Journal Description
Fermentation
Fermentation
is an international, peer-reviewed, open access journal on fermentation process and technology, published monthly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubAg, FSTA, Inspec, CAPlus / SciFinder, and other databases.
- Journal Rank: JCR - Q2 (Biotechnology and Applied Microbiology) / CiteScore - Q1 (Plant Science)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.5 days after submission; acceptance to publication is undertaken in 3.9 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
3.3 (2024);
5-Year Impact Factor:
3.5 (2024)
Latest Articles
Insights into the Feed Additive Inhibitor and Alternative Hydrogen Acceptor Interactions: A Future Direction for Enhanced Methanogenesis Inhibition in Ruminants
Fermentation 2025, 11(12), 680; https://doi.org/10.3390/fermentation11120680 - 5 Dec 2025
Abstract
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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
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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
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
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
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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.
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(This article belongs to the Special Issue The Industrial Feasibility of Biosurfactants)
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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
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.
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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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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
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
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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.
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(This article belongs to the Special Issue Lactic Acid Bacteria Metabolism)
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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
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
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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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Open AccessArticle
Antifungal Effect of Lactiplantibacillus plantarum Y48 Postbiotics Combined with Potassium Sorbate in Bread
by
Yasemin Kaya, Sevda Dere, Fatih Bozkurt, Dilara Devecioglu, Funda Karbancioglu-Guler, Mustafa Sengul and Enes Dertli
Fermentation 2025, 11(12), 675; https://doi.org/10.3390/fermentation11120675 - 1 Dec 2025
Abstract
Mycotoxigenic molds pose a threat to human health and cause economic losses in bread production. To address this issue, postbiotics have emerged as promising natural bioprotective agents due to their antifungal properties. In this study, postbiotics were obtained from Lactiplantibacillus (Lp.) plantarum Y48,
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Mycotoxigenic molds pose a threat to human health and cause economic losses in bread production. To address this issue, postbiotics have emerged as promising natural bioprotective agents due to their antifungal properties. In this study, postbiotics were obtained from Lactiplantibacillus (Lp.) plantarum Y48, Liquorilactobacillus (Lq.) hordei SK-6, and Lp. plantarum VB-29 strains and subsequently lyophilized. The functional groups of the bioactive components in these postbiotics were identified using FTIR spectroscopy. Samples extracted with different solvents were analyzed for their volatile compound profiles by GC-MS, and the results were compared using principal component analysis (PCA). The antifungal activities of postbiotics were tested. Subsequently, the antifungal activity of Lp. plantarum Y48 postbiotic was evaluated on bread contaminated with Aspergillus niger and Penicillium expansum. The postbiotic was incorporated into the bread formulation both alone and in combination with potassium sorbate, and it was also applied to the bread surface as a spray. Notably, the formulation containing 3% postbiotic + 0.1% potassium sorbate completely inhibited the growth of A. niger and P. expansum. These results indicate that the combined use of Lp. plantarum Y48 postbiotic and potassium sorbate can effectively prevent mold growth in bread and holds potential as a natural bioprotective approach in food preservation applications.
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(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods, 2nd Edition)
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Open AccessSystematic Review
Mechanisms Underlying the Effects of Rumen Microbiota Transplantation on the Growth and Development of Ruminants
by
Yirun Zhao, Enkai Li, Yutao Qiu, Xiaokang Ma, Dingfu Xiao and Zhiqing Li
Fermentation 2025, 11(12), 674; https://doi.org/10.3390/fermentation11120674 - 30 Nov 2025
Abstract
The growth and development of ruminants are closely linked to the stability and functional capacity of their rumen microbiota. Rumen microbiota transplantation (RMT), which entails the transfer of ruminal microorganisms and their metabolites from healthy donors to recipient animals, has emerged as a
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The growth and development of ruminants are closely linked to the stability and functional capacity of their rumen microbiota. Rumen microbiota transplantation (RMT), which entails the transfer of ruminal microorganisms and their metabolites from healthy donors to recipient animals, has emerged as a promising strategy for modulating host physiology. Accumulating evidence indicates that RMT can substantially influence nutrient digestion, immune function, and overall growth performance. This review synthesizes current knowledge on the mechanisms through which RMT affects ruminant growth and development, with particular attention to its roles in shaping microbial colonization and succession, enhancing rumen fermentation efficiency, and modulating host metabolic pathways. Together, these regulatory processes contribute to improved rumen maturation in young animals and enhanced production performance in adults. In addition, this review critically examines key factors governing the efficacy of RMT, including transplantation procedures, donor microbiota characteristics, and the physiological status of recipient animals. By integrating these insights, the present synthesis provides a conceptual framework to support the precise and effective application of RMT in the sustainable management of healthy ruminant production systems.
