Fermentation

22 pages, 1117 KB

Open AccessArticle

Lactic Acid Bacteria Fermentation as a Tool for Creating Texture in Plant-Based “Clean-Label” Cheeses

by Valeria Novikova, Anna Shiker, Anastasia Vostrikova, Egor Parkhomenko, Ilya Demyanenko, Olga Korneeva, Zorigto Namsaraev and Alexey Sazonov

Fermentation 2026, 12(2), 111; https://doi.org/10.3390/fermentation12020111 - 12 Feb 2026

Abstract

The growing demand for clean-label plant-based cheese alternatives underscores the need for products with desirable properties. A key technological challenge is replicating the firmness of traditional cheese without synthetic additives. This study explores lactic acid bacteria (LAB) fermentation as a natural texturizing method [...] Read more.

The growing demand for clean-label plant-based cheese alternatives underscores the need for products with desirable properties. A key technological challenge is replicating the firmness of traditional cheese without synthetic additives. This study explores lactic acid bacteria (LAB) fermentation as a natural texturizing method for clean-label plant-based cheeses. We investigated the link between LAB metabolic traits and the firmness of three substrates: cashew, soybean, and sunflower seed. A strong correlation (r ≈ −0.88) was found between final pH and firmness in cashew paste, where strains achieving a pH of ~4.0–4.5 (near the protein isoelectric point) produced the firmest gels (up to 3.35 N). Lactiplantibacillus plantarum 729/23 and Lacticaseibacillus helveticus NK-1 were most effective. Soybean paste firmness increased moderately (to 1.93 N), while sunflower seed paste showed no significant improvement (≤1.14 N) despite active acidification, indicating substrate-specific limitations. This study, supported by a comprehensive analysis of the literature on firmness measurement in plant-based cheeses, demonstrates the potential of targeted selection of natural starter cultures to create clean-label products with minimal ingredients. Full article

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

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5 pages, 150 KB

Open AccessEditorial

Biofuel Production and Processing Technology, 3rd Edition

by Alessia Tropea

Fermentation 2026, 12(2), 110; https://doi.org/10.3390/fermentation12020110 - 12 Feb 2026

Abstract

The rapid growth of the global population and the impending depletion of fossil fuels, currently meeting approximately 80% of the world’s power needs, have intensified interest in biofuels derived from renewable biomass. This editorial refers to the Special Issue, “Biofuel Production and Processing [...] Read more.

The rapid growth of the global population and the impending depletion of fossil fuels, currently meeting approximately 80% of the world’s power needs, have intensified interest in biofuels derived from renewable biomass. This editorial refers to the Special Issue, “Biofuel Production and Processing Technology, 3rd Edition,” which highlights the transition of fermentation-based technologies from isolated processes into integrated, multifunctional biorefinery platforms. The collection includes nine contributions (eight original articles and one review) covering diverse advancements, including: The valorization of industrial intermediates, strategies to improve anaerobic digestion through co-digestion and heat recovery integration, mechanistic insights into syngas fermentation and the development of multi-product microbial systems, emerging frontier technologies, such as biological hydrogen production in depleted oil and gas reservoirs. Collectively, these studies emphasize that the future of sustainable energy relies on system-level optimization, balancing feedstock flexibility, energy integration, and environmental performance within a circular bioeconomy. Full article

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

14 pages, 257 KB

Open AccessArticle

Can Pre-Fermented Juice Be an Alternative Probiotic Helping to Reduce Heat Stress in Laying Japanese Quails (Metabolism and Nutrition)

by Sadık Serkan Aydin, Mehmet Avci, Nurcan Kirar, Ahmet Oruç, Mehmet Savrunlu and Aydin Daş

Fermentation 2026, 12(2), 109; https://doi.org/10.3390/fermentation12020109 - 12 Feb 2026

Abstract

This study aimed to determine the effects of incorporating probiotic fermented natural lactic acid bacteria (PFJ) into the drinking water of laying quails subjected to temperature stress on egg production, egg quality, cecum microbiology, blood parameters, and incubation performance. A total of 260 [...] Read more.

