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Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources

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A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Industrial Fermentation".

Deadline for manuscript submissions: closed (28 February 2026) | Viewed by 12160

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Dr. Yukun Zhang

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Laboratory of Aquatic Animal Nutrition, Faculty of Fisheries, Kagoshima University, Kagoshima 890-0056, Japan
Interests: nutrition; probiotic; aquatic; antioxidant; bio-enzyme; fermentation; immunology; intestinal microorganism
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Dr. Amina Moss

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Institute of Aquaculture, University of Stirling, Stirling, UK
Interests: crustacean; phospholipids; sustainable aquaculture; aquaculture welfare; aquaculture nutrition; feed additives; interaction of aquaculture feed and the environment; aquaponics
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Dr. Weilong Wang

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College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
Interests: aquaculture nutrition; carotenoids metabolism in crustaceans; live food cultivatology; functional feed additive
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Special Issue Information

Dear Colleagues,

In recent years, the global demand for high-quality sustainable animal feed has grown significantly. Fermentation offers a promising approach to address the challenges faced by the feed industry, particularly in enhancing the nutritional value of raw materials and optimizing the use of available resources. By improving the digestibility, protein content, and bioavailability of essential nutrients, fermentation can significantly reduce reliance on conventional feed ingredients such as fish- and soybean meal. Furthermore, fermentation processes can increase the presence of bioactive compounds, probiotics, and antioxidants, contributing to better animal health, growth performance, and environmental sustainability.

This Special Issue focuses on innovative fermentation strategies and their application in the feed industry, exploring novel methods, microbial solutions, and substrates which can enhance feed quality and efficiency. We welcome research papers, reviews, and case studies that contribute to the understanding and development of fermentation technologies aimed at optimizing raw material utilization, improving feed efficiency, and supporting a more sustainable and resource-efficient feed production system.

We look forward to your valuable contributions to this exciting field.

Dr. Yukun Zhang
Dr. Amina Moss
Dr. Weilong Wang
Guest Editors

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

animal feed optimization
waste valorization
nutrient bioavailability
sustainable feed ingredients
microbial fermentation
feed efficiency improvement
protein enhancement in feed
gut health and microbiota
fishmeal replacement
soybean meal replacement

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Published Papers (8 papers)

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Research

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25 pages, 2972 KB

Open AccessArticle

Application of Machine Learning Models (ANN vs. RF) in Optimizing the Fermentation of Sweet-Potato Waste in the Japanese Shochu Industry for Nutritional Enhancement

by Yukun Zhang, Manabu Ishikawa, Shunsuke Koshio, Saichiro Yokoyama, Na Jiang, Jiayi Chen, Yiwen Tong and Xiaoxiao Zhang

Fermentation 2026, 12(4), 191; https://doi.org/10.3390/fermentation12040191 - 9 Apr 2026

Viewed by 375

Abstract

To address the challenge of depleting traditional feed resources, this study aimed to biovalorize sweet potato waste (SPW), a major byproduct of the Japanese shochu industry, into a high-value functional animal feed. An innovative two-stage solid-state fermentation (SSF) was employed, featuring an initial aerobic stage with Aspergillus oryzae for substrate degradation, followed by an anaerobic stage with Lactobacillus plantarum for nutritional enhancement. To optimize this complex, multi-variable process, the predictive performance of Artificial Neural Network (ANN) and Random Forest (RF) machine learning models was compared based on an augmented experimental dataset (N = 80). To ensure statistical robustness and prevent data leakage, a repeated k-fold cross-validation strategy was implemented. The RF model demonstrated significantly superior accuracy and reliability than the ANN model, particularly in predicting the primary metric, crude protein (R² = 0.61 ± 0.04 vs. R² = 0.12 ± 0.15). Subsequently, the validated RF model was integrated with a Constrained Differential Evolution (CDE) algorithm for global parameter optimization. The optimized process was predicted to yield a final product with a crude protein content of 25.0%, alongside significant increases of 114.1% in total amino acids and 123.9% in essential amino acids. These projections were experimentally validated in vitro, confirming the model’s accuracy with a relative error of less than 5%. Furthermore, comprehensive biochemical assays demonstrated a massive degradation of anti-nutritional factors and significant enhancements in total phenolic content and antioxidant activity. This study provides a scientifically validated, data-driven framework for the valorization of SPW. It confirms the superior efficacy of ensemble learning methods for optimizing complex bioprocesses with limited data, offering a contribution to the development of a circular bioeconomy and sustainable feed resources. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

