Fermentation

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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20 pages, 1065 KiB

Open AccessReview

Microbial Genome Editing with CRISPR–Cas9: Recent Advances and Emerging Applications Across Sectors

by Chhavi Dudeja, Amish Mishra, Ansha Ali, Prem Pratap Singh and Atul Kumar Jaiswal

Fermentation 2025, 11(7), 410; https://doi.org/10.3390/fermentation11070410 - 16 Jul 2025

Abstract

CRISPR technology, which is derived from the bacterial adaptive immune system, has transformed traditional genetic engineering techniques, made strain engineering significantly easier, and become a very versatile genome editing system that allows for precise, programmable modifications to a wide range of microbial genomes. [...] Read more.

CRISPR technology, which is derived from the bacterial adaptive immune system, has transformed traditional genetic engineering techniques, made strain engineering significantly easier, and become a very versatile genome editing system that allows for precise, programmable modifications to a wide range of microbial genomes. The economies of fermentation-based manufacturing are changing because of its quick acceptance in both academic and industry labs. CRISPR processes have been used to modify industrially significant bacteria, including the lactic acid producers, Clostridium spp., Escherichia coli, and Corynebacterium glutamicum, in order to increase the yields of bioethanol, butanol, succinic acid, acetone, and polyhydroxyalkanoate precursors. CRISPR-mediated promoter engineering and single-step multiplex editing have improved inhibitor tolerance, raised ethanol titers, and allowed for the de novo synthesis of terpenoids, flavonoids, and recombinant vaccines in yeasts, especially Saccharomyces cerevisiae and emerging non-conventional species. While enzyme and biopharmaceutical manufacturing use CRISPR for quick strain optimization and glyco-engineering, food and beverage fermentations benefit from starter-culture customization for aroma, texture, and probiotic functionality. Off-target effects, cytotoxicity linked to Cas9, inefficient delivery in specific microorganisms, and regulatory ambiguities in commercial fermentation settings are some of the main challenges. This review provides an industry-specific summary of CRISPR–Cas9 applications in microbial fermentation and highlights technical developments, persisting challenges, and industrial advancements. Full article

(This article belongs to the Section Fermentation Process Design)

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15 pages, 4120 KiB

Open AccessArticle

Unlocking the Potential of Lacticaseibacillus rhamnosus 73 as a Ripening Agent in Semi-Hard Cheese After Freeze-Drying and a Six-Month Storage Period

by Mara E. Batistela, Carina V. Bergamini, Elisa C. Ale and Guillermo H. Peralta

Fermentation 2025, 11(7), 409; https://doi.org/10.3390/fermentation11070409 - 16 Jul 2025

Abstract

Dehydration and storage conditions used to preserve dairy cultures in the industry may negatively impact their viability and functionality. This study investigated the effects of freeze-drying and storage on the metabolic activity of Lacticaseibacillus rhamnosus 73 (L73). The strain’s viability after freeze-drying and [...] Read more.

Dehydration and storage conditions used to preserve dairy cultures in the industry may negatively impact their viability and functionality. This study investigated the effects of freeze-drying and storage on the metabolic activity of Lacticaseibacillus rhamnosus 73 (L73). The strain’s viability after freeze-drying and storage, its metabolic activity in cultured milk, and its performance as a ripening agent in miniature cheeses were evaluated. Neither the freeze-drying process nor the storage conditions negatively affected its viability, as L73 maintained its initially high levels (>10 log cfu mL⁻¹) throughout the storage period. L73 improved the overall quality of the cheeses, as a reduction in hydrophobic peptides (i.e., potential bitter peptides) was evidenced in cheese manufactured with L73. Furthermore, L73 exhibited protective properties, as evidenced by the decreased availability of compounds that could be used as energy sources by adventitious microorganisms (e.g., galactose, hippuric acid) and the increased production of lactic acid in both cultured milk and cheese. Full article

(This article belongs to the Special Issue Applications of Lactic Acid Bacteria in Fermented Foods and Beverages: Second Edition)

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2 pages, 125 KiB

Open AccessEditorial

Fermentation Processes: Modeling, Optimization and Control: 2nd Edition

by Ricardo Aguilar López

Fermentation 2025, 11(7), 408; https://doi.org/10.3390/fermentation11070408 (registering DOI) - 16 Jul 2025

Abstract

Fermentation is an important cornerstone of bioengineering, which plays a critical role in the production of a wide array of products including pharmaceuticals, biofuels, food additives, industrial chemicals and enzymes [...] Full article

(This article belongs to the Special Issue Fermentation Processes: Modeling, Optimization and Control: 2nd Edition)