This study aimed to determine the effects of incorporating probiotic fermented natural lactic acid bacteria (PFJ) into the drinking water of laying quails subjected to temperature stress on egg production, egg quality, cecum microbiology, blood parameters, and incubation performance. A total of 260 Japanese quails (Coturnixcoturnix japonica) aged 8 weeks were used, of which 200 were females, and 60 were males. The quails were divided into four groups, each containing 50 individuals, and further split into five subgroups of 10 quails. For every 10 female quails, three male quails were housed together in cages. The experiment was conducted under normal environmental conditions in control, PFJ, heat-stressed control, and heat-stressed PFJ groups. Temperature stress (34–36 °C) was applied for 8 h daily. The results indicated that by the end of weeks 1–4, the feed conversion ratios of all groups were significantly different, with the best feed conversion ratio of 2.36 found in the PFJ group under temperature stress. Throughout the periods of weeks 1–4 and 5–8, there were statistically significant differences (p < 0.01) in the daily average feed consumption and egg weights among all treated groups. Temperature stress and the addition of PFJ significantly affected shell thickness, Haugh units, albumen weight, yolk weight, and yolk color; no significant impacts were observed on egg shape index, yolk percentage (%), albumen percentage (%), and specific gravity (g/cm³). The highest counts of lactic acid bacteria (LAB) were found in the PFJ-treated groups under both normal and temperature-stressed conditions. Under temperature stress, the levels of Enterobacter, coliform, and E. coli decreased with the addition of PFJ. Regarding blood parameters, significant differences (p < 0.05) were observed in total protein values among groups, while differences in chloride, triglycerides, total cholesterol, LDL cholesterol, HDL cholesterol, and triglyceride concentrations were not statistically significant (p > 0.05). Furthermore, the addition of temperature stress and PFJ significantly affected fertility rates, incubation efficiency, and hatchability. In conclusion, these findings suggest that PFJ could be considered a potential probiotic alternative for improving nutrition in laying quails under conditions of temperature stress. Full article

(This article belongs to the Special Issue Application of Fermentation Technology in Animal Nutrition: 3rd Edition)

15 pages, 2508 KB

Open AccessArticle

Genome-Scale Modeling-Guided Metabolic Engineering Enables Heterologous Production of 3-Amino-4-hydroxybenzoic Acid in Streptomyces thermoviolaceus

by Togo Yamada, Pamella Apriliana, Prihardi Kahar, Tomoya Kobayashi, Yutaro Mori and Chiaki Ogino

Fermentation 2026, 12(2), 108; https://doi.org/10.3390/fermentation12020108 - 12 Feb 2026

Abstract

3-Amino-4-hydroxybenzoic acid (3,4-AHBA) is a non-proteinogenic aromatic compound that functions as a key biosynthetic precursor for diverse secondary metabolites with pharmaceutical and industrial value. Microbial production of 3,4-AHBA offers a sustainable alternative to petroleum-based chemical synthesis; however, metabolic complexity and trade-offs between growth [...] Read more.

3-Amino-4-hydroxybenzoic acid (3,4-AHBA) is a non-proteinogenic aromatic compound that functions as a key biosynthetic precursor for diverse secondary metabolites with pharmaceutical and industrial value. Microbial production of 3,4-AHBA offers a sustainable alternative to petroleum-based chemical synthesis; however, metabolic complexity and trade-offs between growth and product formation constrain rational strain design. Here, genome-scale metabolic (GSM) modeling and flux balance analysis (FBA) were integrated with targeted genetic engineering to elucidate and enhance 3,4-AHBA production in Streptomyces thermoviolaceus. A genome-scale metabolic model was constructed and expanded by incorporating the nspH–nspI gene operon, which encodes the 3,4-AHBA biosynthetic pathway. In silico FBA predicted substantial rewiring of central carbon metabolism, with carbon flux redirected from glycolysis and the tricarboxylic acid cycle toward aspartate-derived intermediates and 3,4-AHBA synthesis, accompanied by reduced biomass-associated flux. Guided by these predictions, an engineered strain (St::NspHI) was developed and experimentally evaluated. Consistent with model predictions, the engineered strain exhibited lower growth rates and glucose uptake than the wild type, reflecting a metabolic burden. Nevertheless, 3,4-AHBA production was achieved exclusively in the engineered strain. Comparison of simulated and experimental fluxes revealed overestimation by FBA, likely due to secondary metabolism and incomplete genome annotation. Overall, GSM-guided design enables optimization of precursor production. Full article