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(This article belongs to the Special Issue Research Progress of Rumen Fermentation)
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Open AccessArticle
Genomic and Metabolomic Characterization of Kitasatospora griseola JNUCC 62 from Mulyeongari Oreum and Its Cosmeceutical Potential
by
Mi-Sun Ko, Mi-Yeon Moon and Chang-Gu Hyun
Fermentation 2025, 11(12), 671; https://doi.org/10.3390/fermentation11120671 - 29 Nov 2025
Abstract
The actinobacterial strain Kitasatospora griseola JNUCC 62 was isolated from volcanic wetland soil at Mulyeongari Oreum, Jeju Island, and taxonomically identified through 16S rRNA gene and whole-genome analyses. The complete genome, assembled from PacBio Sequel I reads, spans 8.31 Mb with a GC
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The actinobacterial strain Kitasatospora griseola JNUCC 62 was isolated from volcanic wetland soil at Mulyeongari Oreum, Jeju Island, and taxonomically identified through 16S rRNA gene and whole-genome analyses. The complete genome, assembled from PacBio Sequel I reads, spans 8.31 Mb with a GC content of 72.8% and contains 7265 coding sequences. Comparative genomic indices (Average nucleotide identity, ANI 97.46%; digital DNA–DNA hybridization, dDDH 84.4%) confirmed its conspecific relationship with K. griseola JCM 3339T. Genome mining using antiSMASH 8.0 revealed 30 biosynthetic gene clusters (BGCs), including polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), ribosomally synthesized and post-translationally modified peptide (RiPP), lanthipeptide, and terpene types, accounting for 18.6% of the genome. Several BGCs displayed homology to known formicamycin-, lankacidin-, and lanthipeptide-type clusters, while others were novel or cryptic, reflecting adaptation to the nutrient-poor volcanic environment. Ethyl acetate extraction of the culture broth, especially under tryptophan-supplemented conditions, yielded four metabolites—1-acetyl-β-carboline, perlolyrine, tryptopol, and 1H-pyrrole-2-carboxylic acid—identified by UV and NMR spectroscopy. These compounds correspond to NRPS–PKS hybrid and arylpolyene-type gene clusters predicted in the genome, suggesting precursor-directed biosynthesis of indole and pyrrole alkaloids. The ethyl acetate extract (JNUCC62 EA) exhibited strong antioxidant capacity in the ABTS assay, anti-inflammatory activity via inhibition of nitric oxide (31.09 ± 3.69% of control) and cytokines (IL-6, IL-1β, TNF-α) in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages, and anti-melanogenic effects in α-melanocyte-stimulating hormone (MSH)-stimulated B16F10 melanoma cells, where melanin content and tyrosinase activity decreased to 61.49 ± 1.24% and 24.32 ± 0.31% of the control, respectively, without cytotoxicity. A human primary skin irritation test confirmed no irritation up to 50 µg/mL, establishing excellent dermal safety. Collectively, these findings highlight K. griseola JNUCC 62 from Mulyeongari Oreum as a volcanic wetland-derived actinomycete harboring rich biosynthetic potential for novel indole alkaloids with antioxidant, anti-inflammatory, and whitening properties, supporting its development as a safe and multifunctional cosmeceutical ingredient.