15 pages, 1196 KiB

Open AccessArticle

Assisted Isolation of Camelliagenin B from Camellia oliefera Seed Cake Meal and Microbial Transformation by Bacillus subtilis ATCC 6633, Bacillus megaterium CGMCC 1.1741, and Streptomyces gresius ATCC 13273

by Richa Raj, Jingling Zhang, Yanyan Meng, Xuewa Jiang, Wei Wang, Jian Zhang and Boyang Yu

Fermentation 2025, 11(7), 407; https://doi.org/10.3390/fermentation11070407 - 15 Jul 2025

Abstract

This study investigates the potential for the microbial transformation of camelliagenin B, a saponin derived from Camellia oleifera seed cake meal, to develop novel metabolites. We employed three microbial strains, specifically Bacillus subtilis ATCC 6633, Bacillus megaterium CGMCC 1.1741, and Streptomyces griseus ATCC [...] Read more.

This study investigates the potential for the microbial transformation of camelliagenin B, a saponin derived from Camellia oleifera seed cake meal, to develop novel metabolites. We employed three microbial strains, specifically Bacillus subtilis ATCC 6633, Bacillus megaterium CGMCC 1.1741, and Streptomyces griseus ATCC 13273, to biotransform camelliagenin B into its derivatives. The compounds were purified and separated using chromatographic techniques, such as high-performance liquid chromatography (HPLC). Structural identification was carried out using spectroscopic methods, including nuclear magnetic resonance (NMR) and mass spectrometry (MS). Ten bioactive compounds were obtained (1a-1j), of which nine were novel with multiple tailoring reactions, such as allyl oxidation, C-C double-bond rearrangement, hydroxylation, dehydrogenation, and glycosylation, observed in camelliagenin B analogs. The structures of these compounds were determined by 1D/2D NMR and HR-ESI-MS analysis. Therefore, this study showcases the capacity of microbial transformation as a sustainable and environmentally friendly method for generating bioactive compounds from C. oleifera seed cake meals. The individual chemicals can potentially facilitate the design of novel medicinal agents, functional foods, and natural preservatives. Full article

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18 pages, 8219 KiB

Open AccessArticle

From Lebanese Soil to Antimicrobials: A Novel Streptomyces Species with Antimicrobial Potential

by Razane Hamiyeh, Aya Hanna and Antoine Abou Fayad

Fermentation 2025, 11(7), 406; https://doi.org/10.3390/fermentation11070406 - 15 Jul 2025

Abstract

The ongoing threat of antimicrobial-resistant pathogens has intensified the need for new antimicrobial agents, making the discovery of novel natural products crucial. This study focuses on the isolation and characterization of a novel Streptomyces species from the Anjar region in Lebanon, an area [...] Read more.

The ongoing threat of antimicrobial-resistant pathogens has intensified the need for new antimicrobial agents, making the discovery of novel natural products crucial. This study focuses on the isolation and characterization of a novel Streptomyces species from the Anjar region in Lebanon, an area rich in microbial diversity that is largely unexplored for its biotechnological potential. Soil samples were collected and processed, leading to the isolation of Streptomyces strain ANJ10. Comprehensive morphological, physiological, and genomic analyses were conducted, including whole-genome sequencing (WGS) to identify biosynthetic gene clusters (BGCs) and broth microdilution (BMD) assays to evaluate antimicrobial activity. The ANJ10 genome revealed 42 BGCs, significantly more than the average number in Streptomyces species, suggesting a high potential for secondary metabolite production. Phylogenetic analysis confirmed ANJ10 as a novel species, and BMD assays demonstrated its strong antimicrobial activity against several gram-negative pathogens, specifically, Acinetobacter baumannii. These findings underscore the potential of this strain as a significant source of new antimicrobial compounds, reinforcing the importance of exploring underexploited environments like Lebanon for microbial bioprospecting. Full article

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

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21 pages, 1958 KiB

Open AccessArticle

Potential Prebiotic Effect of Caatinga Bee Honeys from the Pajeú Hinterland (Pernambuco, Brazil) on Synbiotic Alcoholic Beverages Fermented by Saccharomyces boulardii CNCM I-745

by Walter de Paula Pinto-Neto, Luis Loureiro, Raquel F. S. Gonçalves, Márcia Cristina Teixeira Marques, Rui Miguel Martins Rodrigues, Luís Abrunhosa, Aline Magalhães de Barros, Neide Kazue Sakugawa Shinohara, Ana Cristina Pinheiro, Antonio Augusto Vicente, Rafael Barros de Souza and Marcos Antonio de Morais Junior

Fermentation 2025, 11(7), 405; https://doi.org/10.3390/fermentation11070405 - 15 Jul 2025

Abstract

The singular biodiversity of the Brazilian Caatinga inspires innovative solutions in food science. In this study, we evaluated the prebiotic potential of honeys produced by Apis mellifera in the Pajeú hinterland, Pernambuco, Brazil (Caatinga Biome), with different floral origins: Mastic (Aroeira), Mesquite (Algaroba), [...] Read more.

