Fermentation

15 pages, 574 KiB

Open AccessArticle

Influence of Fermentation and Milling Processes on the Nutritional and Bioactive Properties of Pistachio-Based Beverages

by Tiziana Di Renzo, Antonela Guadalupe Garzón, Leonardo Pablo Sciammaro, Maria Cecilia Puppo, Silvina Rosa Drago and Anna Reale

Fermentation 2025, 11(8), 429; https://doi.org/10.3390/fermentation11080429 (registering DOI) - 26 Jul 2025

Abstract

The study aimed to evaluate how different production methods and fermentation processes using two different lactic acid bacteria (LAB) affect the chemical composition and bioactive properties of pistachio beverages. The beverages were prepared with two varieties of pistachios, one from Argentina and the [...] Read more.

The study aimed to evaluate how different production methods and fermentation processes using two different lactic acid bacteria (LAB) affect the chemical composition and bioactive properties of pistachio beverages. The beverages were prepared with two varieties of pistachios, one from Argentina and the other from Italy. The pistachios were processed with two technologies: a domestic processor and a colloidal mill. For the fermentation, pistachio beverages were inoculated with two different LAB strains and incubated at 28 °C for 24 h. The beverages were analyzed for proximal composition (including protein, fat, fiber, and minerals) and bioactive properties such as antioxidant activity, angiotensin-converting enzyme inhibition (ACE-I), and dipeptidyl peptidase-4 inhibition (DPP-4). The colloidal milling allowed the inclusion of the whole pistachio nut, resulting in beverages with higher solid content and no waste. Beverages treated with colloidal milling exhibited higher acidity, improved microbial fermentation performance, and generally showed higher bioactivity compared to those obtained by the domestic processor. Bioactivity varied according to the pistachio variety, the processing method and LAB strains used. Lactic acid bacteria fermentation decreased antioxidant properties of the beverages by ~40% but improved anti-hypertensive and hypoglycaemic activities. Fermented pistachio-based beverages showed promising health-promoting properties, indicating their potential as functional foods. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria: Fermentation)

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19 pages, 890 KiB

Open AccessArticle

Characterization of SCOBY and Lactiplantibacillus plantarum ELB90 Fermented Coffee Kombucha from Different Coffee Sources

by Oznur Saroglu, Yagmur Gulce Irmak, Rusen Metin Yildirim and Ayse Karadag

Fermentation 2025, 11(8), 428; https://doi.org/10.3390/fermentation11080428 - 25 Jul 2025

Abstract

Coffee kombucha beverages were developed by fermenting various coffee substrates, including instant coffee (I), coffee brews of ground coffee beans (G), and additional spent coffee added ground coffee (GSC) using either SCOBY (S) or Lactiplantibacillus plantarum ELB90 (L), or a combination of both [...] Read more.

Coffee kombucha beverages were developed by fermenting various coffee substrates, including instant coffee (I), coffee brews of ground coffee beans (G), and additional spent coffee added ground coffee (GSC) using either SCOBY (S) or Lactiplantibacillus plantarum ELB90 (L), or a combination of both (SL). The combined SL inoculation did not synergistically enhance the growth of acetic and lactic acid bacteria, nor did it increase the acetic and lactic acid concentrations or improve retention of caffeoylquinic acids (CQA) compared to non-fermented controls stored for the incubation period (7 days). Samples fermented with L better preserved the total CQAs during incubation, notably increasing 3-CQA and 4-CQA in L-fermented G and GSC samples by up to 40%, whereas 5-CQA showed a slight decrease (up to 8%) in L-fermented G and GSC samples. After one week, all fermented samples maintained stable levels of 3-CQA compared to the non-fermented SCG control, with significantly elevated 4-CQA. Caffeic acid was detected only in the bound fraction of beans, exhibiting similar concentrations in both fermented and non-fermented samples. SL-fermented coffees showed significant reductions in caffeine contents, except for I coffee substrate, and spent coffee grounds (SCG) filtered from the SL-fermented sample also had significantly lower caffeine content. Panelists preferred coffee kombucha beverages inoculated with S over those fermented with L, which were rated least appealing. The study concludes that fermentation with specific inoculation cultures could mitigate the degradation of coffee phenolic compounds during storage and facilitate the production of beverages with lower caffeine content, potentially enhancing both functional properties and consumer acceptability. Full article

(This article belongs to the Section Fermentation for Food and Beverages)

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21 pages, 2411 KiB

Open AccessSystematic Review

Response of Akkermansia muciniphila to Bioactive Compounds: Effects on Its Abundance and Activity

by Jair Alejandro Temis-Cortina, Harold Alexis Prada-Ramírez, Hulme Ríos-Guerra, Judith Espinosa-Raya and Raquel Gómez-Pliego

Fermentation 2025, 11(8), 427; https://doi.org/10.3390/fermentation11080427 - 24 Jul 2025

Abstract

Introduction: The gut microbiota is vital for human health, and its modulation through dietary and pharmaceutical compounds has gained increasing attention. Among gut microbes, Akkermansia muciniphila has been extensively researched due to its role in maintaining intestinal barrier integrity, regulating energy metabolism, and [...] Read more.