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14 pages, 1042 KB

Open AccessArticle

Effect of Limonene and a Cinnamaldehyde–Carvacrol Blend on the Fermentation, Nutritional Quality, and Aerobic Stability of Corn Silage

by Ronnie Coêlho de Andrade, Marco Antonio Previdelli Orrico Junior, Giuliano Reis Pereira Muglia, Isabele Paola de Oliveira Amaral, Ana Carolina Amorim Orrico and Mábio Silvan José Da Silva

Fermentation 2026, 12(3), 167; https://doi.org/10.3390/fermentation12030167 - 21 Mar 2026

Viewed by 644

Abstract

This study evaluated the effects of essential oils, such as limonene (LIM) and a cinnamaldehyde–carvacrol blend (CCB), on the fermentation, chemical composition, in vitro digestibility, and aerobic stability of corn silage stored for 150 and 200 days. Treatments included a control, CCB (100 and 200 mg/kg DM), and LIM (100 and 200 mg/kg DM). Essential oils improved fermentation by increasing lactic acid (up to 7.46% of DM) and reducing proteolysis (NH₃-N: 0.46–0.59% of total N). Limonene, particularly at 100 mg/kg DM, enhanced the lactic:acetic acid ratio (up to 3.07), better preserved non-fiber carbohydrates (≈32.7%), and increased in vitro DM digestibility (up to 81.5%) compared to the control (≈76.0%). The CCB treatment raised acetic acid concentrations (up to 3.04% of DM). Extending storage to 200 days reduced DM recovery (≈84.0%) versus 150 days (92.5%). Treated silages showed greater aerobic stability, with a lower pH increase after 72 h of air exposure, most notably in the LIM 200 treatment (pH 4.10) compared to the control (pH 5.40). Essential oils, particularly limonene, effectively improve the fermentative quality, nutritional value, and aerobic stability of corn silage under prolonged storage. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

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19 pages, 9449 KB

Open AccessArticle

Two High-Biofilm-Producing Lactiplantibacillus pentosus Strains Maintain Gut Microbiota Balance in Chicks via Antibacterial Activity

by Huibin Qin, Hongyu Liu, Zhiwei Huang, Zhiqiang Zhang, Haigang Wang, Sen Hou, Meng Li, Xiaoning Cao, Zhijun Qiao, Hongjiang Yang and Zhixin Mu

Fermentation 2026, 12(1), 6; https://doi.org/10.3390/fermentation12010006 - 21 Dec 2025

Viewed by 682

Abstract

Lactic acid bacteria can colonize the gut, thereby regulating the gut microbiota and improving intestinal health. The study aimed to screen the suitable strains for Suanzhou fermentation and investigate their roles in the chicken gut in vivo. A total of 70 strains of lactic acid bacteria isolated from Suanzhou were characterized to determine their biofilm formation abilities. The strains with high-yielding biofilms were further characterized for their optimum growth temperature and pH, as well as antibacterial effects. Based on the results of biofilm formation, temperature and pH tolerance, and antibacterial effect experiments, two strains of h8-c and p15-c (Lactiplantibacillus pentosus) with high-yielding biofilms and better antibacterial effects were selected. By establishing a chick Lactobacillus feeding model and using high-throughput techniques to analyze the structure and diversity of the gut microbiota, we investigated changes in the diversity of gut bacteria, fungi, and archaea during and for three weeks after feeding with h8-c and p15-c. The results indicate that h8-c and p15-c may promote the intestinal colonization of lactobacilli, thereby balancing the gut microbiota and enhancing intestinal health in chicks. Furthermore, these strains provide excellent candidates for the industrial fermentation of Suanzhou. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