The singular biodiversity of the Brazilian Caatinga inspires innovative solutions in food science. In this study, we evaluated the prebiotic potential of honeys produced by Apis mellifera in the Pajeú hinterland, Pernambuco, Brazil (Caatinga Biome), with different floral origins: Mastic (Aroeira), Mesquite (Algaroba), and mixed flowers. These were used to formulate synbiotic and alcoholic beverages fermented by Saccharomyces boulardii CNCM I-745. Static and dynamic simulations of the human gastrointestinal tract (GIT) were used, as well as physicochemical, rheological, and microbiological analyses. The results revealed that honey positively influences the viability and resilience of probiotic yeast, especially honey with a predominance of Algaroba, which promoted the highest survival rate (>89%) even after 28 days of refrigeration and in dynamic in vitro simulation of the GIT (more realistic to human physio-anatomical conditions). The phenolic composition of the honeys showed a correlation with this tolerance. The use of complementary methodologies, such as flow cytometry, validated the findings and highlighted the functional value of these natural matrices, revealing an even greater longevity potential compared to conventional microbiological methodology. The data reinforces the potential of the Caatinga as a source of bioactive and sustainable compounds, proposing honey as a promising non-dairy synbiotic vehicle. This work contributes to the appreciation of the biome and the development of functional food products with a positive social, economic, and ecological impact. Full article

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

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19 pages, 1681 KiB

Open AccessArticle

Mixed Inoculation with Lacticaseibacillus casei and Staphylococcus carnosus Improves Safety, Gel Properties and Flavor of Giant Squid Surimi Without Added Seasonings

by Hongliang Mu, Peifang Weng and Zufang Wu

Fermentation 2025, 11(7), 404; https://doi.org/10.3390/fermentation11070404 - 14 Jul 2025

Abstract

The gel performance of giant squid is weak. Researchers have confirmed that adding some substances could improve the texture. However, the flavor has not been taken into account. In a previous study, we proved that mixed inoculation with Lacticaseibacillus casei and Staphylococcus carnosus [...] Read more.

The gel performance of giant squid is weak. Researchers have confirmed that adding some substances could improve the texture. However, the flavor has not been taken into account. In a previous study, we proved that mixed inoculation with Lacticaseibacillus casei and Staphylococcus carnosus with several seasonings adding could improve the texture of squid. Whether the addition of seasonings could affect the quality of samples or not and how fermentation affects the texture and flavor were not clear. In present study, we prepared fermented squid without seasonings. The results showed that compared with fermented samples with added seasonings, samples without seasonings might be safer, with fewer types and lower concentrations of biogenic amines. In samples without seasonings, non-inoculation had a higher pH and higher levels of biogenic amines. Meanwhile, mixed inoculation with L. casei and S. carnosus could ensure safety, improve texture and rheological properties. The water state of the fermented sample was also changed. The microstructure indicated that good network was formed in the fermented sample. After fermentation, the contents of several organic acids, free amino acids and volatile flavor compounds increased, and the results of the electronic nose test were also changed. In addition, starters were dominant during fermentation. These results indicated that mixed inoculation without seasonings might be a safer method than that with seasonings. In addition, mixed inoculation without seasonings could improve the texture and flavor of the squid. These results lay the foundation for improving fermented squid quality in further studies. Full article

(This article belongs to the Special Issue Functional Properties of Microorganisms in Fermented Foods, 2nd Edition)

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18 pages, 1720 KiB

Open AccessArticle

In Vitro Preliminary Characterization of Lactiplantibacillus plantarum BG112 for Use as a Starter Culture for Industrial Dry-Fermented Meats

by María Inés Palacio, María Julia Ruiz, María Fernanda Vega and Analía Inés Etcheverría

Fermentation 2025, 11(7), 403; https://doi.org/10.3390/fermentation11070403 - 14 Jul 2025

Abstract

The objective of this study was to perform a preliminary in vitro characterization of Lactiplantibacillus plantarum BG112, assessing its safety and technological features for potential application as a culture starter for an industrial fermented dry meat product. In vitro assays assessed its viability, [...] Read more.