Introduction: The gut microbiota is vital for human health, and its modulation through dietary and pharmaceutical compounds has gained increasing attention. Among gut microbes, Akkermansia muciniphila has been extensively researched due to its role in maintaining intestinal barrier integrity, regulating energy metabolism, and influencing inflammatory responses. Subject: To analyze and synthesize the available scientific evidence on the influence of various bioactive compounds, including prebiotics, polyphenols, antioxidants, and pharmaceutical agents, on the abundance and activity of A. muciniphila, considering underlying mechanisms, microbial context, and its therapeutic potential for improving metabolic and intestinal health. Methods: A systematic literature review was conducted in accordance with the PRISMA 2020 guidelines. Databases such as PubMed, ScienceDirect, Scopus, Web of Science, SciFinder-n, and Google Scholar were searched for publications from 2004 to 2025. Experimental studies in animal models or humans that evaluated the impact of bioactive compounds on the abundance or activity of A. muciniphila were prioritized. The selection process was managed using the Covidence platform. Results: A total of 78 studies were included in the qualitative synthesis. This review compiles and analyzes experimental evidence on the interaction between A. muciniphila and various bioactive compounds, including prebiotics, antioxidants, flavonoids, and selected pharmaceutical agents. Factors such as the chemical structure of the compounds, microbial environment, underlying mechanisms, production of short-chain fatty acids (SCFAs), and mucin interactions were considered. Compounds such as resistant starch type 2, GOS, 2′-fucosyllactose, quercetin, resveratrol, metformin, and dapagliflozin showed beneficial effects on A. muciniphila through direct or indirect pathways. Discussion: Variability across studies reflects the influence of multiple variables, including compound type, dose, intervention duration, experimental models, and analytical methods. These differences emphasize the need for a contextualized approach when designing microbiota-based interventions. Conclusions: A. muciniphila emerges as a promising therapeutic target for managing metabolic and inflammatory diseases. Further mechanistic and clinical studies are necessary to validate its role and to support the development of personalized microbiota-based treatment interventions. Full article

(This article belongs to the Section Probiotic Strains and Fermentation)

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19 pages, 722 KiB

Open AccessReview

Karst Multi-Source Organic Solid Waste Bio-Enhanced Composting: The Potential of Circular Utilization to Enhance Soil Quality and Control Contaminants

by Chen Huang, Xinyu Zhao, Hui Zhang, Zihan Wang and Beidou Xi

Fermentation 2025, 11(8), 426; https://doi.org/10.3390/fermentation11080426 - 24 Jul 2025

Abstract

The dual environmental challenges of karst areas lie in organic solid waste’s (OSW) massive generation scale and diffuse dispersion, which accelerate bedrock exposure and soil contamination, while simultaneously representing an underutilized resource for soil amendments through optimized composting. Bio-enhanced composting of multi-source OSW [...] Read more.

The dual environmental challenges of karst areas lie in organic solid waste’s (OSW) massive generation scale and diffuse dispersion, which accelerate bedrock exposure and soil contamination, while simultaneously representing an underutilized resource for soil amendments through optimized composting. Bio-enhanced composting of multi-source OSW yields compounds with dual redox/adsorption capabilities, effectively improving soil quality and restoring ecological balance. The recycling and circular utilization of OSW resources become particularly critical in karst regions with vulnerable soil ecosystems, where sustainable resource management is urgently needed to maintain ecological balance. This review elucidates the ecological impacts of multi-source OSW compost applications on soil environments in ecologically fragile karst regions, specifically elucidating the mechanisms of heavy metals (HMs) migration–transformation and organic contaminant degradation (with emphasis on emerging pollutants), and the functional role of microbial carbon pumps in these processes. Furthermore, establishing a sustainable “multi-source OSW−compost−organic matter (adsorption and redox sites)−microorganisms−pollution remediation” cycle creates a green, low-carbon microenvironment for long-term soil remediation. Finally, this study evaluates the application prospects of the refined composting technology utilizing multi-objective regulation for OSW resource recycling and utilization in karst areas. This review provides critical insights for optimizing soil remediation strategies in karst ecosystems through organic waste valorization. Full article

(This article belongs to the Special Issue Turning Organic Solid Waste into Soil Nutrients Using Biological Technology)

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13 pages, 2088 KiB

Open AccessArticle

Assessment of Effects of Storage Time on Fermentation Profile, Chemical Composition, Bacterial Community Structure, Co-Occurrence Network, and Pathogenic Risk in Corn Stover Silage

by Zhumei Du, Ying Meng, Yifan Chen, Shaojuan Cui, Siran Wang and Xuebing Yan

Fermentation 2025, 11(8), 425; https://doi.org/10.3390/fermentation11080425 - 23 Jul 2025

Abstract

In order to achieve the efficient utilization of agricultural by-products and overcome the bottleneck of animal feed shortages in dry seasons, this study utilized corn stover (CS; Zea mays L.) as a material to systematically investigate the dynamic changes in the fermentation quality, [...] Read more.