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14 pages, 461 KB

Open AccessArticle

Modulating Fermentation in Total Mixed Ration Silages Using Lasalocid Sodium and Essential Oils

by Isabele Paola de Oliveira Amaral, Mariany Felex de Oliveira, Marco Antonio Previdelli Orrico Junior, Marciana Retore, Tatiane Fernandes, Yara América da Silva, Ana Carolina Amorim Orrico, Ronnie Coêlho de Andrade and Giuliano Reis Pereira Muglia

Fermentation 2025, 11(8), 468; https://doi.org/10.3390/fermentation11080468 - 15 Aug 2025

Cited by 2 | Viewed by 996

Abstract

This study evaluated the effects of lasalocid sodium (LASA) and essential oils on the fermentation and nutritional quality of total mixed ration (TMR) silages. A 4 × 2 factorial design tested four additives—a control (distilled water), LASA (375 mg/kg DM), limonene essential oil (LEO), and a blend of cinnamaldehyde and carvacrol (EOB), both at 400 mg/kg DM—during summer and autumn. The TMRs were formulated to meet the nutritional requirements of lactating cows producing 20 kg of milk per day. After 110 days of ensiling, silages were analyzed for fermentation losses, pH, short-chain fatty acids, ammoniacal nitrogen (NH₃-N), aerobic stability (AS), and chemical composition. The additives significantly improved dry matter recovery (DMR), especially LASA and EOB in autumn. EOB showed the lowest effluent losses and highest AS, with higher acetic acid and lower NH₃-N contents. LEO and EOB increased lactic acid, while LASA reduced ethanol and butyric acid levels in summer. Crude protein increased with LEO in autumn, and LASA and LEO improved total digestible nutrients (TDNs) in summer. EOB-treated silages had higher fiber fractions in autumn, without compromising feed value. Therefore, LASA, LEO, and particularly EOB enhanced silage fermentation and nutrient preservation, with EOB showing the most consistent results across seasons. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

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15 pages, 1280 KB

Open AccessArticle

The Fermentative and Nutritional Effects of Limonene and a Cinnamaldehyde–Carvacrol Blend on Total Mixed Ration Silages

by Isabele Paola de Oliveira Amaral, Marco Antonio Previdelli Orrico Junior, Marciana Retore, Tatiane Fernandes, Yara América da Silva, Mariany Felex de Oliveira, Ana Carolina Amorim Orrico, Ronnie Coêlho de Andrade and Giuliano Reis Pereira Muglia

Fermentation 2025, 11(7), 415; https://doi.org/10.3390/fermentation11070415 - 18 Jul 2025