The objective of this study was to perform a preliminary in vitro characterization of Lactiplantibacillus plantarum BG112, assessing its safety and technological features for potential application as a culture starter for an industrial fermented dry meat product. In vitro assays assessed its viability, probiotic properties, and safety for use in food formulations. The strain was characterized through morphological and biochemical tests, carbohydrate fermentation profiling, and various in vitro assays based on FAO/WHO criteria for probiotic selection. These included proteolytic activity, auto-aggregation capacity, tolerance to simulated gastric juice and bile salts, antimicrobial activity, and resistance to sodium chloride, nitrite, and low pH. Safety evaluations were also performed by testing antibiotic susceptibility, hemolytic activity, and DNAse production. The results showed that L. plantarum BG112 exhibited strong tolerance to adverse environmental conditions typically found during sausage fermentation and ripening, along with significant inhibitory activity against pathogenic bacteria, such as Escherichia coli O157:H7, Salmonella Typhimurium, and Staphylococcus aureus. The strain also demonstrated no hemolytic or DNAse activity and presented a favorable antibiotic sensitivity profile, meeting key safety requirements for probiotic use. Further studies using meat matrices and in vivo models are needed to validate these findings. This study contributes to the early-stage selection of safe and technologically suitable strains for use in fermented meat products. These findings support the potential application of L. plantarum BG112 as a safe and effective starter culture in the development of high-value, premium fermented meat products, aligned with current consumer demand for health-enhancing and natural foods. Full article

(This article belongs to the Special Issue Probiotic Lactic Acid Bacteria and Their Applications in Food Safety and Animal Health)

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37 pages, 5685 KiB

Open AccessArticle

Enhanced Biofuel Production from Mixed Marine Microalgae Using UV and UV/H₂O₂ Pretreatment: Optimization of Carbohydrate Release and Fermentation Efficiency

by Malak Alsarayreh and Fares AlMomani

Fermentation 2025, 11(7), 402; https://doi.org/10.3390/fermentation11070402 - 14 Jul 2025

Abstract

The robust structure of algal cell walls presents a major barrier in the recovery of fermentable sugars and intracellular lipids for biofuel production. This study investigates the effectiveness of ultraviolet (UV) radiation and UV-assisted hydrogen peroxide (UV/H₂O₂) pretreatment on [...] Read more.

The robust structure of algal cell walls presents a major barrier in the recovery of fermentable sugars and intracellular lipids for biofuel production. This study investigates the effectiveness of ultraviolet (UV) radiation and UV-assisted hydrogen peroxide (UV/H₂O₂) pretreatment on a local mixed marine algal culture to enhance biofuel production through cell wall disruption. Local mixed cultures of marine microalgae (LMCMA) were pretreated with UV for various exposure times (5–30 min) and with UV/H₂O₂ using H₂O₂ concentrations ranging from 0.88 to 3.53 mM. The impact of pretreatment was evaluated based on morphological changes (SEM and TEM), elemental composition (C, H, N), sugar release, and downstream fermentation yields of ethanol, methanol, 1-propanol, 1-butanol, and 1-pentanol using Saccharomyces cerevisiae. UV pretreatment at 20–30 min yielded the highest carbohydrate release (up to 0.025 g/gDCW), while UV/H₂O₂ at 1.76 mM achieved maximum sugar liberation (0.0411 g/gDCW). Fermentation performance was enhanced under optimized conditions, with peak ethanol yields of 0.3668 g ethanol/g carbohydrates (UV, 30 min, 48 h) and 0.251 g ethanol/g (UV/H₂O₂, 0.88 mM, 24 h). This study also demonstrated selective production of higher alcohols under varying fermentation temperatures (30–37 °C). These findings highlight the potential of combining oxidative pretreatment and process optimization to enhance biofuel recovery from environmentally relevant algal biomass. Full article

(This article belongs to the Special Issue Cyanobacteria and Eukaryotic Microalgae (2nd Edition))

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23 pages, 2711 KiB

Open AccessSystematic Review

Electro-Composting: An Emerging Technology

by Ahmad Shabir Hozad and Christian Abendroth

Fermentation 2025, 11(7), 401; https://doi.org/10.3390/fermentation11070401 - 14 Jul 2025

Abstract

This study focuses on electrical stimulation for composting. Using the PSALSAR method, a comprehensive systematic review analysis identified 22 relevant articles. The examined studies fall into four main systems: electric field-assisted aerobic composting (EAAC), electrolytic oxygen aerobic composting (EOAC), microbial fuel cells (MFCs), [...] Read more.

