Exploring Fermentation Strategies for the Valorization of Food By-Products and Their Bioactive Potential—2nd Edition

A Special Issue of Fermentation (ISSN 2311-5637) belonging to the section "Fermentation for Food and Beverages".

Deadline for manuscript submissions: 30 November 2026 | Viewed by 2102

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Guest Editor
Tecnologico de Monterrey, School of Engineering and Sciences, Ave. General Ramón Corona 2514, Zapopan 45138, Mexico
Interests: fermentation strategies; bioactive compounds; food biotechnology; food by-products; food microbiology; food science
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Special Issue Information

Dear Colleagues,

Fermentation using microorganisms such as fungi and lactic acid bacteria has been employed for centuries to improve the nutritional quality and functionality of foods. In recent years, there has been growing interest in the valorization of fruit and food by-products as sustainable sources of bioactive compounds for functional food development, health promotion, and disease prevention in both human and animal nutrition systems. Fermentation strategies, including submerged fermentation (SmF) and solid-state fermentation (SSF), have emerged as powerful tools for converting food by-products into value-added ingredients, enabling enzyme production, enhanced release of bioactive compounds, and modulation of nutritional and functional profiles. However, despite significant progress, important knowledge gaps remain regarding the optimization of fermentation parameters, the comparative performance of SmF and SSF, and the role of indigenous or underexplored microorganisms with enhanced bioconversion capacity. Recent advances have also highlighted the importance of understanding fermentation-driven mechanisms that influence the extraction, transformation, and bioavailability of bioactive compounds, as well as their interactions with gut microbiota and their potential health-related effects in human and animal models. In addition, the environmental and sustainability implications of using food by-products in fermentation-based processes—within the framework of circular bioeconomy—require further investigation. Therefore, this Special Issue aims to provide a platform for high-quality original research and review articles addressing innovative and advanced fermentation strategies for the valorization of food by-products, with particular emphasis on SmF and SSF, bioactive compound functionality, bioavailability, and sustainable food and feed system applications.

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 strategies;
  • Extraction and production of enzymes, metabolites, or bioactive compounds derived from fermentation;
  • Characterization of fermentation-derived metabolites using in vitro, in vivo, and simulated digestion models relevant to human or animal health;
  • Mechanisms governing the release, transformation, and bioavailability of bioactive compounds during fermentation;
  • Role of microbial consortia and underexplored microorganisms in by-product valorization;
  • Fermentation-driven modulation of functional and nutritional properties;
  • Sustainability, circular bioeconomy, and environmental assessment of fermentation-based valorization processes.

Prof. Dr. Tomas García-Cayuela
Guest Editor

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 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-anonymized 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

  • food by-products
  • solid-state fermentation
  • submerged fermentation
  • functional ingredients
  • bioactive compounds
  • fermentation-derived metabolites
  • enzyme production
  • circular bioeconomy
  • food and feed applications

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Published Papers (3 papers)