Cited by 2 | Viewed by 1080

Abstract

This study evaluated the effects of different doses of limonene essential oil (LEO) and a blend of cinnamaldehyde and carvacrol (BCC) on the fermentative quality and chemical–bromatological composition of total mixed ration (TMR) silages. Two independent trials were conducted, each focused on one additive, using a completely randomized design with four treatments (0, 200, 400, and 600 mg/kg of dry matter), replicated across two seasons (summer and autumn), with five replicates per treatment per season. The silages were assessed for their chemical composition, fermentation profile, aerobic stability (AS), and storage losses. In the LEO trial, the dry matter (DM) content increased significantly by 0.047% for each mg/kg added. Dry matter recovery (DMR) peaked at 97.9% at 473 mg/kg (p < 0.01), while lactic acid (LA) production reached 5.87% DM at 456 mg/kg. Ethanol concentrations decreased to 0.13% DM at 392 mg/kg (p = 0.04). The highest AS value (114 h) was observed at 203.7 mg/kg, but AS declined slightly at the highest LEO dose (600 mg/kg). No significant effects were observed for the pH, neutral detergent fiber (NDF), acid detergent fiber (ADF), crude protein (CP), or non-fiber carbohydrates (NFCs). In the BCC trial, DMR reached 98.2% at 548 mg/kg (p < 0.001), and effluent losses decreased by approximately 20 kg/ton DM. LA production peaked at 6.41% DM at 412 mg/kg (p < 0.001), and AS reached 131 h at 359 mg/kg. BCC increased NDF (from 23.27% to 27.73%) and ADF (from 35.13% to 41.20%) linearly, while NFCs and the total digestible nutrients (TDN) decreased by 0.0007% and 0.039% per mg of BCC, respectively. In conclusion, both additives improved the fermentation efficiency by increasing LA and reducing losses. LEO was more effective for DM retention and ethanol reduction, while BCC improved DMR and AS, with distinct effects on fiber and energy fractions. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

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15 pages, 270 KB

Open AccessArticle

Performance, Metabolism, and Economic Implications of Replacing Soybean Meal with Dried Distillers Grains with Solubles in Feedlot Cattle Diets

by Andrei L. R. Brunetto, Guilherme L. Deolindo, Ana Luiza de F. dos Santos, Luisa Nora, Maksuel Gatto de Vitt, Renato S. de Jesus, Bruna Klein, Luiz Eduardo Lobo e Silva, Roger Wagner, Gilberto V. Kozloski and Aleksandro S. da Silva

Fermentation 2025, 11(7), 363; https://doi.org/10.3390/fermentation11070363 - 23 Jun 2025

Cited by 1 | Viewed by 2414

Abstract

The growing demand for biofuels, especially ethanol produced from corn, has driven the production of co-products such as dried distillers grains with solubles (DDGS). With a high protein content (around 30%), fiber, and minerals, DDGS presents an economical alternative for animal nutrition, replacing traditional sources like soybean meal while maintaining productive performance and reducing costs. This study evaluated the total replacement of soybean meal with DDGS in the diet of confined Holstein cattle, focusing on weight gain, feed intake, digestibility, feed efficiency, animal health, meat quality, and economic viability. The 24 animals received diets with 80% concentrate, containing either DDGS or soybean meal, and no significant differences were observed in terms of body weight (p = 0.92), feed intake (p = 0.98), or feed efficiency (p = 0.97) between the two treatments. The average daily gain was 1.25 and 1.28 kg for cattle in the DDGS and soybean meal groups, respectively (p = 0.92). Regarding metabolic and digestive parameters, no relevant changes were found in blood levels, except for higher serum cholesterol (p = 0.03) levels in animals fed DDGS. The digestibility of neutral detergent fiber (NDF) (p = 0.03) and acid detergent fiber (ADF) (p = 0.05) was lower in the DDGS group, while the digestibility of ether extract was higher (p = 0.02). Rumen fluid analysis revealed an increase in the production of short-chain fatty acids (p = 0.01), such as acetic and butyric acids (p = 0.01), in the DDG-fed animals. In terms of meat quality, animals fed DDGS produced meat with lower levels of saturated fatty acids (SFA) (p = 0.05) and higher levels of unsaturated fatty acids (UFA) (p = 0.02), especially oleic acid (p = 0.05). This resulted in a healthier lipid profile, with a higher UFA/SFA ratio (p = 0.01). In terms of economic viability, DDGS-based diets were 10.5% cheaper, reducing the cost of production per animal by 7.67%. Profitability increased by 110% with DDGS compared to soybean meal, despite the high transportation costs. Therefore, replacing soybean meal with DDGS is an efficient and economical alternative for feeding confined cattle, maintaining zootechnical performance, increasing meat lipid content and improving fatty acid profile, and promoting higher profitability. This alternative is particularly advantageous in regions with easy access to the product. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

