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Fermentation
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Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques
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Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques

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

Deadline for manuscript submissions: 20 November 2025 | Viewed by 4726

Special Issue Editors

Dr. Paola Foti

E-Mail Website
Guest Editor
Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Rome, Italy
Interests: fermentation; functional food; bioactive compounds; omics; microorganisms
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Flora Valeria Romeo

E-Mail Website
Guest Editor
Council for Agricultural Research and Economics (CREA), Research Centre for Olive, Fruit and Citrus Crops, Acireale, CT, Italy
Interests: food by-products as nutraceuticals or antimicrobials; polyphenols; development of new functional foods

Special Issue Information

Dear Colleagues,

The reuse and valorization of the by-products of the agro-food industry represents a functional strategy to reduce waste along the production chain, contain costs, and obtain new matrices that can be reused as “co-products”. Indeed, agro-food by-products provide a source of bioactive molecules that can be effectively recovered and valorized across various application sectors, including food, cosmetics, pharmaceuticals, and animal feeds. Although several conventional strategies have been proposed for the recovery of these by-products, green technologies are playing an increasingly important role from the perspective of sustainability and the transition towards circular models. In this context, fermentation, based on the use of microbial cultures, appears to be a low-cost and low-energy process capable of generating highly added-value products from residual matrices. Biotransformation enables the desired changes, such as improved microbiological safety, nutritional and sensory properties, and extended shelf-life, and fermentation, therefore, represents a promising technological strategy to produce new foods and/or functional ingredients, contributing significantly to the implementation of a sustainable circular model.

Dr. Paola Foti
Dr. Flora Valeria Romeo
Guest Editors

Manuscript Submission Information

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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • by-product
  • fermentation
  • starter cultures
  • bioactive molecules
  • biotechnology approaches

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Published Papers (5 papers)