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Research

17 pages, 1952 KB  
Article
Furan Inhibitor Effects on Native Lactic Acid Bacteria from Maule Region: Growth Kinetics and Lactic Acid Production from Agroindustrial Waste
by Vicente Barros, Maribel Mamani, Benjamín Castillo, Sara Cuadros-Orellana, Nidia Torres-Ponce and Cristian Valdés
Fermentation 2026, 12(9), 422; https://doi.org/10.3390/fermentation12090422 - 3 Sep 2026
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Abstract
Native Lactic Acid Bacteria (LAB) isolated from fruits and vegetables in Chile’s Maule Region were identified as Lactiplantibacillus plantarum and L. pentosus. Their growth and lactic acid production were evaluated under furan inhibitor stress (furfural and 5-methylfurfural (5-MF)) relevant to agroindustrial waste [...] Read more.
Native Lactic Acid Bacteria (LAB) isolated from fruits and vegetables in Chile’s Maule Region were identified as Lactiplantibacillus plantarum and L. pentosus. Their growth and lactic acid production were evaluated under furan inhibitor stress (furfural and 5-methylfurfural (5-MF)) relevant to agroindustrial waste valorization. In fruit hydrolysates containing natural furans (11–57 mg/L), LAB grew similarly to inhibitor-free controls and produced 17–25 g/L lactic acid. Under controlled conditions, furfural at 12 g/L reduced bacterial growth by over 80% and decreased lactic acid production to only 2 g/L. In contrast, 5-MF at the same concentration allowed substantially higher tolerance, with up to 7 g/L lactic acid. Benchmarked directly against the commercial reference strain Lactiplantibacillus plantarum PL8014 under identical conditions, the native isolate B1 matched or exceeded PL8014’s lactic acid output in most furfural and 5-MF concentrations tested, including the two most severe 5-MF conditions. Logistic growth and Luedeking–Piret models accurately described both bacterial growth dynamics and lactic acid production kinetics under all inhibitory conditions (R2 > 0.96). Inhibitor concentration proved more critical than inhibitor type, although furfural consistently showed stronger potency. These findings confirm the biotechnological potential of native Maule LAB and provide quantitative kinetic parameters for optimizing lactic acid production from lignocellulosic waste, supporting circular economy strategies. Full article
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17 pages, 2557 KB  
Article
From Waste to Resource: The Development of a Sustainable Bacterial Culture Medium from Wine Lees and Toxicity Evaluation in the Zebrafish Model
by Marina Edith Navarro, Emma Elizabeth Tymczyszyn, Carolina Soledad Martinez, María Jimena Prieto and Bárbara Mercedes Bravo-Ferrada
Fermentation 2026, 12(9), 415; https://doi.org/10.3390/fermentation12090415 - 1 Sep 2026
Viewed by 167
Abstract
Wine lees (WL) are one of the main byproducts generated during winemaking and are usually disposed of in landfills or incorporated into the soil as an organic amendment; nevertheless, these practices can have negative environmental impacts. Reusing agro-industrial byproducts is a key step [...] Read more.
Wine lees (WL) are one of the main byproducts generated during winemaking and are usually disposed of in landfills or incorporated into the soil as an organic amendment; nevertheless, these practices can have negative environmental impacts. Reusing agro-industrial byproducts is a key step toward more sustainable production cycles, and WL represent a promising alternative for formulating culture media for the production of lactic acid bacteria (LAB) biomass, microorganisms widely used in the food and wine industries. In this work, we aim to evaluate the ecotoxicity of WL using a bioassay with zebrafish (Danio rerio) embryos and to analyze their potential as a source of nitrogen and growth factors for the production of UNQLp 11 Lactiplantibacillus plantarum strain biomass in whey permeate. Trials conducted with zebrafish showed that embryos exposed to WL exhibited increased mortality in a concentration-dependent response and the appearance of sublethal effects, such as alterations in embryonic development. Regarding WL biotechnological application, the results obtained confirm that the growth of Lpb. plantarum depends largely on the composition of the culture medium. Whey permeate media (WP) without supplementation showed nutritional limitations, reflected in lower cell counts. While supplementation with WL significantly improved bacterial growth, in some cases reaching values comparable to those obtained with MRS. The results demonstrated that WL can act as an efficient nutrient source, with the potential to replace commercial yeast extract in Lpb. plantarum culture media. Full article
17 pages, 2076 KB  
Article
Microbial Succession and Functional Metabolite Formation During SCOBY Fermentation of Pomelo Peel Substrates
by Tomoki Kono, Yi-Chung Lai, Bang-Yuan Chen and Meng-I Kuo
Fermentation 2026, 12(5), 219; https://doi.org/10.3390/fermentation12050219 - 28 Apr 2026
Cited by 1 | Viewed by 1219
Abstract
This study investigated the fermentation kinetics, microbial community succession, and potential functional metabolite formation in Symbiotic culture of bacteria and yeast (SCOBY)-mediated fermentation using pomelo peel substrates. Pomelo peel substrates were prepared using 1% and 6% (w/w) SCOBY combined [...] Read more.
This study investigated the fermentation kinetics, microbial community succession, and potential functional metabolite formation in Symbiotic culture of bacteria and yeast (SCOBY)-mediated fermentation using pomelo peel substrates. Pomelo peel substrates were prepared using 1% and 6% (w/w) SCOBY combined with 10 g and 25 g pomelo peel and fermented at 30 °C for 25 days. The results showed that higher SCOBY inoculum significantly accelerated acid production, resulting in a rapid decrease in pH and an increase in titratable acidity. Total soluble solids continuously decreased due to microbial utilization of sugars. The highest lactic acid bacteria count (6.04 log CFU/mL) and total viable count (7.23 log CFU/mL) were observed in S6-P25 at day 25. Bioactive compound analysis revealed that total flavonoid content reached its maximum in S6-P25 at day 20 (15.34 ± 0.70 mg RE/g dry weight, DW), while the highest total phenolic content was found in S1-P25 (151.5 ± 1.29 mg GAE/g DW), suggesting that a lower SCOBY level may favor polyphenol production. Antioxidant activity (DPPH and TEAC) increased with fermentation time and was highest in S6-P25. Microbiome analysis demonstrated that Firmicutes was the dominant phylum, with Apilactobacillus ozensis accounting for 99% of the relative abundance, indicating strong microbial selection and its potential role in acid production and fermentation ability. This microbial structure was consistent with the improved fermentation performance and enhanced bioactive properties observed in the pomelo peel substrates. These findings highlight SCOBY fermentation as a promising biotechnological strategy for converting citrus processing by-products into fermented ingredients for food applications. Full article
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