Exploring Fermentation Strategies for the Valorization of Food By-Products and Their Bioactive Potential

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Fermentation for Food and Beverages".

Deadline for manuscript submissions: 30 January 2026 | Viewed by 10706

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Escuela de Ingeniería y Ciencias, Food and Biotech Lab, Tecnologico de Monterrey, Ave. General Ramón Corona 2514, Zapopan 45138, Jalisco, México
Interests: cloning; food microbiology; microbial molecular biology; biotechnology; microbiology; PCR; food microbiology and safety; food safety; food science and technology; antimicrobials
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Special Issue Information

Dear Colleagues,

The process of fermentation via microorganisms (e.g., fungi and lactic acid bacteria) has been used for centuries to improve the nutritional value of foods. There is a growing interest in utilizing fruit and food by-products as sources of bioactive substances for functional food development, disease prevention, and overall health improvement. Fermentation methods such as submerged fermentation (SmF) and solid-state fermentation (SSF) have emerged as novel strategies for the valorization of by-products, enabling the production of microbial enzymes, the extraction of bioactive compounds, and the enrichment of nutritional profiles, while also improving the bioactivity of these compounds. Despite the potential of these methods, there is limited research on optimizing specific fermentation parameters and conditions, while the comparison of submerged fermentation (SmF) and solid-state fermentation (SSF) remains insufficiently studied. Further investigation is also needed regarding indigenous and less-studied microorganisms with enhanced fermentative capabilities and bioactive compound production. Although some studies have noted the antioxidant and anti-inflammatory properties of fermented food by-products, comprehensive evaluations of their health benefits are still lacking, as is information related to the mechanisms that enhance the extraction and bioavailability of bioactive compounds post-fermentation. Additionally, the environmental benefits of utilizing food by-products in these fermentation processes remain unexplored. Therefore, the aim of this Special Issue is to provide a platform for the publication of valuable articles related to the fermentation strategies of food by-products, with a focus on SmF and SSF to enhance the extraction and bioavailability of bioactive compounds for functional food development.

Original research articles and reviews are both welcome. Research areas may include (but are not limited to) the following:

  • Optimization of solid-state and submerged fermentation processes;
  • Comparative analyses of fermentation processes;
  • Extraction of enzymes or bioactive molecules derived from fermentation;
  • Characterization of metabolites after the fermentation process using in vitro and in vivo models;
  • Mechanisms of bioactive compounds released during fermentation.

Prof. Dr. Tomas García-Cayuela
Guest Editor

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Keywords

  • by-products
  • solid-state fermentation
  • submerged fermentation
  • health benefits
  • bioactive compounds
  • extraction
  • enzymes

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Published Papers (8 papers)