Full article
(This article belongs to the Special Issue Microbial Metabolism Focusing on Bioactive Molecules)
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Open AccessArticle
Development of a Semi-Industrial Kefalotyri-Type Cheese Using Thermized Milk from Native Epirus Sheep Breeds and Autochthonous Starter and Adjunct Cultures
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Loulouda Bosnea, Ioanna Kosma, Athanasia Kakouri, Spiros Paramithiotis and John Samelis
Fermentation 2025, 11(12), 673; https://doi.org/10.3390/fermentation11120673 - 28 Nov 2025
Abstract
Autochthonous starter and adjunct cultures have gained increasing practical research interest for use in traditional cheese-making in recent years. This study evaluated the performance of a native starter comprising Streptococcus thermophilus ST1 and two wild Lactococcus lactis strains, including the M78 nisin A-producer,
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Autochthonous starter and adjunct cultures have gained increasing practical research interest for use in traditional cheese-making in recent years. This study evaluated the performance of a native starter comprising Streptococcus thermophilus ST1 and two wild Lactococcus lactis strains, including the M78 nisin A-producer, during the semi-industrial production of Kefalotyri cooked hard cheese from thermized sheep milk (TM; 65 °C, 30 s) in the absence (C-cheese) or presence of the native adjunct strains Lactiplantibacillus plantarum H25 and Leuconostoc mesenteroides KFM7 + KFM9 (N-cheese). The growth of the native starter was optimal in all three cheese trials within the first 24 h of processing, but afterward, ST1 failed to exceed 8 log CFU/g in favor of total mesophilic LAB, comprising both L. lactis starter strains, and the prevalent (ca. 8.5 log CFU/g) H25 adjunct in the ripening N-cheeses. Instead, in the C-cheeses, indigenous non-Enterococcus NSLAB survivors from TM prevailed, whereas enterococci failed to increase above 6 log CFU/g in all cheeses. Although the mature (90-day-old) N-cheeses presented no statistically significant differences regarding the pH value, gross composition, and hydrophobic (HO)/hydrophilic (HI) peptide ratios from the mature C-cheeses, they had lower total LAB counts and contained less residual lactose, more acetate, and an overall less diversified volatilome (VOC) profile. The most abundant VOCs in both cheeses were acetone, butyric acid, methyl butyrate, ethyl ether, and ethanol. All mature cheeses were safe and graded of ‘excellent quality’ (i.e., moisture < 35%; fat-in-dry-matter > 47%).
Full article
(This article belongs to the Special Issue Fermented Dairy Products: From Artisanal Production to Functional Products and Beyond)
Open AccessArticle
Effects of Autochthonous Starter Cultures on the Quality Characteristics of Traditionally Produced Sucuk
by
Mükerrem Kaya, Bilge Sayın, Kübra Çinar Topçu and Güzin Kaban
Fermentation 2025, 11(12), 672; https://doi.org/10.3390/fermentation11120672 - 28 Nov 2025
Abstract
This study aimed to evaluate the impact of autochthonous strains (Pediococcus pentosaceus 128b, Latilactobacillus sakei S15, Lactiplantibacillus plantarum S91, L. plantarum S24 and Staphylococcus carnosus G109) used as mono and mixed starter cultures on the quality attributes of traditionally produced sucuk, a
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This study aimed to evaluate the impact of autochthonous strains (Pediococcus pentosaceus 128b, Latilactobacillus sakei S15, Lactiplantibacillus plantarum S91, L. plantarum S24 and Staphylococcus carnosus G109) used as mono and mixed starter cultures on the quality attributes of traditionally produced sucuk, a Turkish dry fermented sausage, in a local small-scale facility. At the end of ripening, samples underwent comprehensive microbiological and physicochemical analyses. The use of autochthonous starter cultures (ASC) showed no statistically significant influence on thiobarbituric acid-reactive substances and water activity value. Lower pH values were observed in groups with autochthonous lactic acid bacteria strains (ALABS) compared to the control group. However, ALABS inhibited Micrococcus/Staphylococcus growth by rapidly lowering the pH, except in the groups with S. carnosus G109. The use of ASC led to an increase in the L* values of sucuk samples, except monoculture L. plantarum S91. The correlation heat map illustrating the relationships between the starter cultures and volatile compounds revealed that all groups containing L. plantarum S91 exhibit a volatile compound profile different from other single or mixed cultures. According to the results of the principal component analysis performed to determine the relationship between the chemical groups of the starter cultures and volatile compounds, the groups containing L. plantarum S91 differed from the other groups and showed positive correlations with phenols, furans, acids, terpenes, aromatic hydrocarbons, ketones, nitrogenous compounds, esters, and aliphatic hydrocarbons.