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

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16 pages, 3468 KB

Open AccessArticle

Study on Microbial Diversity and Product Quality of Corn Gluten Meal-Based Fermented Feed

by Nan Hu, Hongji Zhao, Jingyi Sun, Kerui Liu, Shuying Li, Yongping Xu and Shanzi Cong

Fermentation 2026, 12(2), 107; https://doi.org/10.3390/fermentation12020107 - 12 Feb 2026

Abstract

This study aimed to evaluate the effects of mixed strain fermentation on the microbial diversity, fermentation quality, and flavor of corn gluten meal-based fermented feed (CGMFF). High-throughput sequencing techniques (16S rDNA and ITS) and GC-MS technology were used to determine microbial community succession [...] Read more.

This study aimed to evaluate the effects of mixed strain fermentation on the microbial diversity, fermentation quality, and flavor of corn gluten meal-based fermented feed (CGMFF). High-throughput sequencing techniques (16S rDNA and ITS) and GC-MS technology were used to determine microbial community succession and flavor changes during the fermentation and storage stages of CGMFF and to explore their correlations. The results showed that Xeromyces and Lactobacillus became the dominant genera at the end of storage, with a relative abundance exceeding 96%. During fermentation and storage, the contents of soluble protein and ammonia nitrogen increased while the crude protein content decreased. The protein molecular weight was concentrated in the range of 75–1100 Da (96.98%), and the free amino acid (FAA) content increased by 1.42 times. This reduction in the proportion of bitter amino acids enhanced the palatability of CGMFF. The aroma gradually developed characteristics dominated by esters and alkanes. This study is intended to provide a theoretical basis for the application of corn gluten meal as a protein-rich raw material in fermented feed. 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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16 pages, 320 KB

Open AccessArticle

Biotechnological Valorization of Almond Hulls via Solid-State Fermentation with Saccharomyces cerevisiae and Fibrolytic Enzyme Supplementation: Enhancing Ruminal Fermentation and Reducing Greenhouse Gas Emissions

by Khalil Abid

Fermentation 2026, 12(2), 106; https://doi.org/10.3390/fermentation12020106 - 12 Feb 2026

Abstract

Valorization of agricultural by-products is a key component of circular strategies aimed at enhancing the sustainability of livestock systems. Almond hulls (AHs), a major residue of the almond-processing industry, are characterized by their high non-fiber carbohydrate (NFC) content, but low crude protein (CP) [...] Read more.

Valorization of agricultural by-products is a key component of circular strategies aimed at enhancing the sustainability of livestock systems. Almond hulls (AHs), a major residue of the almond-processing industry, are characterized by their high non-fiber carbohydrate (NFC) content, but low crude protein (CP) content and ruminal fermentation. This study evaluated the effects of treating AHs with exogenous fibrolytic enzymes (EFEs) and Saccharomyces cerevisiae (SC) via solid-state fermentation. Treatments were applied individually or in combination (SC + EFEs). The effects on chemical composition and ruminal fermentation were assessed. EFEs reduced the fiber content and increased the NFC content. This accelerated ruminal fermentation and reduced the lag time. However, it did not change the overall fermentation extent. SC increased the CP content and ether extract but reduced the NFC content. This modification promoted the growth of ruminal bacteria. As a result, the ruminal fermentation extent, ruminal degradability and volatile fatty acid (VFA) content improved. However, methane (CH₄) and carbon dioxide (CO₂) emissions relative to the substrate, degraded substrate and total gas emission were not affected. SC + EFEs had synergistic effects. This further increased the CP content and ether extract and reduced the NFC and fiber contents. The treatment modulated ruminal microbiota by decreasing protozoa and increasing bacteria. It also reduced the fermentation lag time and enhanced the fermentation extent, degradability and VFA production favoring propionate formation. Additionally, it reduced CH₄ and CO₂ emissions per unit of degraded substrate and the total gas emission. Overall, the SC + EFEs represent an effective approach to enhance the nutritional value of AHs while partially mitigating greenhouse gas emissions relative to substrate utilization and fermentation pathways. Full article