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Research

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16 pages, 641 KB  
Article
A Strategy for Sustainable Production of Isoflavones from Black Soybean Okara via Solid-State Co-Fermentation
by Yi-Chung Lai, Bang-Yuan Chen, Jung-Feng Hsieh, Chien-Cheng Yeh, Cheng Huang, Meng-I Kuo and Chun-Ping Lu
Fermentation 2025, 11(11), 619; https://doi.org/10.3390/fermentation11110619 - 29 Oct 2025
Viewed by 745
Abstract
Okara, the soybean residue generated during soymilk and tofu production, is nutrient-rich but underutilized due to its high moisture content and perishability. This study established a sustainable solid-state co-fermentation strategy using Rhizopus oligosporus (BCRC 31631) and Yarrowia lipolytica (BCRC 21252) to enhance the [...] Read more.
Okara, the soybean residue generated during soymilk and tofu production, is nutrient-rich but underutilized due to its high moisture content and perishability. This study established a sustainable solid-state co-fermentation strategy using Rhizopus oligosporus (BCRC 31631) and Yarrowia lipolytica (BCRC 21252) to enhance the bioactive value of black soybean okara from two Taiwanese cultivars—Tainan No. 3 (TN.3) and Tainan No. 5 (TN.5). Co-fermentation markedly enhanced β-glucosidase activity, reaching 0.75 U/g DW at 30 °C after 48 h in TN.3 and 0.68 U/g DW after 24 h in TN.5, approximately 3.5-fold higher than single-strain fermentation. Near-complete (97–100%) hydrolysis of daidzin, glycitin, and genistin occurred within 24–48 h, producing 672.9 µg/g DM of total aglycone-type isoflavones—an ~11-fold increase compared with unfermented okara (61.5 µg/g DM), where most isoflavones (~740 µg/g DM) remained glycosylated. Varietal structure affected conversion efficiency: TN.3 exhibited stronger enzymatic responsiveness and higher aglycone yield, whereas TN.5 showed faster but less extensive transformation. The process also revealed a bioactive–pigment trade-off, as enhanced isoflavone activation coincided with anthocyanin degradation. These findings demonstrate that ambient-temperature solid-state co-fermentation effectively boosts β-glucosidase activity and isoflavone bioconversion, transforming low-value okara into a high-value functional ingredient consistent with circular bioeconomy and sustainable food system goals. Full article
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17 pages, 658 KB  
Article
Diet Formulated with Rice Bran Fermented by Rhizopus oryzae and Saccharomyces cerevisiae: Impacts on Zootechnical Performance and Intestinal Gene Expression in Zebrafish (Danio rerio)
by Gabriela Lenz, Rejane Macedo Martins, Jade Riet, Raíza dos Santos Azevedo, Arthur Cardoso, Bruna Félix da Silva Nornberg, Martín Bessonart, Larisa Magnone, Luis Fernando Fernandes Marins, Iuri Salim Abou Anni, Tatiane Penteado Gonçalves, Anelise Christ-Ribeiro and Marcelo Borges Tesser
Fermentation 2025, 11(10), 567; https://doi.org/10.3390/fermentation11100567 - 30 Sep 2025
Viewed by 773
Abstract
The growing demand for aquaculture has driven the search for sustainable practices and utilization of agro-industrial residues. Brown rice bran, an abundant and low-cost by-product, has emerged as a promising raw material. This dissertation aimed to evaluate solid-state fermentation (SSF) of rice bran [...] Read more.
The growing demand for aquaculture has driven the search for sustainable practices and utilization of agro-industrial residues. Brown rice bran, an abundant and low-cost by-product, has emerged as a promising raw material. This dissertation aimed to evaluate solid-state fermentation (SSF) of rice bran using the fungus Rhizopus oryzae and the yeast Saccharomyces cerevisiae with the goal of improving its nutritional value for use in diets formulated for zebrafish (Danio rerio). Proximate composition analyses revealed the strong biotransformation potential of Rhizopus oryzae. Fermentation with this fungus resulted in a significant 36.45% increase in protein content, a 51.62% increase in total polyphenols, and a 13.7% reduction in lipid content. In an in vivo experiment, zebrafish fed a diet containing rice bran fermented by R. oryzae showed the best zootechnical performance, with higher weight gain, specific growth rate, and improved feed conversion. Gene expression analysis showed a significant difference only for glut6, which is related to glucose transport. In summary, the fermentation of brown rice bran with Rhizopus oryzae represents an effective strategy to enhance its nutritional profile, establishing it as a viable alternative for the formulation of more sustainable and efficient diets in aquaculture. Full article
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21 pages, 719 KB  