In order to achieve the efficient utilization of agricultural by-products and overcome the bottleneck of animal feed shortages in dry seasons, this study utilized corn stover (CS; Zea mays L.) as a material to systematically investigate the dynamic changes in the fermentation quality, bacterial community structure, and pathogenic risk of silage under different fermentation times (0, 3, 7, 15, and 30 days). CS has high nutritive value, including crude protein and sugar, and can serve as a carbon source and a nitrogen source for silage fermentation. After ensiling, CS silage (CSTS) exhibited excellent fermentation quality, characterized by relatively high lactic acid content, low pH, and ammonia nitrogen content within an acceptable range. In addition, neither propionic acid nor butyric acid was detected in any of the silages. CS exhibited high α-diversity, with Serratia marcescens being the dominant bacterial species. After ensiling, the α-diversity significantly (p < 0.05) decreased, and Lactiplantibacillus plantarum was the dominant species during the fermentation process. With the extension of fermentation days, the relative abundance of Lactiplantibacillus plantarum significantly (p < 0.05) increased, reaching a peak and stabilizing between 15 and 30 days. Ultimately, lactic acid bacteria dominated and constructed a microbial symbiotic network system. In the bacterial community of CSTS, the abundance of “potential pathogens” was significantly (p < 0.01) lower than that of CS. These results provide data support for establishing a microbial regulation theory for silage fermentation, thereby improving the basic research system for the biological conversion of agricultural by-products and alleviating feed shortages in dry seasons. Full article

(This article belongs to the Special Issue Application of Fermentation Technology in Animal Nutrition: 2nd Edition)

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19 pages, 5882 KiB

Open AccessArticle

Targeted Redesign and Optimization of Culture Media for Ethylene Glycol Biosynthesis in Komagataella phaffii

by Thályta Fraga Pacheco and João Ricardo Moreira de Almeida

Fermentation 2025, 11(8), 424; https://doi.org/10.3390/fermentation11080424 - 23 Jul 2025

Abstract

Tailoring culture media and supplementation strategies to the specific requirements of a target product is essential for enhancing microbial production efficiency. This work addresses an unexplored aspect of K. phaffii cultivation: optimizing culture media for metabolite production from xylose, diverging from the conventional [...] Read more.

Tailoring culture media and supplementation strategies to the specific requirements of a target product is essential for enhancing microbial production efficiency. This work addresses an unexplored aspect of K. phaffii cultivation: optimizing culture media for metabolite production from xylose, diverging from the conventional focus on recombinant protein expression and the use of glycerol or methanol as primary substrates. Ethylene glycol biosynthesis in an engineered K. phaffii strain was improved by evaluating media and nutrient supplementation. Among the seven evaluated formulations, FM22 and d’Anjou were the most effective, with inositol and thiamine dichloride playing key roles in enhancing production. Salt concentrations in both media were optimized using Central Composite Design (CCD), reducing complexity while increasing yields. Ethylene glycol production increased by 54% in FM22 and 21% in d’Anjou, accompanied by a threefold and 26% reduction in the total salt content, respectively. The vitamin solution was streamlined from seven to two components, each at half the standard concentration. Trace element solutions were reduced to 25% of the original volume without compromising productivity. These findings underscore the dual benefit of culture medium optimization: improved ethylene glycol yields and simplified formulations, establishing a foundation for the development of more efficient and cost-effective bioprocesses using K. phaffii. Full article

(This article belongs to the Section Microbial Metabolism, Physiology & Genetics)

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18 pages, 1090 KiB

Open AccessArticle

Enhancing Soy Yogurt with Microencapsulated Limosilactobacillus reuteri: Viability and Sensory Acceptability

by Ricardo H. Hernández-Figueroa, Yani D. Ramírez, Aurelio López-Malo and Emma Mani-López

Fermentation 2025, 11(8), 423; https://doi.org/10.3390/fermentation11080423 - 22 Jul 2025

Abstract

This study aimed to microencapsulate Limosilactobacillus reuteri DSM 17938 to enrich soy yogurt flavored with peach jam. The effect of three concentrations of alginate and coating chitosan were evaluated in terms of probiotic viability, and the physicochemical and sensory properties of soy yogurt. [...] Read more.