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(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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Open AccessArticle
Applications of Enzymatic-Ultrasonic Treatment for the Integrated Processing of Secondary Fish Raw Materials and the Production of Food Ingredients
by
Natalia Naumenko, Anastasia Antonova, Irina Kalinina and Rinat Fatkullin
Fermentation 2025, 11(12), 670; https://doi.org/10.3390/fermentation11120670 - 28 Nov 2025
Abstract
The rapidly developing food industry necessitates the efficient use of raw materials, which can be achieved through the production of functional ingredients with high nutritional value. Secondary fish raw materials generated during the filleting of Atlantic cod (Gadus morhua), including vertebral
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The rapidly developing food industry necessitates the efficient use of raw materials, which can be achieved through the production of functional ingredients with high nutritional value. Secondary fish raw materials generated during the filleting of Atlantic cod (Gadus morhua), including vertebral bones with residual muscle tissue, skin, tails, and fins, represent a promising source of both biologically active compounds and highly digestible protein substances. The aim of this study was to evaluate the properties of protein hydrolysates obtained from secondary Atlantic cod raw materials by conventional enzymatic hydrolysis and combined enzymatic-ultrasonic treatment. The best results were achieved at a power of 320 W and a treatment duration of 3.5 min prior to the addition of the enzyme preparation (Protozyme C). The application of ultrasound enhanced the degree of hydrolysis by 4–5% while simultaneously reducing the amount of enzyme used. Electrophoretic analysis demonstrated a predominance of smaller peptides in the 10–15 kDa range compared to the control sample (43–95 kDa). Infrared spectroscopy confirmed structural changes in the samples under study, manifested in an increase in the number of terminal groups and partial disaggregation of the peptide mixture. Particle size distribution analysis revealed a more uniform distribution and a decrease in the median particle size in samples with ultrasonic pretreatment. The safety and antioxidant activity assessment did not show any toxic effects, but manifested a significant increase in antioxidant indicators (2.5–3.2 times) compared to the control sample. The results obtained show the enzymatic-ultrasonic treatment to be promising for the integrated processing of fish raw materials and the production of functional food ingredients with improved properties.
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(This article belongs to the Section Fermentation for Food and Beverages)
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Machine Learning-Based Discovery of Antimicrobial Peptides and Their Antibacterial Activity Against Staphylococcus aureus
by
Yuetong Fu, Zeyu Yan, Jingtao Yuan, Yishuai Wang, Wenqiang Zhao, Ziguang Wang, Jingyu Pan, Jing Zhang, Yang Sun and Ling Jiang
Fermentation 2025, 11(12), 669; https://doi.org/10.3390/fermentation11120669 - 28 Nov 2025
Abstract
The escalating crisis of antibiotic resistance, particularly concerning foodborne pathogens such as Staphylococcus aureus and its biofilm contamination, has emerged as a major global challenge to food safety and public health. Biofilm formation significantly enhances the pathogen’s resistance to environmental stresses and disinfectants,
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The escalating crisis of antibiotic resistance, particularly concerning foodborne pathogens such as Staphylococcus aureus and its biofilm contamination, has emerged as a major global challenge to food safety and public health. Biofilm formation significantly enhances the pathogen’s resistance to environmental stresses and disinfectants, underscoring the urgent need for novel antimicrobial agents. In this study, we isolated Bacillus strain B673 from the saline–alkali environment of Xinjiang, conducted whole-genome sequencing, and applied antiSMASH analysis to identify ribosomally synthesized and post-translationally modified peptide (RiPP) gene clusters. By integrating an LSTM-Attention-BERT deep learning framework, we screened and predicted nine novel antimicrobial peptide sequences. Using a SUMO-tag fusion tandem strategy, we achieved efficient soluble expression in an E. coli system, and the purified products exhibited remarkable inhibitory activity against Staphylococcus aureus (MIC = 3.13 μg/mL), with inhibition zones larger than those of the positive control. Molecular docking and dynamic simulations demonstrated that the peptides can stably bind to MurE, a key enzyme in cell wall synthesis, with negative binding free energy, suggesting an antibacterial mechanism via MurE inhibition. This study provides promising candidate molecules for the development of anti-drug-resistant agents and establishes an integrated research framework for antimicrobial peptides, spanning gene mining, intelligent screening, efficient expression, and mechanistic elucidation.
Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)
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Open AccessArticle
Isolation and Partial Characterization of Lactic Acid Bacteria from Natural Whey Starter Culture
by
Ida De Chiara, Rosangela Marasco, Milena Della Gala, Alberto Alfano, Darshankumar Parecha, Noemi Costanzo, Chiara Schiraldi and Lidia Muscariello
Fermentation 2025, 11(12), 668; https://doi.org/10.3390/fermentation11120668 - 28 Nov 2025
Abstract
Natural whey starter (NWS) cultures are microbial consortia characterized by high microbial diversity in terms of genus and species, as well as strains, accounting for the variety of different characteristics and quality of the artisanal fermented food. By means of a combined approach,
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Natural whey starter (NWS) cultures are microbial consortia characterized by high microbial diversity in terms of genus and species, as well as strains, accounting for the variety of different characteristics and quality of the artisanal fermented food. By means of a combined approach, using plate counts, bacterial isolation, molecular identification, and genotyping, we analyzed 41 colonies isolated from NWS of cow milk used in the production of caciocavallo, a typical pasta filata Italian cheese. Results revealed that 27 of them were lactic acid bacteria (LAB), including Lactococcus lactis as the dominant species, followed by Streptococcus thermophilus, Enterococcus faecium, Limosilactobacillus fermentum, Lactobacillus helveticus, and Lacticaseibacillus rhamnosus. The remaining isolates were taxonomically identified as non-LAB, probably due to environmental contamination. These results were mostly confirmed by metagenomic analysis, with the exception of only three species. Finally, small-scale fermentation experiments were performed in both standard media and skimmed milk to further characterize the newly isolated LAB strains. Overall, our results show that, except for four of the Lactococcus isolates and one Streptococcus, which show multi-drug resistance, the isolated strains under study exhibit levels of acidifying, metabolic properties, and safety parameters, suggesting their potential as starter cultures in cheese production.
Full article
(This article belongs to the Special Issue Probiotic Lactic Acid Bacteria and Their Applications in Food Safety and Animal Health)
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Open AccessArticle
An Engineered Multi-Enzyme Cascade with Low-Cost ATP Regeneration for Efficient D-Allulose Production from D-Fructose
by
Yutong Lu, Huayang Tang, Dexun Fan, Qingzhu Wang and Shuangyan Han
Fermentation 2025, 11(12), 667; https://doi.org/10.3390/fermentation11120667 - 28 Nov 2025
Abstract
D-Allulose is a promising low-calorie rare sugar with significant health benefits. However, its industrial production is hindered by the low catalytic efficiency (≤33% conversion) and unfavorable equilibrium of the key enzyme, D-allulose 3-epimerase (DAE). To overcome this thermodynamic bottleneck, an in vitro synthetic
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D-Allulose is a promising low-calorie rare sugar with significant health benefits. However, its industrial production is hindered by the low catalytic efficiency (≤33% conversion) and unfavorable equilibrium of the key enzyme, D-allulose 3-epimerase (DAE). To overcome this thermodynamic bottleneck, an in vitro synthetic enzymatic cascade based on a phosphorylation–dephosphorylation strategy was constructed. This engineered system comprises four synergistically operating enzymes: D-allulose-3-epimerase (DAE), L-rhamnulose kinase (RhaB), polyphosphate kinase (PPK), and acid phosphatase (AP). Through rational design and systematic optimization, the cascade achieved an exceptional 84.5% conversion yield from 50 mM D-fructose. Importantly, the system also maintained high conversion rates of 64.4% and 61.1% at high D-fructose loadings (50–100 g L−1). This performance, together with the integration of a low-cost PolyP6–PPK ATP regeneration module, underscores the potential industrial applicability of the proposed cascade strategy.