17 pages, 2461 KB

Open AccessArticle

Optimization of Palm Kernel Cake Bioconversion with P. ostreatus: An Efficient Lignocellulosic Biomass Value-Adding Process for Ruminant Feed

by Aldo Ibarra-Rondón, Dinary Eloisa Durán-Sequeda, Andrea Carolina Castro-Pacheco, Pedro Fragoso-Castilla, Rolando Barahona-Rosales and José Edwin Mojica-Rodríguez

Fermentation 2025, 11(5), 251; https://doi.org/10.3390/fermentation11050251 - 1 May 2025

Cited by 2 | Viewed by 2313

Abstract

This study aims to optimize the bioconversion of palm kernel cake (PKC) by Pleurotus ostreatus to improve fungal biomass production, lignocellulolytic enzyme expression, and the nutritional value of the substrate as ruminant feed. Three inorganic nitrogen sources (ammonium sulfate, ammonium nitrate, and urea) were evaluated for fungal biomass production using a central composite design (CCD) in liquid fermentations. The formulated culture medium (18.72 g/L glucose and 0.39 g/L urea) effectively yielded better fungal biomass production (8 g/L). Based on these results, an extreme vertex design, mixtures with oil palm by-products (PK, hull, and fiber) supplemented with urea, were formulated, finding that PKC stimulated the highest biomass production and laccase enzyme activity in P. ostreatus. The transcriptome of P. ostreatus was obtained, and the chemical composition of the fermented PKC was determined. Transcriptomic analysis revealed the frequency of five key domains with carbohydrate-activated enzyme (CAZy) function: GH3, GH18, CBM1, AA1, and AA5, with activities on lignocellulose. In the fermented PKC, lignin was reduced by 46.9%, and protein was increased by 69.8%. In conclusion, these results show that urea is efficient in the bioconversion of PKC with P. ostreatus as a supplement for ruminants. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

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Review

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29 pages, 501 KB

Open AccessReview

Fermentation-Based Strategies for the Feed Industry: Nutritional Augmentation, Environmental Sustainability

by Yukun Zhang, Manabu Ishikawa, Na Jiang and Xiaoxiao Zhang

Fermentation 2026, 12(2), 103; https://doi.org/10.3390/fermentation12020103 - 11 Feb 2026

Viewed by 1843

Abstract

Global agriculture faces unprecedented challenges, including a projected population of 10 billion by 2050, declining arable land, and the urgent need to phase out antibiotic growth promoters (AGPs) to stem antimicrobial resistance (AMR). This review evaluates fermentation technology as a sustainable solution to the “food–feed–fuel” three competing land uses. We systematically compare solid-state fermentation (SSF) and submerged fermentation (SmF), highlighting their quantitative advantages: SSF offers 2–3× higher volumetric productivity and 70–90% lower water usage for solid wastes (e.g., soybean meal, wheat bran), while SmF provides superior process control for high-value products (e.g., single-cell protein). Key molecular mechanisms are discussed, including enzymatic degradation of anti-nutritional factors (up to 95% phytate and 98.8% tannin removal), mycotoxin detoxification (60–80% reduction), and biosynthesis of bioactive compounds (e.g., vitamin B12 enrichment up to 15-fold). Fermented feeds benefit many livestock species, particularly in organic and high-density farming systems, improving growth performance, gut health, and disease resistance while reducing environmental footprints. Advanced technologies such as AI-driven digital twins, CRISPR-based strain engineering, and precision fermentation are explored to overcome bottlenecks, including heat dissipation, strain stability, and process control. Despite challenges in scale-up, economics, and divergent global regulations (EU, USA, China, Southeast Asia, and Africa), fermentation is a critical biotechnological paradigm for circularity—the circular bioeconomy—and long-term food security. Future research should prioritize cost-effective large-scale implementation and the harmonization of regulatory frameworks. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

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