This study aimed to microencapsulate Limosilactobacillus reuteri DSM 17938 to enrich soy yogurt flavored with peach jam. The effect of three concentrations of alginate and coating chitosan were evaluated in terms of probiotic viability, and the physicochemical and sensory properties of soy yogurt. Lim. reuteri was microencapsulated in alginate (1, 2, and 3%) and coated with chitosan (0, 0.4, and 0.8%). Soymilk was fermented using Lactobacillus bulgaricus and Streptococcus thermophilus. Soy yogurt was combined with probiotic beads and peach jam and stored for 27 days at 4 °C. The pH, titratable acidity, and probiotic viability of probiotic peach soy yogurt (PPSY) were determined during storage. Alginate at 3% and alginate (2%) coated with 0.4% chitosan maintained probiotic counts at 8 and 7.5 log CFU/g after 27 days. The pH of PPSY decreases rapidly and drastically during storage when probiotic-free cells are added. The PPSY containing alginate (3%) beads, alginate (2%) coated with chitosan (0.4%), and probiotic-free cells had a similar level of acceptance in color, texture, and odor (p > 0.05), while flavor and overall acceptability were significantly higher (p < 0.05) in PPSY with probiotic beads. These findings support the use of microencapsulation strategies in developing functional plant-based probiotic foods. Full article

(This article belongs to the Special Issue Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and Health Bioprocesses)

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14 pages, 1604 KiB

Open AccessArticle

Elicitation-Induced Enhancement of Lovastatin and Pigment Production in Monascus purpureus C322

by Sirisha Yerramalli, Stephen J. Getting, Godfrey Kyazze and Tajalli Keshavarz

Fermentation 2025, 11(8), 422; https://doi.org/10.3390/fermentation11080422 - 22 Jul 2025

Abstract

Monascus purpureus is a filamentous fungus renowned for producing bioactive secondary metabolites, including lovastatin and azaphilone pigments. Lovastatin is valued for its cholesterol-lowering properties and cardiovascular benefits, while Monascus pigments exhibit anti-cancer, anti-inflammatory, and antimicrobial activities, underscoring their pharmaceutical and biotechnological relevance. This [...] Read more.

Monascus purpureus is a filamentous fungus renowned for producing bioactive secondary metabolites, including lovastatin and azaphilone pigments. Lovastatin is valued for its cholesterol-lowering properties and cardiovascular benefits, while Monascus pigments exhibit anti-cancer, anti-inflammatory, and antimicrobial activities, underscoring their pharmaceutical and biotechnological relevance. This study evaluated the impact of carbohydrate-derived elicitors—mannan oligosaccharides, oligoguluronate, and oligomannuronate—on the enhancement of pigment and lovastatin production in M. purpureus C322 under submerged fermentation. Elicitors were added at 48 h in shake flasks and 24 h in 2.5 L stirred-tank fermenters. All treatments increased the production of yellow, orange, and red pigments and lovastatin compared to the control, with higher titres upon scale-up. OG led to the highest orange pigment yield (1.2 AU/g CDW in flasks; 1.67 AU/g CDW in fermenters), representing 2.3- and 3.0-fold increases. OM yielded the highest yellow and red pigments (1.24 and 1.35 AU/g CDW in flasks; 1.58 and 1.80 AU/g CDW in fermenters) and the highest lovastatin levels (10.46 and 12.6 mg/g CDW), corresponding to 2.03–3.03-fold improvements. These results highlight the potential of carbohydrate elicitors to stimulate metabolite biosynthesis and facilitate scalable optimisation of fungal fermentation. Full article

(This article belongs to the Section Industrial Fermentation)

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14 pages, 4866 KiB

Open AccessArticle

Effect of Ohmic Heating Pretreatment on Enzyme Production by Solid-State Fermentation of Brewer’s Spent Grain

by Bruna F. Silva, Luís Machado, Ana M. Fernandes, Ricardo N. Pereira and Isabel Belo

Fermentation 2025, 11(8), 421; https://doi.org/10.3390/fermentation11080421 - 22 Jul 2025

Abstract

Solid-state fermentation (SSF) involves the growth of microorganisms on solid substrates, mimicking natural environments of many species. Due to sustainability concerns, transforming agro-industrial by-products into value-added products through SSF has been increasingly studied. Brewer’s spent grain (BSG), the main by-product of beer production, [...] Read more.

Solid-state fermentation (SSF) involves the growth of microorganisms on solid substrates, mimicking natural environments of many species. Due to sustainability concerns, transforming agro-industrial by-products into value-added products through SSF has been increasingly studied. Brewer’s spent grain (BSG), the main by-product of beer production, mostly consists of barley grain husks, making BSG a great support for microorganism cultivation. Although autoclaving remains the standard sterilization and pretreatment method of substrates, electric field technologies and their attendant ohmic heating (OH) have great potential as an alternative technology. In the present work, pretreatment of BSG by OH was explored in SSF with Aspergillus niger to produce commercially valuable enzymes. OH favored the solubilization of phenolic compounds, total protein, and reducing sugars significantly higher than autoclaving. SSF of treated BSG led to the production of lignocellulosic enzymes, with xylanases being the most active, reaching 540 U/g, a 1.5-fold increase in activity compared to autoclaved BSG. Protease activity was also improved 1.6-fold by OH, resulting in 49 U/g. Our findings suggest that OH treatment is an effective alternative to autoclaving and that its integration with SSF is a sustainable strategy to enhance by-product valorization through enzyme production with many industrial applications, according to circular economy guidelines. Full article

(This article belongs to the Special Issue Fermentative Production of Valuable Chemicals from Lignocellulosic Biomass)

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13 pages, 1239 KiB

Open AccessArticle

Assessing the Fermentation Quality, Bacterial Composition and Ruminal Degradability of Caragana korshinskii Ensiled with Oat Grass

by Yao Shen, Kun Wang, Benhai Xiong, Fuguang Xue, Yajie Kang, Shichao Liu and Liang Yang

Fermentation 2025, 11(7), 420; https://doi.org/10.3390/fermentation11070420 - 20 Jul 2025

Abstract

The purpose of this study was to explore the effects of co-ensiling Caragana korshinskii with different proportions of oat grass on silage fermentation quality, chemical composition, in situ rumen degradability and in vitro rumen fermentation characteristics. C. korshinskii and oat grass were mixed [...] Read more.