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(This article belongs to the Special Issue Microbial Production of Industrial Enzymes)
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Nutritional and Physicochemical Attributes of Sourdough Breads Fermented with a Novel Pediococcus acidilactici ORE 5 Strain
by
Ioanna Mantzourani, Athanasios Alexopoulos, Gregoria Mitropoulou, Yiannis Kourkoutas and Stavros Plessas
Fermentation 2025, 11(12), 666; https://doi.org/10.3390/fermentation11120666 - 28 Nov 2025
Abstract
This study evaluated the application of Pediococcus acidilactici ORE 5 (applied in free or immobilized form in a prebiotic matrix called “trahanas”) in sourdough bread production. Specific volumes of all the produced bread samples varied at approximately the same levels (2.50 to 2.54
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This study evaluated the application of Pediococcus acidilactici ORE 5 (applied in free or immobilized form in a prebiotic matrix called “trahanas”) in sourdough bread production. Specific volumes of all the produced bread samples varied at approximately the same levels (2.50 to 2.54 mL/g), indicating a satisfactory dough expansion. In contrast, acidity differed significantly (p < 0.05). Sourdough bread produced with immobilized cells (IB) exhibited the lowest pH (4.30) and the highest titratable acidity (9.13 mL NaOH N/10), followed by the sourdough bread produced with free cells (FB) and the control bread (CB), reflecting the enhanced metabolic activity of immobilized cells supported by the prebiotic matrix. The organic acid analysis revealed higher levels of lactic (2.96 g/kg) and acetic acid (0.99 g/kg) in the IB sample, along with increased minor acids. The high organic acid content contributed to a delayed rope (14.7 days) and mold spoilage (7.3 days) compared to the CB sample, enhancing microbial stability. In addition, the nutritional properties of the produced sourdough breads containing P. acidilactici ORE 5 were improved significantly. The IB sample demonstrated the highest total phenolic content (85 mg GAE/100 g), followed by the FB sample (61 mg/100 g) and the CB sample (48 mg/100 g), while phytic acid levels were markedly reduced (93% in IB and 80% in FB). A sensory evaluation confirmed the maintained overall acceptability, with enhanced flavor scores for sourdough breads containing P. acidilactici ORE 5. These findings indicate that P. acidilactici ORE 5, particularly in immobilized form, could be an effective functional starter culture for sourdough bread, highlighting its potential for applications in functional bakery products.
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(This article belongs to the Special Issue Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and Health Bioprocesses)
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Open AccessReview
Utilization of Non-Saccharomyces to Address Contemporary Winemaking Challenges: Species Characteristics and Strain Diversity
by
Spiros Paramithiotis, Jayanta Kumar Patra, Yorgos Kotseridis and Maria Dimopoulou
Fermentation 2025, 11(12), 665; https://doi.org/10.3390/fermentation11120665 - 27 Nov 2025
Abstract
Winemaking is facing significant challenges caused by industrialization of the process, climate change, and increased consumer awareness regarding the use of chemical preservatives. Although several solutions have been proposed, the utilization of non-Saccharomyces species seems to be the most efficient one. Several
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Winemaking is facing significant challenges caused by industrialization of the process, climate change, and increased consumer awareness regarding the use of chemical preservatives. Although several solutions have been proposed, the utilization of non-Saccharomyces species seems to be the most efficient one. Several non-Saccharomyces species have been employed for this purpose, with Hanseniaspora uvarum, H. vineae, Kluyveromyces marxianus, Lachancea thermotolerans, Metschnikowia pulcherrima, Pichia fermentans, P. kluyveri, Schizosaccharomyces pombe, Starmerella bacillaris, Torulaspora delbrueckii, and Wickerhamomyces anomalus being the most promising ones. However, only a restricted amount of metabolic activities can be reliably attributed to the species level, while most of them are characterized by strain variability and are also affected by the Saccharomyces cerevisiae strains used to carry out alcoholic fermentation, as well as the efficient supply of precursor molecules by the grape varieties and the conditions for their effective bioconversion. This variability necessitates the application of optimization strategies, taking into consideration all these parameters. This review article aims to assist in this direction by collecting the data referring to the winemaking practice of the most interesting non-Saccharomyces species, presenting clearly and comprehensively their most relevant features, and highlighting the effect of strain diversity.