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Research

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16 pages, 1477 KB  
Article
Valorization of Oat Husk for the Production of Fermentable Sugars, Xylooligosaccharides, and Inulinase via Deep Eutectic Solvent and Microwave-Assisted Pretreatment
by Hatice Gözde Hosta Yavuz, Ibrahim Yavuz and Irfan Turhan
Fermentation 2025, 11(10), 561; https://doi.org/10.3390/fermentation11100561 - 28 Sep 2025
Viewed by 700
Abstract
This study presents an integrated valorization strategy for oat husks through microwave-assisted pretreatment using a deep eutectic solvent (DES) composed of choline chloride and glycerol (1:2). The process was designed to enhance the release of fermentable sugars, enable xylooligosaccharide (XOS) production, and support [...] Read more.
This study presents an integrated valorization strategy for oat husks through microwave-assisted pretreatment using a deep eutectic solvent (DES) composed of choline chloride and glycerol (1:2). The process was designed to enhance the release of fermentable sugars, enable xylooligosaccharide (XOS) production, and support inulinase production by Aspergillus niger A42 via submerged fermentation of the hydrolysate and solid-state fermentation of the residual biomass. Response surface methodology (RSM) was applied to evaluate the effects of microwave power, treatment time, and liquid-to-solid ratio (LSR) on fermentable sugar content (FSC) and total phenolic compounds (TPCs). Following pretreatment, the biomass was hydrolyzed using 1.99% sulfuric acid for 1 min. Optimal pretreatment conditions (350 W, 30 s, LSR 4 w/w) yielded an FSC of 51.14 g/L. Additionally, 230.78 mg/L xylohexaose and 6.47 mg/L xylotetraose were detected. Submerged fermentation of the liquid fraction with A. niger A42 resulted in inulinase and invertase activities of 60.45 U/mL and 21.83 U/mL, respectively. Solid-state fermentation of the pretreated solids produced 37.03 U/mL inulinase and 17.64 U/mL invertase. The integration of microwave-assisted DES pretreatment, dilute acid hydrolysis, and fungal fermentation established a robust strategy for the sequential production of XOS, fermentable sugars, and inulinase from oat husks, supporting their comprehensive utilization within a sustainable biorefinery framework. Full article
(This article belongs to the Special Issue Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques)
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15 pages, 607 KB  
Article
Improvement of Thermophilic Butanol Production by Thermoanaerobacterium thermosaccharolyticum from Waste Figs Through the Gradual Addition of Butyric Acid
by Ebru Özkan and Hidayet Argun
Fermentation 2025, 11(10), 548; https://doi.org/10.3390/fermentation11100548 - 23 Sep 2025
Viewed by 513
Abstract
This study focuses on determining the optimal fig and butyric acid concentrations for butanol production under thermophilic conditions. Waste fig is a potentially rich substrate in sugars, minerals, and vitamins, but it is insufficient for effective butanol formation when butyrate is not present [...] Read more.
This study focuses on determining the optimal fig and butyric acid concentrations for butanol production under thermophilic conditions. Waste fig is a potentially rich substrate in sugars, minerals, and vitamins, but it is insufficient for effective butanol formation when butyrate is not present in the media because butanol is produced by butyrate reduction. Therefore, butyric acid was supplemented gradually in certain concentrations to fig-containing fermentation broth. The best combination of butyric acid and fig was determined using the Box–Wilson statistical experiment design. Fig and butyric acid concentrations were set as independent variables, while butanol concentration was the objective function. When the concentrations of butyric acid and fig were near the middle of the ranges under inspection, more butanol was produced. Butanol production was the lowest as fig and butyric acid values got closer to the extremes, particularly at high concentrations. Maximum butanol of 0.32 g/L was obtained with 16 g fig/L and 1.6 g butyric acid/L. The quadratic model generated was found to be significant, and its reliability was tested with verification experiments with reproducible results. This study showed that butanol could be produced from butyrate-supplemented fig waste under thermophilic conditions with a consolidated bioprocessing approach. Full article
(This article belongs to the Special Issue Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques)
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15 pages, 2645 KB  
Article
Bioconversion of a Glycerol- and Methanol-Rich Residue from Biodiesel Industry into 1,3-Propanediol: The Role of Magnesium
by Rafael de Moraes Altafini, Giovana Masson Fachin and Valeria Reginatto
Fermentation 2025, 11(7), 370; https://doi.org/10.3390/fermentation11070370 - 26 Jun 2025
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Abstract
Biodiesel is one of the most important biofuels worldwide. Besides glycerol, the residual aqueous phase of the transesterification reaction (RAPTR) from the biodiesel industry contains a high concentration of methanol. Here, we propose using RAPTR as substrate for Clostridium beijerinckii Br21 to produce [...] Read more.
Biodiesel is one of the most important biofuels worldwide. Besides glycerol, the residual aqueous phase of the transesterification reaction (RAPTR) from the biodiesel industry contains a high concentration of methanol. Here, we propose using RAPTR as substrate for Clostridium beijerinckii Br21 to produce 1,3-propanediol (1,3-PDO). 1,3-PDO is a valuable chemical compound widely used in the production of polymers, cosmetics, and pharmaceuticals. To diminish the methanol content, we pretreated RAPTR by low-pressure evaporation, which minimized water evaporation and prevented other contaminants from being concentrated. We optimized the evaporation conditions by using a 22 central composite rotational design to establish optimal temperature and time of 55 °C and 51.3 min, respectively. Pretreated RAPTR diluted at 20% (v v−1) with a nutrient solution allowed the bacterium to grow, but no glycerol was consumed. Supplementing the nutrient solution with 0.4 g L−1 MgCl2, defined in another experimental design, led the bacterium to consume glycerol and to produce 1,3-PDO. In the optimized conditions, pretreated RAPTR supplemented with MgCl2 gave 2.78 ± 0.01 g L−1 1,3-PDO in higher yield (Y1,3-PDO/glycerol) compared to the theoretical one, 0.61 and 0.50 g g−1, respectively. This result is relevant for biodiesel biorefineries, which could implement the innovative and customized strategy proposed herein to obtain 1,3-PDO, a high-value-added product, from a glycerol- and methanol-rich residue. Full article
(This article belongs to the Special Issue Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques)
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17 pages, 1694 KB  
Article
Enhancing Bioconversion of Crude Glycerol into Butanol and 1,3-Propanediol After Pretreatment by Coupling Fermentation and In Situ Recovery: Effect of Initial pH Control
by Alejandro Ortega, Alejo Valles, Miguel Capilla, Carmen Gabaldón, Francisco Javier Álvarez-Hornos and Paula Marzal
Fermentation 2025, 11(6), 339; https://doi.org/10.3390/fermentation11060339 - 11 Jun 2025
Viewed by 1140
Abstract
The sharp rise in the worldwide production of biodiesel has created an excess in the crude glycerol market, so it is essential to develop new added-value alternatives for crude glycerol. This paper describes a study on fermenting high concentrations of two types of [...] Read more.
The sharp rise in the worldwide production of biodiesel has created an excess in the crude glycerol market, so it is essential to develop new added-value alternatives for crude glycerol. This paper describes a study on fermenting high concentrations of two types of medium-pure crude glycerol to solvents by Clostridium pasteurianum. The effect of media composition (iron, yeast extract, and vitamins) on solvents production was assessed by a full factorial design with pure glycerol. Granular activated carbon (GAC) adsorption was highly effective in removing impurities from crude glycerol. Following GAC pretreatment, fermentation of glycerol at initial concentration as high as 60 g L−1 was possible, resulting in a butanol production of ~9 g L−1. Based on these results, a batch fermentation with in situ gas stripping and pH controlled at ≥6.5 was shown to be the best alternative to enhance biomass growth, glycerol uptake, and solvent production. The combination of controlling pH in the early stages of fermentation with in situ butanol removal stabilised the metabolism of the strain and showed that the fermentation performance with crude glycerol is very similar to that of pure glycerol. With a notable uptake of glycerol (>83%), solvent production was >11 g L−1 butanol (yield > 0.21 g g−1glycerol consumed) and >6 g L−1 1,3-propanediol (yield > 0.13 g g−1glycerol consumed). Setting the fermentation conditions to achieve a high uptake of high levels of glycerol with a similar product distribution is of great interest for the viability of the industrial processing of crude glycerol into chemicals via biological conversion. Full article
(This article belongs to the Special Issue Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques)
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Review