(This article belongs to the Special Issue Biotechnological Approaches to the Valorization of Agro-Industrial By-Products)

14 pages, 2211 KB

Open AccessArticle

Mechanisms of Ofloxacin Exposure Inhibiting Hydrogen Production in Anaerobic Fermentation

by Luyao Zhou, Jiasheng Zhang, Jianning Chang and Panyue Zhang

Fermentation 2026, 12(2), 105; https://doi.org/10.3390/fermentation12020105 - 11 Feb 2026

Abstract

Ofloxacin (OFL) exists widely in raw materials of organic fermentation, which can inhibit hydrogen production of dark fermentation. In this study, the inhibition of OFL on hydrogen production was studied from the aspects of hydrogen production performance, bacterial community and functional genes using [...] Read more.

Ofloxacin (OFL) exists widely in raw materials of organic fermentation, which can inhibit hydrogen production of dark fermentation. In this study, the inhibition of OFL on hydrogen production was studied from the aspects of hydrogen production performance, bacterial community and functional genes using glucose as a model substrate. The results showed that OFL exposure ≥ 10 mg/L significantly decreased the hydrogen production. With an OFL exposure concentration of 500 mg/L, the hydrogen yield reduced to 48.35 ± 2.13 mL/g glucose and the lag period prolonged to 26.48 ± 0.40 h, compared with those of control without ofloxacin exposure (169.99 ± 9.68 mL/g glucose and 8.98 ± 0.07 h), respectively. The efficient hydrogen-producing bacteria, Clostridium, were inhibited and the dominant microbial population was transformed, leading to change in metabolic pathway of fermentation from butyric acid type to ethanol type. Correspondingly, the proportion of butyrate in metabolites decreased from 66.46% to 0.00%, the proportion of acetate decreased from 26.12% to 3.69%, and the proportion of ethanol increased from 3.13% to 96.31%. OFL exposure showed significant downregulation of predicted functional genes involved in glycolysis and hydrogen production, such as K00845, K00532, and K03737, fundamentally resulting in significant inhibition of glycolysis and pyruvate metabolism for hydrogen production. Full article

(This article belongs to the Special Issue Recent Advancements in Fermentation Technology: Biofuels Production)

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14 pages, 893 KB

Open AccessReview

Recent Updates on Autochthonous Lactic Acid Bacteria in the Food Industry: A Bibliometric Analysis

by Jayuri Susy Fernandes de Araújo, Genésio José da Silva Neto, Bruno Fonsêca Feitosa, Winnie Alencar Luciano, Bárbara Fernanda Figueiredo dos Santos, Emmanuel Moreira Pereira, Mônica Correia Gonçalves, Mônica Tejo Cavalcanti, Maria Manuela Pintado and Osvaldo Soares da Silva

Fermentation 2026, 12(2), 104; https://doi.org/10.3390/fermentation12020104 - 11 Feb 2026

Abstract

This bibliometric review aimed to map recent scientific production (2020–2026) on autochthonous bacterial strains applied to the food industry, focusing on experimental studies retrieved from the Scopus^® database. Boolean operators and truncation were applied to refine searches and exclude yeast-related terms, and [...] Read more.