The purpose of this study was to explore the effects of co-ensiling Caragana korshinskii with different proportions of oat grass on silage fermentation quality, chemical composition, in situ rumen degradability and in vitro rumen fermentation characteristics. C. korshinskii and oat grass were mixed at different ratios of 100:00, 90:1, 80:2, 70:30, 60:40 and 50:50. Each ratio of mixture was ensiled for 7, 14, 30, 45 and 60 days at room temperature (25 °C), with 30 bags per ratio, for a total of 180 bags. We further investigated the dynamic profiles of the bacterial community during ensiling and in vitro rumen fermentation. The results showed that co-ensiling C. korshinskii and oat grass decreased the pH values and increased the content of lactic acid and acetic acid compared with ensiling C. korshinskii alone. C. korshinskii ensiled with oat grass at a ratio of 70:30 (70% C. korshinskii) showed the best fermentation quality, which was related to higher relative abundance of Lactobacillus and Weissella. The silage with the ratio of 70:30 (70% C. korshinskii) showed higher dry matter digestibility and the more production of gas and total volatile fatty acids, compared with fresh C. korshinskii. In conclusion, C. korshinskii co-ensiled with oat grass at a ratio of 70:30 could enhance the fermentation quality and digestibility of C. korshinskii. Full article

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22 pages, 2637 KiB

Open AccessArticle

Anti-Obesity and Hepatoprotective Effects of Probiotic Goat Milk in Mice: Insights from Hepatic Proteomics

by Antonela Marquez, Estefanía Andrada, Matias Russo, Jaime Daniel Babot, Roxana Medina and Paola Gauffin-Cano

Fermentation 2025, 11(7), 419; https://doi.org/10.3390/fermentation11070419 - 20 Jul 2025

Abstract

Dietary administration of fermented goat milk (FGM) with the starter strain Lactobacillus delbrueckii subsp. indicus CRL1447 and supplemented with different functional cultures (FCs) of lactobacilli strains (FC1: Limosilactobacillus fermentum CRL1446 + Lactiplantibacillus paraplantarum CRL1449 + Lactiplantibacillus paraplantarum CRL1472; FC2: CRL1446 + CRL1449; FC3: [...] Read more.

Dietary administration of fermented goat milk (FGM) with the starter strain Lactobacillus delbrueckii subsp. indicus CRL1447 and supplemented with different functional cultures (FCs) of lactobacilli strains (FC1: Limosilactobacillus fermentum CRL1446 + Lactiplantibacillus paraplantarum CRL1449 + Lactiplantibacillus paraplantarum CRL1472; FC2: CRL1446 + CRL1449; FC3: CRL1446 + CRL1472; and FC4: CRL1449 + CRL1472) was investigated in mice fed a high-fat diet (HFD). FGM supplemented with different FCs, referred to as Probiotic Goat Milk (PGM), demonstrated significant anti-obesity activity by reducing body weight and improving blood lipid profiles in obese mice. The animals that received the PGM showed less fat infiltration in the hepatocytes compared to the obese mice fed FGM. Hepatic proteomics data show that HFD generally upregulates proteins involved in fatty acid oxidation and downregulates proteins implicated in lipid synthesis, whereas the administration of FGM supplemented with FC3 (PGM3) improves the proteomic profile. These results suggest that PGM exerts systemic metabolic effects through modulation of the gut–liver axis, highlighting its potential as a dietary strategy against obesity-related disorders. Full article

(This article belongs to the Special Issue Fermented Dairy Products: Processing Technology, Microbiology and Health Benefits: 2nd Edition)

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15 pages, 1576 KiB

Open AccessArticle

Interactive Effects of Sulfide Addition and Heat Pretreatment on Hydrogen Production via Dark Fermentation

by Tae-Hoon Kim, Yun-Ju Jeon, Sungjin Park, Ji-Hye Ahn, Junsu Park and Yeo-Myeong Yun

Fermentation 2025, 11(7), 418; https://doi.org/10.3390/fermentation11070418 - 20 Jul 2025

Abstract

Despite being recognized as toxic in anaerobic systems, sulfide’s potential to enhance hydrogen fermentation via microbial modulation remains underexplored. This study evaluated the combined effects of sulfide concentration (0–800 mg S/L) and heat pretreatment on hydrogen production during dark fermentation (DF). Without pretreatment, [...] Read more.