This study focuses on electrical stimulation for composting. Using the PSALSAR method, a comprehensive systematic review analysis identified 22 relevant articles. The examined studies fall into four main systems: electric field-assisted aerobic composting (EAAC), electrolytic oxygen aerobic composting (EOAC), microbial fuel cells (MFCs), and thermoelectric generators (TEGs). Apart from the main systems highlighted above, bioelectrochemically assisted anaerobic composting (AnC_{BE, III}) is discussed as an underexplored system with the potential to improve the efficiency of anaerobic degradation. Each system is described in terms of key materials, composter design, operating conditions, temperature evolution, compost maturity, microbial community, and environmental outcomes. EAAC and EOAC systems accelerate organic matter decomposition by improving oxygen distribution and microbial activity, whereas MFC and TEG systems have dual functioning due to the energy generated alongside waste degradation. These innovative systems not only significantly improve composting efficiency by speeding up organic matter breakdown and increasing oxygen supply but also support sustainable waste management by reducing greenhouse gas emissions and generating bioelectricity or heat. Together, these systems overcome the drawbacks of conventional composting systems and promote future environmental sustainability solutions. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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15 pages, 5632 KiB

Open AccessArticle

Characterization and Multi-Omics Basis of Biofilm Formation by Lactiplantibacillus plantarum

by Ruitang Ma, Dong Zhao, Rongqing Zhou, Jia Zheng and Chongde Wu

Fermentation 2025, 11(7), 400; https://doi.org/10.3390/fermentation11070400 - 12 Jul 2025

Abstract

Lactiplantibacillus plantarum is a kind of common lactic acid bacteria, which plays an important role in the production of fermented foods. In general, the formation of biofilm is conducive to the adaptability of cells in the face of fierce competition and an increasingly [...] Read more.

Lactiplantibacillus plantarum is a kind of common lactic acid bacteria, which plays an important role in the production of fermented foods. In general, the formation of biofilm is conducive to the adaptability of cells in the face of fierce competition and an increasingly harsh fermentation environment. In this work, optimum conditions for the formation of biofilm by L. plantarum were investigated, and scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) analysis showed the morphology of biofilm cells and 3D architecture of biofilm under different conditions, respectively. In addition, cells in the biofilms showed higher cell viability under heat stress, acid stress, and oxidative stress compared with planktonic cells. RNA-seq technology and TMT-based proteomic technology were employed to reveal the differential expression of profiles between biofilm cells and planktonic cells. The shelter provided by biofilm and the differential expression of genes and proteins involved in PTS, the TCA cycle, alanine, and teichoic acid biosynthesis may be involved in the formation of biofilm cells. The results presented in this study will help to understand the formation of biofilms in L. plantarum and regulate the industrial performance of cells in the food industry. Full article

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16 pages, 2079 KiB

Open AccessArticle

Biogas Production from Agave durangensis Mezcal Bagasse Pretreated Using Chemical Processes

by Refugio Hernández-López, Iván Moreno-Andrade, Blanca E. Barragán-Huerta, Edson B. Estrada-Arriaga and Marco A. Garzón-Zúñiga

Fermentation 2025, 11(7), 399; https://doi.org/10.3390/fermentation11070399 - 12 Jul 2025

Abstract

This study evaluated the viability of using the solid residues (bagasse) of the mezcal industry produced with Agave durangensis as a substrate for biogas production, using two chemical pretreatments, acid (HCl) and alkaline (KOH + Ca(OH)₂), to enhance its biodegradability and [...] Read more.

This study evaluated the viability of using the solid residues (bagasse) of the mezcal industry produced with Agave durangensis as a substrate for biogas production, using two chemical pretreatments, acid (HCl) and alkaline (KOH + Ca(OH)₂), to enhance its biodegradability and improve the anaerobic digestion (AD) process. The chemical composition of bagasse was analyzed before and after the chemical pretreatments and then AD experiments were conducted in anaerobic sequential batch reactors (A-SBR) to analyze the effect of pretreatments on biogas production performance. The results showed that acid pretreatment increased cellulose content to 0.606 g, which represented an increase of 34%, and significantly reduced hemicellulose. In contrast, alkaline pretreatment did not show significant changes in cellulose composition, although it caused a swelling of the Agave durangensis mezcal bagasse (Ad-MB) fibers. In terms of biogas production, Ad-MB pretreated with acid (Ad-MB-acid) increased cumulative production by 76% compared to the Agave durangensis mezcal bagasse that was not pretreated (Ad-MB-not pretreated) and by 135% compared to Agave durangensis mezcal bagasse pretreated with an alkaline solution (Ad-MB-alkaline). These results confirmed that Agave durangensis solid waste from the mezcal industry that receives acidic chemical pretreatment has the potential to generate biogas as a sustainable biofuel that can be used to reduce the ecological footprint of this industry. Full article