This bibliometric review aimed to map recent scientific production (2020–2026) on autochthonous bacterial strains applied to the food industry, focusing on experimental studies retrieved from the Scopus^® database. Boolean operators and truncation were applied to refine searches and exclude yeast-related terms, and keyword co-occurrence analysis was performed using VOSviewer (v1.6.20). A total of 44,095 experimental articles were analyzed. Results revealed a stable annual output exceeding 8000 papers between 2021 and 2024, indicating sustained scientific interest in the topic. China and the United States accounted for over 55% of total publications, with Chinese institutions and funding agencies showing predominant activity. Research was mainly distributed across Biochemistry, Genetics, Molecular Biology, Medicine, and Microbiology, reflecting applied and mechanistic approaches. Two major thematic clusters were identified: one focused on gastrointestinal health and microbiota modulation and another centered on microbial metabolism, probiotic functionality, and biochemical characterization. The findings confirm the growing scientific and technological relevance of autochthonous strains in improving food quality, safety, and functionality, especially in fermented products, and provide valuable insights for guiding future research and innovation in food microbiology and biotechnology. Full article

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

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29 pages, 501 KB

Open AccessReview

Fermentation-Based Strategies for the Feed Industry: Nutritional Augmentation, Environmental Sustainability

by Yukun Zhang, Manabu Ishikawa, Na Jiang and Xiaoxiao Zhang

Fermentation 2026, 12(2), 103; https://doi.org/10.3390/fermentation12020103 - 11 Feb 2026

Abstract

Global agriculture faces unprecedented challenges, including a projected population of 10 billion by 2050, declining arable land, and the urgent need to phase out antibiotic growth promoters (AGPs) to stem antimicrobial resistance (AMR). This review evaluates fermentation technology as a sustainable solution to [...] Read more.

Global agriculture faces unprecedented challenges, including a projected population of 10 billion by 2050, declining arable land, and the urgent need to phase out antibiotic growth promoters (AGPs) to stem antimicrobial resistance (AMR). This review evaluates fermentation technology as a sustainable solution to the “food–feed–fuel” three competing land uses. We systematically compare solid-state fermentation (SSF) and submerged fermentation (SmF), highlighting their quantitative advantages: SSF offers 2–3× higher volumetric productivity and 70–90% lower water usage for solid wastes (e.g., soybean meal, wheat bran), while SmF provides superior process control for high-value products (e.g., single-cell protein). Key molecular mechanisms are discussed, including enzymatic degradation of anti-nutritional factors (up to 95% phytate and 98.8% tannin removal), mycotoxin detoxification (60–80% reduction), and biosynthesis of bioactive compounds (e.g., vitamin B12 enrichment up to 15-fold). Fermented feeds benefit many livestock species, particularly in organic and high-density farming systems, improving growth performance, gut health, and disease resistance while reducing environmental footprints. Advanced technologies such as AI-driven digital twins, CRISPR-based strain engineering, and precision fermentation are explored to overcome bottlenecks, including heat dissipation, strain stability, and process control. Despite challenges in scale-up, economics, and divergent global regulations (EU, USA, China, Southeast Asia, and Africa), fermentation is a critical biotechnological paradigm for circularity—the circular bioeconomy—and long-term food security. Future research should prioritize cost-effective large-scale implementation and the harmonization of regulatory frameworks. Full article

(This article belongs to the Special Issue Fermentation Strategies to Enhance Feed Nutritional Value and Optimize Industry Resources)

20 pages, 5069 KB

Open AccessArticle

Screening of Non-Saccharomyces for Citrus reticulata cv. ‘Dahongpao’ Fruit Wine and Volatile Organic Compounds Analyzed by Gas Chromatography–Ion Mobility Spectrometry

by Xun Fu, Qingyu Nie, Xiang Li, Penghao Tan, Tingting Feng, Chunmei Xiong, Wenling Zhang, Yan Zhang, Sujin Li and Lixin Zhang

Fermentation 2026, 12(2), 102; https://doi.org/10.3390/fermentation12020102 - 11 Feb 2026

Abstract

In recent years, there has been substantial global progress in screening yeasts for fermenting various specialty fruits, especially non-Saccharomyces species known for their contributions to aroma enhancement. This study focused on mature fruits and soil samples collected from orchards located in the main [...] Read more.