Article
Changes in Ruminal Dynamics and Microbial Populations Derived from Supplementation with a Protein Concentrate for Cattle with the Inclusion of Non-Conventional Feeding Sources
by Diana Sofía Torres-Velázquez, Daniel Francisco Ramos-Rosales, Manuel Murillo-Ortiz, Jesús Bernardo Páez-Lerma, Juan Antonio Rojas-Contreras, Karina Aide Araiza-Ponce and Damián Reyes-Jáquez
Fermentation 2025, 11(8), 438; https://doi.org/10.3390/fermentation11080438 - 30 Jul 2025
Viewed by 902
Abstract
Feed supplementation strategies are essential for optimizing cattle productivity, and the incorporation of non-conventional feed resources may reduce both production costs and environmental impact. This study evaluated the effects of pelletized protein concentrates (including Acacia farnesiana, A. schaffneri, and Agave duranguensis [...] Read more.
Feed supplementation strategies are essential for optimizing cattle productivity, and the incorporation of non-conventional feed resources may reduce both production costs and environmental impact. This study evaluated the effects of pelletized protein concentrates (including Acacia farnesiana, A. schaffneri, and Agave duranguensis bagasse) on rumen fermentation parameters, microbial communities, and gas emissions. Fistulated bullocks received the concentrate daily, and ruminal contents were collected and filtered before and after supplementation to assess in vitro gas and methane production, pH, and microbial composition using high-throughput sequencing of 16S rRNA and mcrA amplicons. In addition, in situ degradability was evaluated during and after the supplementation period. Supplementation led to a significant (p < 0.05) reduction in degradability parameters and methane production, along with a marked decrease in the abundance of Methanobrevibacter and an increase in succinate-producing taxa. These effects were attributed to the enhanced levels of non-fiber carbohydrates, hemicellulose, crude protein, and the presence of bioactive secondary metabolites and methanol. Rumen microbiota composition was consistent with previously described core communities, and mcrA-based sequencing proved to be a valuable tool for targeted methanogen detection. Overall, the inclusion of non-conventional ingredients in protein concentrates may improve ruminal fermentation efficiency and contribute to methane mitigation in ruminants, although further in vivo trials on a larger scale are recommended. Full article
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15 pages, 1100 KB  
Article
Silage of the By-Products of Mollar de Elche and Wonderful Pomegranate Varieties Preserves Nutritional Value and Antioxidant Activity of Ruminant Feed
by Marina Galvez-Lopez, Jihed Zemzmi, Mihaela Iasmina Madalina Ilea, Francisca Hernández, Martín Rodríguez, José Ramón Díaz and Gema Romero
Fermentation 2025, 11(7), 392; https://doi.org/10.3390/fermentation11070392 - 8 Jul 2025
Viewed by 911
Abstract
The valorization of agro-industrial by-products for their use in animal feed leads to a reduction in inputs, creating the opportunity to optimize the sustainability of the agri-food chain, a priority of the SDG 2030 strategy; it also leads to a reduction in production [...] Read more.
The valorization of agro-industrial by-products for their use in animal feed leads to a reduction in inputs, creating the opportunity to optimize the sustainability of the agri-food chain, a priority of the SDG 2030 strategy; it also leads to a reduction in production costs. The objective of this study was to examine the changes that occur during the silage process of the pomegranate varieties Mollar de Elche (PDO) and Wonderful in terms of their nutritional and antioxidant characteristics for subsequent use in ruminant feed. Microsilos were created with the by-products of these two different pomegranate varieties. Two different microsilos for each variety were monitored on days 0 (raw material), 14, 35, 60, and 180. The variables studied included microbiology tracks, fermentation products, pH, dry matter (DM), macronutrient composition, organic acid and sugar contents, and antioxidant activity. The results show that, for both varieties, the silage process was successful; the stability of the fermentation process was determined by day 35, and its viability was ensured for a minimum period of 6 months. Furthermore, the nutritional characteristics of the raw material were preserved in the ensiled product. An evaluation of the total phenols and antioxidant capacity (ABTS and DPPH) showed that they remained stable throughout the monitoring period, despite the decrease in bioactive compounds (total phenols) at the end of the study period. It was concluded that silage is an effective preservation method for the by-products of Mollar de Elche and Wonderful pomegranate varieties, and its outcome presents valuable potential as a sustainable nutritional resource for ruminants. Full article