(This article belongs to the Special Issue Biofuels Production and Processing Technology, 3rd Edition)

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22 pages, 2129 KiB

Open AccessArticle

Biological Hydrogen Production Through Dark Fermentation with High-Solids Content: An Alternative to Enhance Organic Residues Degradation in Co-Digestion with Sewage Sludge

by Rodolfo Daniel Silva-Martínez, Oscar Aguilar-Juárez, Lourdes Díaz-Jiménez, Blanca Estela Valdez-Guzmán, Brenda Aranda-Jaramillo and Salvador Carlos-Hernández

Fermentation 2025, 11(7), 398; https://doi.org/10.3390/fermentation11070398 - 11 Jul 2025

Abstract

Adequate treatment of the organic fraction of municipal solid waste (OFMSW) in co-digestion with sewage sludge (SS) through dark fermentation (DF) technologies has been widely studied and recognized. However, there is little experience with a high-solids approach, where practical and scalable conditions are [...] Read more.

Adequate treatment of the organic fraction of municipal solid waste (OFMSW) in co-digestion with sewage sludge (SS) through dark fermentation (DF) technologies has been widely studied and recognized. However, there is little experience with a high-solids approach, where practical and scalable conditions are established to lay the groundwork for further development of feasible industrial-scale projects. In this study, the biochemical hydrogen potential of OFMSW using a 7 L batch reactor at mesophilic conditions was evaluated. Parameters such as pH, redox potential, temperature, alkalinity, total solids, and substrate/inoculum ratio were adjusted and monitored. Biogas composition was analyzed by gas chromatography. The microbial characterization of SS and post-reaction percolate liquids was determined through metagenomics analyses. Results show a biohydrogen yield of 38.4 NmLH₂/gVS OFMSW, which forms ~60% of the produced biogas. Aeration was proven to be an efficient inoculum pretreatment method, mainly to decrease the levels of methanogenic archaea and metabolic competition, and at the same time maintain the required total solid (TS) contents for high-solids conditions. The microbial community analysis reveals that biohydrogen production was carried out by specific anaerobic and aerobic bacteria, predominantly dominated by the phylum Firmicutes, including the genus Bacillus (44.63% of the total microbial community), Clostridium, Romboutsia, and the phylum Proteobacteria, with the genus Proteus. Full article

(This article belongs to the Special Issue Valorization of Food Waste Using Solid-State Fermentation Technology)

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16 pages, 2368 KiB

Open AccessArticle

Isolation and Characterization of a Thermaerobacillus caldiproteolyticus-like Strain Producing Extracellular Amylase from the Nelumwewa Geothermal Spring, Sri Lanka

by Sarath Bandara, Buddhika Dharmasena, Lakshani Pathirana, Prasad Jayasooriya and Aruna Weerasooriya

Fermentation 2025, 11(7), 397; https://doi.org/10.3390/fermentation11070397 - 11 Jul 2025

Abstract

The growing demand for efficient sustainable biocatalysts for industrial applications has driven the exploration of extremozymes from extremophiles, particularly those thriving in geothermal environments. This study aimed to isolate and characterize extracellular amylase-producing thermophilic bacteria from the Nelumwewa geothermal spring in Sri Lanka, [...] Read more.

The growing demand for efficient sustainable biocatalysts for industrial applications has driven the exploration of extremozymes from extremophiles, particularly those thriving in geothermal environments. This study aimed to isolate and characterize extracellular amylase-producing thermophilic bacteria from the Nelumwewa geothermal spring in Sri Lanka, an underexplored ecosystem. Among the isolated thermophilic bacterial strains, NW2 isolates exhibited a prominent extracellular amylase activity. Molecular characterization by 16S rRNA gene sequencing confirmed the close phylogenetic relationship between NW2 and Thermaerobacillus caldiproteolyticus, which is well-known for thermostable proteases. Biochemical assays revealed optimal amylase activity of NW2 isolate at 60 °C and pH 8.0, with a crude enzyme activity of 0.85 U/mL. The enzyme demonstrated efficient hydrolysis of raw cassava starch, highlighting its potential for industrial applications in food, biofuel, and detergent industries. This study reports the first T. caldiproteolyticus-like strain from Sri Lanka with significant extracellular amylase activity, emphasizing the biotechnological potential of geothermal springs as sources of novel extremozymes. These findings contribute to the growing repository of thermostable enzymes, highlighting the need for further exploration of Sri Lanka’s geothermal microbial diversity for industrial biocatalysts. Full article