In recent years, there has been substantial global progress in screening yeasts for fermenting various specialty fruits, especially non-Saccharomyces species known for their contributions to aroma enhancement. This study focused on mature fruits and soil samples collected from orchards located in the main production region of C. reticulata cv. ‘Dahongpao’ (CRCD) in China, with the objective of isolating specialized non-Saccharomyces yeasts suitable for producing CRCD fruit wine. After enrichment cultivation, seven characteristic yeast strains were isolated and purified. These isolates were identified as Candida parapsilosis, Meyerozyma caribbica, Candida quercitrusa, and Meyerozyma guilliermondii through a combination of microscopic morphology and molecular biology methods, which also included Pichia fermentans, Pichia kudriavzevii, and Pichia kluyveri. The strains’ fermentation potential, ethanol production rates, and tolerance levels were assessed, leading to the selection of Candida parapsilosis, Candida quercitrusa, Pichia fermentans, Pichia kudriavzevii, and Pichia kluyveri for further fermentation experiments. The commercial yeast La-Ma was used as a control. Analysis of volatile organic compounds (VOCs) in the fruit wine samples was performed using Gas Chromatography–Ion Mobility Spectrometry (GC-IMS). A total of 42 different VOCs were identified, with esters being the most prevalent. The fingerprint profiles demonstrated notable differences between the fruit wine samples fermented with selected yeasts and those fermented with commercial yeasts. Principal component analysis (PCA) indicated that Pichia kluyveri displayed the most significant divergence from both commercial and other selected yeasts. The samples contained notable VOCs such as 2-methyl-1-butanol, pentanal, 3-methyl-2-butenal, propyl acetate, butyl acetate, isobutyl acetate, isopentyl acetate, and 3-methyl-2-butenyl acetate, while the methanol production was observed to be lower compared to other samples. Consequently, this strain has the potential to produce distinctive fruit wine. Full article

(This article belongs to the Section Yeast)

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15 pages, 3209 KB

Open AccessArticle

Native Carbonic Anhydrase Activity Provides a Critical and Sufficient CO₂ Concentrating Mechanism for Escherichia coli Succinate Fermentation

by Amanda G. Godar, Francesca Cristobal, Luis Taquillo, Xuan Wang and David R. Nielsen

Fermentation 2026, 12(2), 101; https://doi.org/10.3390/fermentation12020101 - 11 Feb 2026

Abstract

While the biobased, fermentative production of succinate by Escherichia coli represents a sustainable alternative to its conventional synthesis from petroleum, this process requires substantial amounts of inorganic carbon (C_i) to support CO₂-fixing reactions in the reductive branch of the [...] Read more.

While the biobased, fermentative production of succinate by Escherichia coli represents a sustainable alternative to its conventional synthesis from petroleum, this process requires substantial amounts of inorganic carbon (C_i) to support CO₂-fixing reactions in the reductive branch of the tricarboxylic acid (rTCA) cycle. Accordingly, intracellular C_i availability represents a potential limiting factor during E. coli succinate fermentations. Here, we first investigate the role and importance of E. coli’s native CO₂ concentrating mechanism (CCM)—comprising two carbonic anhydrases (CAs), Can and CynT—by comparing and contrasting the behaviors of wild-type E. coli and the engineered succinate-producing strain, KJ122. Deletion of can and cynT significantly impaired the aerobic growth of both strains under low CO₂ atmosphere and/or low pH, outcomes that were further exacerbated under anaerobic conditions for KJ122. During bioreactor fermentations, KJ122 Δcan ΔcynT further exhibited a prolonged lag phase (~48 h) and 44% reduced succinate production relative to KJ122 by 96 h. Next, the relative functions and performance of mechanistically diverse, heterologous CCM components were investigated by characterizing their ability to restore growth and/or succinate production. While the cyanobacterial bicarbonate transporter SbtA and the C_i transporter DabAB from Halothiobacillus neapolitanus each complemented growth at 0.05% CO₂ and pH 6.5–7.5, neither fully restored succinate production by KJ122 Δcan ΔcynT. Moreover, individual overexpression of sbtA, dabAB, or can in KJ122 rendered no additional improvements to succinate production. Collectively, while these results point to the critical importance of CA for supporting efficient fermentative succinate production by E. coli, they also suggest that this native CCM alone is sufficient for ensuring C_i acquisition at requisite levels under the conditions examined. Full article