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14 pages, 1182 KB  
Article
Formulation of a Functional Probiotic Beverage Using Maesil (Prunus mume) Syrup By-Product Fermented by Lactiplantibacillus plantarum KFOM 0042
by Chan-Il Bae, Yoon-Soo Gwak, Dasol Nam, Tae Gyu Nam, Hyun-Seok Kim and Mi-Ju Kim
Fermentation 2025, 11(7), 368; https://doi.org/10.3390/fermentation11070368 - 26 Jun 2025
Viewed by 1191
Abstract
Maesil (Prunus mume) syrup is the most common form of maesil consumption in Korea; however, its production generates large quantities of by-products. This study aimed to develop a functional probiotic beverage through the lactic acid fermentation of maesil syrup by-products (MSBs). [...] Read more.
Maesil (Prunus mume) syrup is the most common form of maesil consumption in Korea; however, its production generates large quantities of by-products. This study aimed to develop a functional probiotic beverage through the lactic acid fermentation of maesil syrup by-products (MSBs). To optimize fermentation, eight strains of Lactiplantibacillus plantarum were tested, and KFOM 0042 was selected based on its superior acid production in MSBs. The effects of MSB concentration (5%, 10%, 15%, or 20%), pH levels (3, 4, or 5), and sugar type (none, glucose, fructose, or sucrose) were evaluated. The optimal conditions were found to be 20% MSB at pH 4 or 5, either without added sugar or with sucrose. After fermenting under these conditions for 4 days, the probiotic beverages were stored at 4 °C for 30 days to assess stability. All formulations maintained LAB counts above 7 log CFU/mL for 18 days, but only the beverage with sucrose sustained these levels for 25 days. Additionally, antioxidant activity, total polyphenol, and flavonoid content increased post-fermentation, with the highest lactic acid levels observed at pH 5. Overall, this study presents a novel strategy for upcycling MSB into a probiotic beverage with enhanced functional and microbial stability. Full article
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15 pages, 367 KB  
Article
The Effects of Solid-State Fermentation by Aspergillus spp. on the Nutritional Profile of Selected Agro-Industrial by-Products as Potential Feedstuffs for Weaner Rabbits
by Adedoyin Titi Amos, Damilola Uthman Kareem, Tolulope Modupe Adeleye, Emmanuel Abiodun Adeyeye, Munirat Olaide Abatan, Olusola Sarah Ayorinde, Esther Oluwasayo Adeboye, Maicon Sbardella, Adeboye Olusesan Fafiolu, Abimbola Oladele Oso and Olusegun Mark Obafemi Idowu
Fermentation 2025, 11(6), 356; https://doi.org/10.3390/fermentation11060356 - 19 Jun 2025
Cited by 1 | Viewed by 1241
Abstract
This study evaluates the effects of solid-state fermentation inoculated with Aspergillus spp. on the nutritional profile of selected agro-industrial by-products (AIBPs: cowpea shell, groundnut shell, soybean hull, and maize shaft). These AIBPs were assessed as potential feedstuffs in weaner rabbit diets, which often [...] Read more.
This study evaluates the effects of solid-state fermentation inoculated with Aspergillus spp. on the nutritional profile of selected agro-industrial by-products (AIBPs: cowpea shell, groundnut shell, soybean hull, and maize shaft). These AIBPs were assessed as potential feedstuffs in weaner rabbit diets, which often exhibit digestive disorders when introduced to highly lignified feed ingredients. The AIBPs were milled to a particle size of 2 mm, sterilized, and subjected to fermentation with Aspergillus spp. under microaerophilic conditions at 28 ± 2 °C for 10 days. Samples (four replicates per treatment) were analyzed for chemical constituents (mineral and proximate composition, anti-nutritional factors, and fibre fractions) before and after fermentation. Digestible energy and digestibility coefficient of gross energy were calculated. Data were subjected to two-way analysis of variance (ANOVA). There was an increase (p < 0.05) in mineral profile, proximate composition, digestible energy, digestibility coefficient of gross energy, and dry matter, with a reduction (p < 0.05) in crude fibre, fibre fractions, and anti-nutritional factors. It was concluded that fermentation with Aspergillus spp. improved the nutritional value of the selected agro-industrial by-products. Therefore, fermented materials possess a better nutritional profile to be used in feeding programs for weaner rabbits. This will ensure sustainable animal production and add value to agricultural waste, which would otherwise constitute an environmental nuisance. Full article
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Review