Full article
(This article belongs to the Topic The Biotechnological Potential of Non-Saccharomyces Yeasts)
Open AccessArticle
Engineering Saccharomyces cerevisiae to Enhance Fatty Acid Production via Formate Electrolytes
by
Yu Hou, Yubo Wang, Tianpeng Ma, Shuobo Shi, Zheng Wang, Chun Shen, Yunming Fang, Fenghui Ye and Zihe Liu
Fermentation 2025, 11(12), 664; https://doi.org/10.3390/fermentation11120664 - 27 Nov 2025
Abstract
Fossil fuel overuse drives excessive CO2 emissions, exacerbating environmental degradation and climate change. Coupling electrochemistry with microbial fermentation provides a promising route to convert CO2 into fuels and chemicals. However, microbial electrolytic solution tolerance remains a critical bottleneck, as observed in
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Fossil fuel overuse drives excessive CO2 emissions, exacerbating environmental degradation and climate change. Coupling electrochemistry with microbial fermentation provides a promising route to convert CO2 into fuels and chemicals. However, microbial electrolytic solution tolerance remains a critical bottleneck, as observed in model organisms like Saccharomyces cerevisiae (S. cerevisiae). To address this, we engineered S. cerevisiae to utilize electrochemically derived formate, thereby boosting free fatty acids (FFAs) production. By optimizing culture conditions and heterologously expressing formate dehydrogenase (FDH), we improved formate assimilation efficiency. Additionally, we introduced stress-resistant genes for a better electrolytic solution tolerance to sustain growth and FFAs synthesis under harsh electrolytic conditions (e.g., high formate/salt ion concentrations), eliminating the need to separate formate from the electrolyte post-electrolysis. In the presence of 4 g/L formate electrolytic medium, the engineered strain YB061 achieved a 41.9% increase in biomass and a formate conversion rate exceeding 97.0%. Compared to the parental strain, YB061 enhanced FFAs production by 92.8% by utilizing formate-containing electrolytes, demonstrating great potential for bio-electrochemical manufacturing. However, further work is needed to improve yeast tolerance to high formate concentrations and to enable direct coupling of CO2 electroreduction with microbial cultivation.
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(This article belongs to the Special Issue Yeast Fermentation, 2nd Edition)
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Open AccessReview
Secondary Metabolites from Actinokineospora spp.: Insights into a Sparsely Studied Genus of Actinomycetes
by
Oleksandr Yushchuk
Fermentation 2025, 11(12), 663; https://doi.org/10.3390/fermentation11120663 - 27 Nov 2025
Abstract
The genus Actinokineospora (family Pseudonocardiaceae) has recently emerged as a prolific source of structurally diverse, biologically active specialized metabolites. Actinokineospora spp. are filamentous actinomycetes isolated from various terrestrial biotopes. The genus is still sparsely represented taxonomically, with only 19 species holding validly
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The genus Actinokineospora (family Pseudonocardiaceae) has recently emerged as a prolific source of structurally diverse, biologically active specialized metabolites. Actinokineospora spp. are filamentous actinomycetes isolated from various terrestrial biotopes. The genus is still sparsely represented taxonomically, with only 19 species holding validly published names and genome sequences available for an additional six strains. Nevertheless, Actinokineospora appears to have one of the highest biosynthetic novelty index values among actinomycetes, making it a prime candidate for the discovery of new specialized metabolites. To date, several Actinokineospora strains have shown antimicrobial activity, including Actinokineospora acnipugnans R434T, Actinokineospora alba 03-9939T, Actinokineospora fastidiosa NRRL B-16697T, Actinokineospora riparia C-39162T, Actinokineospora sp. G85, and Actinokineospora sp. PR83; the active compounds from these strains remain to be identified and characterized. By contrast, detailed chemical characterization has been achieved for several producers: Actinokineospora spheciospongiae EG49T (polyketides actinospene and actinosporins; the lasso peptide actinokineosin), Actinokineospora bangkokensis 44EHWT (polyene thailandins), Actinokineospora fastidiosa ATCC 202099 (nocathiacin thiopeptides), Actinokineospora sp. UTMC 2448 (persiathiacin thiopeptides), and Actinokineospora auranticolor DSM 44650T (kineomіcin glycopeptides). Collectively, these findings establish Actinokineospora as a promising yet underexplored genus for antibiotic discovery and biosynthetic engineering. In this review, we summarize current knowledge on Actinokineospora spp. and provide an in-depth account of specialized metabolite production for those compounds whose structures have been elucidated.