Despite being recognized as toxic in anaerobic systems, sulfide’s potential to enhance hydrogen fermentation via microbial modulation remains underexplored. This study evaluated the combined effects of sulfide concentration (0–800 mg S/L) and heat pretreatment on hydrogen production during dark fermentation (DF). Without pretreatment, hydrogen yield reached 83 ± 2 mL/g COD at 0 mg S/L but declined with increasing sulfide, becoming negligible at 800 mg S/L. In contrast, heat-pretreated inocula showed markedly improved performance: peak cumulative production (4628 ± 17 mL) and yield (231 ± 1 mL/g COD) were attained at 200 mg S/L, while the maximum production rate (1462 ± 64 mL/h) occurred at 400 mg S/L. These enhancements coincided with elevated acetic and butyric acids, indicating a metabolic shift toward hydrogen-producing pathways. The microbial analysis of heat-pretreated samples revealed an enrichment of Clostridium butyricum (from 73.1% to 87.5%) and Clostridium perfringens, which peaked at 13.5% at 400 mg S/L. This species contributed to butyric acid synthesis. At 800 mg S/L, Clostridium perfringens declined sharply to 0.6%, while non-hydrogenogenic Levilinea saccharolytica proliferated, correlating with reduced butyric acid and hydrogen output. These findings indicate that sulfide supplementation, when combined with heat pretreatment, selectively restructures microbial communities and metabolic pathways, enhancing DF performance. Full article

(This article belongs to the Special Issue Fermentative Biohydrogen Production, 2nd Edition)

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22 pages, 558 KiB

Open AccessReview

Microbial Fermentation Assisted by Pulsed Electric Fields, Magnetic Fields and Cold Atmospheric Plasma: State of the Art

by Nahed Yousfi, Nofel Merbahi, Jalloul Bouajila, Patricia Taillandier and Mohamed Debouba

Fermentation 2025, 11(7), 417; https://doi.org/10.3390/fermentation11070417 - 19 Jul 2025

Abstract

Microbial fermentation is a fundamental bioconversion mechanism widely used in diverse industrial sectors, notably in food processing and bioenergy production. Over the years, the wealth of information and scientific and technological advances in the field of fermentation have made considerable progress. Most recent [...] Read more.

Microbial fermentation is a fundamental bioconversion mechanism widely used in diverse industrial sectors, notably in food processing and bioenergy production. Over the years, the wealth of information and scientific and technological advances in the field of fermentation have made considerable progress. Most recent research studies are currently devoted to the implementation of innovative technological processes in order to increase fermentation effectiveness while consuming less energy and processing time. The aim of the present review is to investigate the impact of innovative physical techniques (pulsed electric field, PEFs; cold atmospheric plasma, CAP; and magnetic fields, MFs) on fermentation processes. The bibliographic analysis will mainly focus on recent advances towards non-destructive methods (PEF, CAP, and MF) and their induced changes in fermentation dynamics, fermented product quality, metabolite synthesis, and microbial growth kinetics. Various databases, including PubMed, ScienceDirect, Google Scholar, ResearchGate, Scopus, and Web of Science, were used to collect pertinent scientific literature on the impact of innovative physical techniques on microorganisms and fermentation processes and to investigate the potential applications of these emerging technologies in the food and health sectors. According to the results, all techniques have the potential to optimize fermentation dynamics, boost metabolite synthesis, and enhance product quality. However, each technology displayed its own specific advantages and disadvantages. Full article

(This article belongs to the Special Issue Fermentation Processes: Modeling, Optimization and Control: 3rd Edition)

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23 pages, 3679 KiB

Open AccessArticle

Influence of Pediococcus acidilactici and Bacillus coagulans on In Vitro Ruminal Greenhouse Gas Production of Fermented Devilfish in Livestock Rumen Contents

by José Luis Ponce-Covarrubias, Mona M. M. Y. Elghandour, Germán Buendía Rodríguez, Moyosore Joseph Adegbeye, Maximilian Lackner and Abdelfattah Z. M. Salem

Fermentation 2025, 11(7), 416; https://doi.org/10.3390/fermentation11070416 - 18 Jul 2025

Abstract

This study aimed to evaluate the effect of including silage from devilfish waste (SF-Hypostomus plecostomus) and probiotics (PB-Pediococcus acidilactici BX-B122 and Bacillus coagulans BX-B118) in ruminants on greenhouse gas production. The diets evaluated contained 0, 8, 14 and 20% of [...] Read more.