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

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21 pages, 4047 KiB

Open AccessArticle

Valorization of Spent Coffee Grounds as a Substrate for Fungal Laccase Production and Biosorbents for Textile Dye Decolorization

by Eduardo da Silva França, Adriana Ferreira de Souza, Dayana Montero Rodríguez, Nazareth Zimiani de Paula, Anna Gabrielly Duarte Neves, Kethylen Barbara Barbosa Cardoso, Galba Maria de Campos-Takaki, Marcos Antonio Barbosa de Lima and Ana Lucia Figueiredo Porto

Fermentation 2025, 11(7), 396; https://doi.org/10.3390/fermentation11070396 - 10 Jul 2025

Abstract

Spent coffee grounds (SCG) are a widely available agro-industrial residue rich in carbon and phenolic compounds, presenting significant potential for biotechnological valorization. This study evaluated the use of SCG as a suitable substrate for fungal laccase production and the application of the resulting [...] Read more.

Spent coffee grounds (SCG) are a widely available agro-industrial residue rich in carbon and phenolic compounds, presenting significant potential for biotechnological valorization. This study evaluated the use of SCG as a suitable substrate for fungal laccase production and the application of the resulting fermented biomass (RFB), a mixture of fermented SCG and fungal biomass as a biosorbent for textile dye removal. Two fungal strains, namely Lentinus crinitus UCP 1206 and Trametes sp. UCP 1244, were evaluated in both submerged (SmF) and solid-state fermentation (SSF) using SCG. L. crinitus showed superior performance in SSF, reaching 14.62 U/g of laccase activity. Factorial design revealed that a lower SCG amount (5 g) and higher moisture (80%) and temperature (30 °C ± 0.2) favored enzyme production. Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) analyses confirmed significant structural degradation of SCG after fermentation, especially in SSF. Furthermore, SCG and RFB were chemically activated and evaluated as biosorbents. The activated carbon from SCG (ACSCG) and RFB (ACRFB) exhibited high removal efficiencies for Remazol dyes, comparable to commercial activated carbon. These findings highlight the potential of SCG as a low-cost, sustainable resource for enzyme production and wastewater treatment, contributing to circular bioeconomy strategies. Full article

(This article belongs to the Special Issue Application and Research of Solid State Fermentation, 2nd Edition)

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37 pages, 3498 KiB

Open AccessReview

Pigments from Microorganisms: A Sustainable Alternative for Synthetic Food Coloring

by Akshay Chavan, Jaya Pawar, Umesh Kakde, Mekala Venkatachalam, Mireille Fouillaud, Laurent Dufossé and Sunil Kumar Deshmukh

Fermentation 2025, 11(7), 395; https://doi.org/10.3390/fermentation11070395 - 10 Jul 2025

Abstract

Microbial pigments are gaining acceptance as a green, sustainable substitute for synthetic food pigments due to growing health issues and their adverse health impacts. This review provides an overview of the potential of microbial pigments as natural food colorants and the advantages of [...] Read more.

Microbial pigments are gaining acceptance as a green, sustainable substitute for synthetic food pigments due to growing health issues and their adverse health impacts. This review provides an overview of the potential of microbial pigments as natural food colorants and the advantages of microbial pigments over synthetic pigments. Microbial pigments are a natural source of color with medicinal properties like anticancer, antimicrobial, and antioxidant activity. Important pigments covered are astaxanthin, phycocyanin, prodigiosin, riboflavin, β-carotene, violacein, melanin, and lycopene, and their microbial origins and characteristics. The review also covers commercial production of microbial pigments, i.e., strain development and fermentation processes. Microbial pigments also find extensive applications in food industries, including preservatives for food. Also covered are their pharmacological activity and other applications, such as in the formation of nanoparticles. Finally, the challenges and future directions of microbial pigment production are covered, including the need for cost-effective production, regulatory acceptability, and the potential of genetic engineering and fermentation-based technologies to enhance pigment yield and quality. Full article

(This article belongs to the Special Issue Metabolic Engineering in Microbial Synthesis)

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14 pages, 684 KiB

Open AccessArticle

Diversity and Biological Activity of Secondary Metabolites Produced by the Endophytic Fungus Penicillium ochrochlorae

by Jian Hu and Dan Qin

Fermentation 2025, 11(7), 394; https://doi.org/10.3390/fermentation11070394 - 10 Jul 2025

Abstract

In order to investigate bioactive natural products derived from the endophytic fungus Penicillium ochrochloron SWUKD4.1850, a comprehensive study focusing on secondary metabolites was conducted. This research led to the isolation of twenty distinct compounds, including a novel nortriterpenoid (compound 20), alongside nineteen [...] Read more.