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14 pages, 5867 KB  
Review
Fermentation of Organic Wastes for Feed Protein Production: Focus on Agricultural Residues and Industrial By-Products Tied to Agriculture
by Dan He and Can Cui
Fermentation 2025, 11(9), 528; https://doi.org/10.3390/fermentation11090528 - 10 Sep 2025
Viewed by 1181
Abstract
Global population growth and dietary transition have intensified demand for livestock and aquaculture products, thereby escalating demand for high-quality animal feed. Conventional protein sources, including soybean meal and fishmeal, face severe supply constraints driven by intense competition for arable land, worsening water scarcity, [...] Read more.
Global population growth and dietary transition have intensified demand for livestock and aquaculture products, thereby escalating demand for high-quality animal feed. Conventional protein sources, including soybean meal and fishmeal, face severe supply constraints driven by intense competition for arable land, worsening water scarcity, overexploitation of fishery resources, and rising production costs. These challenges are especially pronounced within agricultural systems. Evidence demonstrates that converting agriculturally derived organic wastes and agri-industrial by-products into feed protein can simultaneously alleviate these pressures, address agricultural waste disposal challenges, and reduce the carbon footprint associated with agricultural production. This review synthesizes fermentation processes for generating feed protein from agricultural organic wastes by employing functionally adapted microorganisms or microbial consortia. This distinguishes it from prior studies, which focused solely on single waste streams or individual microbial strains. It aims to advance feed protein production through an integrated approach that unites agricultural organic wastes, microorganisms, and fermentation processes, thereby promoting resource-oriented utilization of agricultural organic wastes and providing actionable solutions to alleviate feed protein scarcity. Full article
(This article belongs to the Special Issue Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques)
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