This study aimed to evaluate the effect of including silage from devilfish waste (SF-Hypostomus plecostomus) and probiotics (PB-Pediococcus acidilactici BX-B122 and Bacillus coagulans BX-B118) in ruminants on greenhouse gas production. The diets evaluated contained 0, 8, 14 and 20% of silage made from SF and the addition of PB at a dose of 0.2 mL/g of diet, using steers and sheep (rams) as rumen inoculum donors in a completely randomized statistical design with a 2 × 4 × 2 factorial arrangement. Asymptotic gas production (GP) was influenced (p < 0.01) by the interactions between rumen liquor (RL), SF, and PB. The inclusion of SF and PB resulted in a higher (p < 0.01) GP rate in sheep; however, the values were reduced with increasing levels of SF. Asymptotic CH₄ in the rumen fluid of steers decreased with an increasing SF percentage up to 14%. Probiotics had different effects on the rumen fluid of sheep and steers. In steers, probiotics substantially reduced (p < 0.01) CH₄ synthesis while supplementation increased it in sheep rumen fluid. Similarly, diets with probiotics had higher CO formation (p < 0.05) in sheep and steer liquor. Similarly, CO decreased (p < 0.05) with increasing levels of SF. In the rumen fluid of sheep and steers, the probiotics were found to reduce H₂S, while there was an SF-dose-dependent decrease in H₂S concentration. The ruminal pH and dry matter digestibility of sheep were higher than in steers. It can be concluded that increasing SF levels generally reduced the total gas and CH₄ production, with probiotics further enhancing this reduction, especially in CH₄ per unit of gas. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section "Probiotic Strains and Fermentation")

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15 pages, 1280 KiB

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

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 [...] Read more.

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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16 pages, 527 KiB

Open AccessArticle

An Assessment of the Functional Properties of Black Amaranth Flour During Fermentation with Probiotic Lactic Acid Bacteria

by Mamadou Lamarana Souare, Alpha Oumar Sily Diallo, Nicoleta Balan, Mihaela Aida Vasile, Lounceny Traore, Gabriela Elena Bahrim, Mihaela Cotârleț and Caterina Nela Dumitru

Fermentation 2025, 11(7), 414; https://doi.org/10.3390/fermentation11070414 - 18 Jul 2025

Abstract

This study aimed to ferment protein-rich amaranth flour with different strains of lactic acid bacteria (LAB) and to analyse the fermented dough’s functional properties. The fermented dough analysis was conducted using titrimetric, spectrophotometric, and chromatographic methods. The antioxidant activity of the fermented doughs [...] Read more.

This study aimed to ferment protein-rich amaranth flour with different strains of lactic acid bacteria (LAB) and to analyse the fermented dough’s functional properties. The fermented dough analysis was conducted using titrimetric, spectrophotometric, and chromatographic methods. The antioxidant activity of the fermented doughs was evaluated using the DPPH (2,2-Diphenyl-1-picrylhydrazyl) and ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) methods, finding ABTS radical scavenging values ranging from 26.00 ± 1.05% to 58.92 ± 6.05%, while the DPPH values ranged from 21.29 ± 0.83% to 28.24 ± 5.48%. By RP-HPLC (Reversed Phase-High Performance Liquid Chromatography) characterisation, several phenolic acids and flavonoids were identified and quantified. Among these compounds, epigallocatechin was the most abundant, with the highest concentration recorded at 7789.88 ± 17.0 ng/µL in the control sample. This was followed by a 6942.47 ± 5.632 ng/µL concentration in the dough fermented with Lacticaseibacillus rhamnosus MIUG BL38 strain and 4983.16 ± 7.29 ng/µL in the dough fermented with Lactiplantibacillus pentosus MIUG BL24 strain. These two LAB strains (Lc. rhamnosus MIUG BL38 and Lp. pentosus MIUG BL24), with probiotic properties previously demonstrated, were selected based on their acidification potential, antioxidant activity, and bioactivity for future optimisation studies. Lactic acid fermentation significantly enhances bioactive characteristics of the amaranth flour, enabling the design of diverse gluten-free products with increased functional properties based on the attributes induced by the prebiotic, probiotic and postbiotic contents (tribiotics). Full article

(This article belongs to the Special Issue Antioxidant Activity of Fermented Foods)

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15 pages, 2591 KiB

Open AccessArticle

Adding Ethanol to the Batch and Continuous Transplantation Co-Culture of Maize Straw Fermented by Rumen Fluid for the Production of Caproic Acid

by Zhiqiang Cheng, Zitong Meng, Yue Shen, Wengboyang Liu, Li Liu, Guoqi Zhao, Lin Wang and Miao Lin

Fermentation 2025, 11(7), 413; https://doi.org/10.3390/fermentation11070413 - 18 Jul 2025

Abstract

In this study, to enhance the concentration of caproic acid generated from maize straw fermentation and clarify the structures of bacterial and fungal communities within the serially subcultured rumen microbial fermentation system, maize straw was used as the substrate. In a continuous subculture [...] Read more.

