crucial for replacing synthetic emulsifiers in the food industry, provided their production costs can be reduced through the use of sustainable and low-cost substrates. This study evaluated the viability of licuri oil as a carbon source for BS production by Candida utilis and assessed the product’s functional stability in food formulations. Production kinetics confirmed the yeast’s efficiency, reducing the water surface tension to a minimum of 31.55 mN·m⁻¹ at 120 h. Factorial screening identified a high carbon-to-nitrogen ratio as the key factor influencing ST reduction. The isolated BS demonstrated high surface activity, with a Critical Micelle Concentration of 0.9 g·L⁻¹. Furthermore, the cell-free broth maintained excellent emulsifying activity (E₂₄ > 70%) against canola and motor oils across extreme pH, temperature, and salinity conditions. Twelve mayonnaise-type dressings were formulated, utilizing licuri oil, and tested for long-term physical stability. Six formulations, featuring the BS in combination with lecithin and/or egg yolk, remained stable without phase segregation after 240 days of refrigeration, maintaining a stable pH and suitable microbiological conditions for human consumption. The findings confirm that the valorization of licuri oil provides a route to produce a highly efficient and robust BS, positioning it as a promising co-stabilizer for enhancing the shelf-life and natural appeal of complex food emulsions. Full article

(This article belongs to the Special Issue The Industrial Feasibility of Biosurfactants)

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15 pages, 1072 KB

Open AccessReview

High-Protein Diets: Characteristics of Bacterial Fermentation and Its Consequences on Intestinal Health

by Fatima Omer, Xin Song, Enting Qiao, Xuezhao Sun, Hao Zhang, Mengzhi Wang and Yujia Jing

Fermentation 2025, 11(12), 678; https://doi.org/10.3390/fermentation11120678 - 4 Dec 2025

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Abstract

Although high-protein diets are widespread, the fate of dietary protein, its fermentation by gut microbiota, and the resulting effects on intestinal health are not yet fully understood. This article provides a comprehensive overview of microbial protein fermentation and its impact on intestinal health. [...] Read more.

Although high-protein diets are widespread, the fate of dietary protein, its fermentation by gut microbiota, and the resulting effects on intestinal health are not yet fully understood. This article provides a comprehensive overview of microbial protein fermentation and its impact on intestinal health. We focus on the bacterial anabolic and catabolic pathways involved in microbial protein metabolism and the generation of metabolites such as ammonia, biogenic amines (BAs), and short-chain fatty acids (SCFAs). This review also examines how excessive dietary protein affects intestinal health. Elevated protein levels may disrupt microbial homeostasis, promoting the proliferation of pathogenic bacteria while reducing beneficial microbiota. Furthermore, enhanced bacterial metabolic activity can lead to greater production of harmful compounds such as BAs. These alterations are associated with impaired intestinal barrier function, immune dysregulation, and elevated inflammatory responses. Further research is necessary to clarify the metabolism of high-protein diets and their consequences for intestinal health. Full article

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

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24 pages, 1759 KB

Open AccessArticle

Metabolic and Safety Characterization of Lactiplantibacillus plantarum Strains Isolated from Traditional Rye Sourdough

by Liis Lutter, Pavel Sahharov, Sana Ben Othman, Lisbeth Luik, Naatan Pikkel, Anna Schneider and Helena Andreson

Fermentation 2025, 11(12), 677; https://doi.org/10.3390/fermentation11120677 - 3 Dec 2025

Viewed by 665

Abstract

Lactiplantibacillus plantarum is a versatile lactic acid bacterium (LAB) with broad ecological and metabolic adaptability, contributing to both technological and probiotic functions. The prevalence and functional diversity of locally adapted L. plantarum strains in traditional sourdough fermentations remain poorly understood. This study aimed [...] Read more.

Lactiplantibacillus plantarum is a versatile lactic acid bacterium (LAB) with broad ecological and metabolic adaptability, contributing to both technological and probiotic functions. The prevalence and functional diversity of locally adapted L. plantarum strains in traditional sourdough fermentations remain poorly understood. This study aimed to characterize ten L. plantarum strains isolated from traditional Estonian rye sourdoughs, focusing on safety, enzymatic and carbohydrate metabolism, fermentation performance, exopolysaccharide (EPS) production, and genotype-associated functional diversity, including interaction with aflatoxin B₁ (AFB₁). Strains were γ-hemolytic and susceptible to major antibiotics. Strong aminopeptidase and β-glucosidase activities were observed, whereas α-glucosidase and α-galactosidase activities varied among strains and genotypes. Strains efficiently utilized mono- and disaccharides, with genotype-specific patterns for complex carbohydrates. During sourdough fermentation, all strains acidified the dough (pH < 4.5) and produced lactic and acetic acids in optimal ratios, while fermentation kinetics differed in a genotype-dependent manner. EPS yields (131–225 mg/L) were stable across genotypes. All strains retained fermentative activity in the presence of AFB₁ and exhibited high binding capacity (~100%). These findings demonstrate the safety, metabolic versatility, and genotype-structured functional diversity of L. plantarum from traditional Estonian rye sourdoughs, supporting their application as robust, multifunctional starter cultures for sustainable food fermentations. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria Metabolism)

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12 pages, 481 KB

Open AccessArticle

2G Ethanol Production from a Cellulose Derivative

by Elton C. Grossi, Romulo D. A. Andrade, Paulo A. Z. Suarez and Sarah S. Brum

Fermentation 2025, 11(12), 676; https://doi.org/10.3390/fermentation11120676 - 3 Dec 2025

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Abstract

The conversion of cellulose into glucose has been a major challenge in improving the competitiveness of 2G ethanol production due to the inefficiency of pre-treatment and the high degree of crystallinity of the cellulose. This study examined the effect of replacing cellulose hydroxyl [...] Read more.

The conversion of cellulose into glucose has been a major challenge in improving the competitiveness of 2G ethanol production due to the inefficiency of pre-treatment and the high degree of crystallinity of the cellulose. This study examined the effect of replacing cellulose hydroxyl groups with acetyl groups on the hydrolysis yield. Cellulose compounds and cellulose acetate were characterized using FTIR, and the degree of substitution of the cellulose acetate was determined chemically. The crystallinity of the materials was analyzed using X-ray diffraction. The results of the hydrolysis reaction analysis showed that the substitution of hydroxyl groups in cellulose with acetyl groups favored acid hydrolysis, yielding high glucose yields. For the fermentation test of the hydrolysate, yeast (Saccharomyces cerevisiae) was used. Fermentation reached values close to maximum efficiency. These results open up new avenues for acid hydrolysis based on the chemical modification of cellulose.: Full article

(This article belongs to the Special Issue Towards the Sustainable Treatment of Organic Wastes via Various Novel Biotechnologies, 2nd Edition)

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Fermentation, Volume 11, Issue 12 (December 2025) – 52 articles

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