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24 pages, 346 KB  
Review
Valorization of Food Processing Wastewater for Astaxanthin Production by the Mixotrophic Fermentation of Microalgae: A Review
by Qian Lu, Limin Yang and Xiaowei Zhang
Fermentation 2025, 11(10), 580; https://doi.org/10.3390/fermentation11100580 - 9 Oct 2025
Viewed by 664
Abstract
Food processing wastewater (FPW) poses significant environmental risks due to its high nutrient load yet offers untapped potential as a low-cost feedstock for high-value compound production. This review critically evaluates the valorization of FPW for astaxanthin production through the mixotrophic fermentation of microalgae. [...] Read more.
Food processing wastewater (FPW) poses significant environmental risks due to its high nutrient load yet offers untapped potential as a low-cost feedstock for high-value compound production. This review critically evaluates the valorization of FPW for astaxanthin production through the mixotrophic fermentation of microalgae. Key microalgal species (e.g., Haematococcus pluvialis and Chromochloris zofingiensis) effectively remediate nutrients (nutrients removal of up to 100%) while synthesizing astaxanthin under stress-inducing conditions, such as nutrient starvation, salinity, and oxidative stress. Advanced strategies, such as two-stage cultivation, nutrient profile adjustment, and microbial co-cultivation, which could enhance astaxanthin yields and wastewater treatment efficiency were reviewed comprehensively. The resulting astaxanthin-rich biomass demonstrates multifunctional benefits in animal feed, improving meat quality, immunity, growth, and shelf life. However, this review identifies some challenges, including wastewater management risks, low digestibility of microalgae biomass, and astaxanthin instability during feed processing, which should be addressed properly in real-world applications. This integrated approach aligns with circular bio-economy principles, transforming FPW from an environmental liability into a resource for sustainable biotechnology. Full article
23 pages, 638 KB  
Review
Solid-State Fermentation as a Biotechnological Tool to Reduce Antinutrients and Increase Nutritional Content in Legumes and Cereals for Animal Feed
by Andrés Álvarez, Alejandra Rodríguez, Sandra Chaparro, Luis Miguel Borrás, Leidy Y. Rache, Maria H. Brijaldo and José J. Martínez
Fermentation 2025, 11(7), 359; https://doi.org/10.3390/fermentation11070359 - 20 Jun 2025
Cited by 2 | Viewed by 3671
Abstract
Antinutritional Factors (ANFs) are compounds produced by plants as defense mechanisms, and in high concentrations, they inhibit nutritional properties. Reducing these ANFs increases the presence of proteins, antioxidants, and vitamins, which is crucial for optimizing animal feed, particularly in developing countries where traditional [...] Read more.
Antinutritional Factors (ANFs) are compounds produced by plants as defense mechanisms, and in high concentrations, they inhibit nutritional properties. Reducing these ANFs increases the presence of proteins, antioxidants, and vitamins, which is crucial for optimizing animal feed, particularly in developing countries where traditional methods may be costly. Solid-state fermentation (SSF) has the potential to improve the nutritional quality of animal feed derived from cereals and legumes cultivated and non-commercially cultivated by reducing antinutrients and enhancing nutrient availability. This review also considers the potential of non-native species, including those exhibiting invasive behavior and taxonomic similarity to cultivated varieties, as alternative substrates for SSF. Additionally, SSF highlights the biological properties of ANFs when extracted and utilized for technological and industrial advancements. Solid-state fermentation with lactic acid bacteria could be an effective and straightforward method for reducing these antinutritional factors while simultaneously enriching protein content. The aim is to present solid-state fermentation as a biotechnological tool to reduce antinutritional factors and enhance the nutritional content of legumes and cereals that are not cultivated for animal feed. This perspective contributes to expanding the range of raw materials considered for SSF by including taxonomically related but underutilized and ecologically problematic plant resources. Full article
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