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(This article belongs to the Special Issue Novel and Old Insights for Biotechnological Exploitation of Actinobacterial Strain Fermentations)
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Open AccessArticle
In Situ Digestibility and In Vitro Ruminal Fermentation of Foliage from Native Trees of the Chaco Region: Effects of Tree Species and Tannins
by
María Paz Corrales Marmol, Gilberto Vilmar Kozloski, Patricia Criscioni, Alejandro René Argüello, Maria Eduarda Pieniz Hamerski, Sandro José Giacomini, Celeste Maricel Bonnet, Orlando Rafael Miszczuk, Iván Daniel Filip and Claudio Antonio Pozo
Fermentation 2025, 11(12), 662; https://doi.org/10.3390/fermentation11120662 - 26 Nov 2025
Abstract
Ruminant production in the Chaco region relies on pastures and native forest foliage, whose nutritional value is poorly characterized and may be influenced by tannins. This study evaluated the in situ digestibility and in vitro ruminal fermentation of foliage from Prosopis affinis (PA),
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Ruminant production in the Chaco region relies on pastures and native forest foliage, whose nutritional value is poorly characterized and may be influenced by tannins. This study evaluated the in situ digestibility and in vitro ruminal fermentation of foliage from Prosopis affinis (PA), Prosopis nigra (PN), Acacia polyphylla (AP), Phyllostylon rhamnoides (PR), and Tabebuia nodosa (TN), incubated with or without polyethylene glycol (PEG) to assess the effects of tannin on gas production and nitrogen (N) compounds degradability. Foliage contained ≥17% crude protein (CP) and ≥40% fiber-bound N. Tannin concentration was >4% dry matter (DM) in PN and PA and <1% DM in PR, AP, and TN. In situ digestibility was ≤51% in all species except PR (73%; p < 0.05). Gas production was higher in PA, PR, and TN (p < 0.05), with no PEG effect. Methane production was not affected by tree species or PEG (p ≤ 0.277). Both species and PEG affected the effective N compounds degradability (END), with PEG increasing it in PN and AP (p < 0.05). Although foliage is high in CP, its digestibility is low; N is largely fiber-bound, and tannins may further limit END, factors to consider when including them in ruminant diets.
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(This article belongs to the Special Issue Research Progress of Rumen Fermentation)
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Characterization, Production, and Application of Antifungal Metabolites from Probiotic Levilactobacillus and Lactiplantibacillus Strains Isolated from Fermented Olives
by
Houssam Abouloifa, Sara Gaamouche, Nabil Ghabbour, Ismail Hasnaoui, Nour Eddine Bentouhami, Yahya Rokni, Salwa Karboune and Abdeslam Asehraou
Fermentation 2025, 11(12), 661; https://doi.org/10.3390/fermentation11120661 - 26 Nov 2025
Abstract
In this study, the characterization, production, and application of antifungal metabolites obtained from the Levilactobacillus (L. brevis S27) and two Lactiplantibacillus (L. pentosus S42 and L. plantarum S62) strains were evaluated. The lactic acid bacteria (LAB) cells showed antifungal activity against
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In this study, the characterization, production, and application of antifungal metabolites obtained from the Levilactobacillus (L. brevis S27) and two Lactiplantibacillus (L. pentosus S42 and L. plantarum S62) strains were evaluated. The lactic acid bacteria (LAB) cells showed antifungal activity against molds. The cell-free supernatant (CFS) of Levilactobacillus and Lactiplantibacillus presented antimicrobial activity against fungi and foodborne pathogenic bacteria, and the antifungal activity was significantly (p < 0.05) higher than that of the antibacterial activity. Moreover, the antifungal metabolites were characterized as proteinaceous compounds that remained stable under both high and low temperatures and demonstrated activity across a broad pH range. Additionally, metabolite production was significantly higher (p < 0.05) at an initial pH of 5 when incubated at either 25 °C or 37 °C. All strains and their CFSs exhibited strong bio-preservative effects against Penicillium digitatum in yogurt and against Aspergillus niger on orange fruit. Consequently, these Lactobacilli strains and their antifungal metabolites represent a novel approach to biocontrol in the agri-food industry and agricultural products.
Full article
(This article belongs to the Special Issue Recent Trends in Lactobacillus and Fermented Food, 3rd Edition)
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