In this study, to enhance the concentration of caproic acid generated from maize straw fermentation and clarify the structures of bacterial and fungal communities within the serially subcultured rumen microbial fermentation system, maize straw was used as the substrate. In a continuous subculture system, the impacts of ethanol addition on pH and gas production were explored, with a focus on the caproic acid yield in the final (eighth generation) generation and alterations in bacterial and fungal communities. The results showed that the relative abundances of unidentified_Clostridiales, Shuttleworthia, and Syntrophococcus in ethanol-driven caproic acid production were enriched by 5.36-fold, 2.61-fold, and 2.25-fold, respectively. This consequently increased the concentration of caproic acid in the fermentation broth to 1492 mg/L, representing a 3.7-fold increase. These findings are highly significant for the high-value utilization of maize straw waste to produce caproic acid via the carboxylic acid platform using rumen microorganisms in industrial processing. Full article

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13 pages, 2175 KiB

Open AccessArticle

Light and Temperature Effects on the Accumulation of Carotenoids in Rhodotorula spp. Yeasts

by Regina Losinska-Sičiūnienė, Živilė Strazdaitė-Žielienė, Saulė Pranckevičiūtė and Elena Servienė

Fermentation 2025, 11(7), 412; https://doi.org/10.3390/fermentation11070412 - 17 Jul 2025

Abstract

Carotenoids are widely recognized for their antioxidant and health-beneficial properties, making them attractive for applications in the food, pharmaceutical, medical, and agricultural sectors. Rhodotorula yeasts are considered one of the most suitable alternatives for carotenoid synthesis due to their rapid biomass growth and [...] Read more.

Carotenoids are widely recognized for their antioxidant and health-beneficial properties, making them attractive for applications in the food, pharmaceutical, medical, and agricultural sectors. Rhodotorula yeasts are considered one of the most suitable alternatives for carotenoid synthesis due to their rapid biomass growth and high pigment yield. During this study, based on the sequences of the ITS region between 18S and 28S rRNA genes, the yeast strains were identified as belonging to Rhodotorula babjevae, R. dairenensis, R. diobovata, R. glutinis, R. graminis, R. ingeniosa, R. kratochvilovae, and R. mucilaginosa. The production of carotenoids by different Rhodotorula yeast strains was analyzed under the combined effects of lighting and temperature. Among all tested strains, the isolate identified as R. ingeniosa exhibited the lowest carotenoid content, ranging from 0.18 to 0.23 mg/g biomass. The highest levels of pigment were accumulated in dark conditions by R. babjevae (0.86 mg/g biomass) and R. graminis (0.76 mg/g biomass) cultivated for 14 days at a constant temperature of 26 °C, and by R. glutinis (0.89 mg/g biomass) after incubation at 4 °C. The majority of yeasts tested produced more carotenoids at a higher temperature. It was observed that in R. babjevae, R. glutinis, and R. graminis, lighting negatively affected the pigment content regardless of incubation temperature. In these strains, the pigment content decreased by 1.2- to 1.4-fold after one week of cultivation under light conditions at 26 °C, compared to cultures grown in the dark. The results suggest that the isolated Rhodotorula strains could be attractive candidates for the efficient synthesis of carotenoids. Full article

(This article belongs to the Special Issue Pigment Production in Submerged Fermentation: Second Edition)

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22 pages, 4837 KiB

Open AccessArticle

Leveraging Historical Process Data for Recombinant P. pastoris Fermentation Hybrid Deep Modeling and Model Predictive Control Development

by Emils Bolmanis, Vytautas Galvanauskas, Oskars Grigs, Juris Vanags and Andris Kazaks

Fermentation 2025, 11(7), 411; https://doi.org/10.3390/fermentation11070411 - 17 Jul 2025

Abstract

Hybrid modeling techniques are increasingly important for improving predictive accuracy and control in biomanufacturing, particularly in data-limited conditions. This study develops and experimentally validates a hybrid deep learning model predictive control (MPC) framework for recombinant P. pastoris fed-batch fermentations. Bayesian optimization and grid [...] Read more.

Hybrid modeling techniques are increasingly important for improving predictive accuracy and control in biomanufacturing, particularly in data-limited conditions. This study develops and experimentally validates a hybrid deep learning model predictive control (MPC) framework for recombinant P. pastoris fed-batch fermentations. Bayesian optimization and grid search techniques were employed to identify the best-performing hybrid model architecture: an LSTM layer with 2 hidden units followed by a fully connected layer with 8 nodes and ReLU activation. This design balanced accuracy (NRMSE 4.93%) and computational efficiency (AICc 998). This architecture was adapted to a new, smaller dataset of bacteriophage Qβ coat protein production using transfer learning, yielding strong predictive performance with low validation (3.53%) and test (5.61%) losses. Finally, the hybrid model was integrated into a novel MPC system and experimentally validated, demonstrating robust real-time substrate feed control in a way that allows it to maintain specific target growth rates. The system achieved predictive accuracies of 6.51% for biomass and 14.65% for product estimation, with an average tracking error of 10.64%. In summary, this work establishes a robust, adaptable, and efficient hybrid modeling framework for MPC in P. pastoris bioprocesses. By integrating automated architecture searching, transfer learning, and MPC, the approach offers a practical and generalizable solution for real-time control and supports scalable digital twin deployment in industrial biotechnology. Full article

(This article belongs to the Special Issue Computer and Mathematical Simulation of Microbial Fermentations: The Choice of Models, Parameter Estimation and Applications)

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