In order to investigate bioactive natural products derived from the endophytic fungus Penicillium ochrochloron SWUKD4.1850, a comprehensive study focusing on secondary metabolites was conducted. This research led to the isolation of twenty distinct compounds, including a novel nortriterpenoid (compound 20), alongside nineteen compounds that had been previously characterized (compounds 1–19). The chemical structures of these compounds were elucidated using spectroscopic techniques and nuclear magnetic resonance (NMR) analyses. Compounds 1–17 were isolated for the first time as metabolites of P. ochrochloron. Except for compounds 1–14, significant structural similarity was discerned between the metabolites of the endophytic fungus and those of the host plant. Compound 20 is noted as the inaugural instance of a naturally occurring 27-nor-3,4-secocycloartane schinortriterpenoid, while compound 17 was identified in fungi for the first time. An antifungal assay showed that compound 10 displayed a broader antifungal spectrum and a stronger inhibitory effect towards four important plant pathogens, at inhibitory rates of 74.9 to 85.3%. The in vitro radical scavenging activities of compounds 1, 3, 8, 15, and 16 showed higher antioxidant activity than vitamin C. Moreover, a cytotoxic assay revealed that compound 20 had moderate cytotoxicity against the HL-60, SMMC-7721, and MCF-7 cell lines (IC₅₀ 6.5–17.8 μM). Collectively, these findings indicate that P. ochrochloron has abundant secondary metabolite synthesis ability in microbial metabolism and that these metabolites have good biological activity and have the potential to enhance plant disease resistance. Full article

(This article belongs to the Special Issue Fermentation-Driven Biological Structural Modification of Natural Products)

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28 pages, 1598 KiB

Open AccessArticle

Development of Antimicrobial and Antioxidative Chicken Patties Using Liquid-Fermented Ganoderma lucidum and Pleurotus djamor Fruiting Body Biomass

by Nur Asyiqin Zahia-Azizan, Chong Shin Yee, Muhammad Ameer Ushidee-Radzi, Zul Ilham, Muhamad Hafiz Abd Rahim, Siva Raseetha, Nazimah Hamid, Adi Ainurzaman Jamaludin and Wan Abd Al Qadr Imad Wan-Mohtar

Fermentation 2025, 11(7), 393; https://doi.org/10.3390/fermentation11070393 - 9 Jul 2025

Abstract

Medicinal mushroom production utilising rural cultivation (solid state fermentation) requires approximately six months compared to culinary mushroom production (7 days). Urban cultivation (submerged liquid fermentation) can be used as a sustainable method of producing medicinal mushroom biomass. In this study, chicken patties were [...] Read more.

Medicinal mushroom production utilising rural cultivation (solid state fermentation) requires approximately six months compared to culinary mushroom production (7 days). Urban cultivation (submerged liquid fermentation) can be used as a sustainable method of producing medicinal mushroom biomass. In this study, chicken patties were fortified with liquid-fermented Ganoderma lucidum flour (GLF) and Pleurotus djamor mushroom biomass flour (PDF) at concentrations of 3%, 6%, and 9%. These were compared to a negative control (0% mushroom flour chicken patty) and a commercial patty. Chicken patties fortified with 3% PDF and 9% GLF recorded the lowest cooking loss, at 5.55% and 10.3%, respectively. Mushroom chicken patties exhibited lower cooking losses and significant changes in colour and texture compared to control samples. Notably, 3% GLF chicken patty achieved the highest overall acceptability score of 6.55 followed by 9% PDF chicken patty (6.08) (p < 0.05). Biomass flour of liquid-fermented Ganoderma lucidum (ENS-GL) and Pleurotus djamor (ENS-PD) were extracted for their endopolysaccharide and analysed for their functional properties. All elemental, FT-IR, and NMR spectroscopy analyses revealed the existence of a comparable beta-glucan polymer structure, linkages, and absorptions when compared to the Laminarin standard. In addition, ENS-GL also proved to possess higher antimicrobial activities and significant antioxidant levels (DPPH-scavenging activity, ferric reduction potential and total phenolic content) compared to ENS-PD. Overall, this study revealed that sustainable liquid-fermented Ganoderma lucidum, a medicinal mushroom, outperformed Pleurotus djamor, a culinary mushroom, as a potential alternative flour for combating hunger in the future. Full article

(This article belongs to the Special Issue Advances in Fermented Foods and Beverages)

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