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

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22 pages, 904 KB

Open AccessArticle

Isolation and Reassembly of Cultivable Bacteria and Yeasts for Kombucha Tea Fermentation

by Lara Signorello, Marcello Brugnoli, Mattia Pia Arena and Maria Gullo

Fermentation 2026, 12(2), 100; https://doi.org/10.3390/fermentation12020100 - 10 Feb 2026

Abstract

Kombucha tea fermentation is driven by microbial consortia composed of yeasts, acetic acid bacteria (AAB) and lactic acid bacteria (LAB), whose metabolic interactions determine the product’s functional and sensory characteristics. This study focused on the isolation and characterization of cultivable microorganisms from kombucha [...] Read more.

Kombucha tea fermentation is driven by microbial consortia composed of yeasts, acetic acid bacteria (AAB) and lactic acid bacteria (LAB), whose metabolic interactions determine the product’s functional and sensory characteristics. This study focused on the isolation and characterization of cultivable microorganisms from kombucha tea and the reassembly of four defined communities to evaluate their contribution to the chemical composition of the beverage based on the physicochemical parameters and multivariate analysis (PCA) of sugars, organic acids and ethanol. Microbial isolates, identified in this study, belonged to yeast (Saccharomyces cerevisiae and Brettanomyces bruxellensis), AAB (Novacetimonas hansenii, Komagataeibacter europaeus, Komagataeibacter intermedius and Acetobacter pasteurianus) and LAB (Liquorilactobacillus nagelii). Selected strains were combined to reassemble simplified communities. Fermentation trials demonstrated that community composition markedly influenced metabolite production and acidification (acetic acid and ethanol concentration ranged from 0.30 ± 0.08 and 2.29 ± 0.03 g/L, and from not determined to 27.31 ± 3.41 g/L, respectively). Consortia combining yeasts, AAB and LAB most closely reproduced the chemical composition of the original Kombucha tea, whereas simpler yeast–bacteria consortia produced chemically distinct beverages. Overall, these findings enhance our understanding of the ecological roles of kombucha-associated microorganisms and demonstrate that community composition is a key factor in shaping the chemical profile of the beverage. Moreover, the reassembly of defined microbial communities represents a promising strategy for selecting and applying functional microorganisms to valorize agri-food by-products through sustainable fermentation processes. Kombucha-derived communities, due to their ability to grow under acidic conditions, tolerate osmotic stress and metabolize complex sugar mixtures, could be versatile biofactories for the development of new fermented beverages or functional ingredients from low-value agri-food residues, contributing to circular bioeconomy strategies and waste reduction. Full article

(This article belongs to the Special Issue Fermentations of Agri-Food By-Products for the Development of Functional Foods)

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21 pages, 2692 KB

Open AccessArticle

Effect of Operational Parameters on Dark Fermentative Hydrogen Production and Volatile Fatty Acids from Agro-Industrial By-Products

by Angeliki Maragkaki, Andreas Kaliakatsos, Nikolaos Markakis, Emmanouela Maragkaki, Napoleon Christoforos Stratigakis, Iosifina Gounaki, Danae Venieri, Kelly Velonia and Thrassyvoulos Manios

Fermentation 2026, 12(2), 99; https://doi.org/10.3390/fermentation12020099 - 10 Feb 2026

Abstract

The purpose of this study was to examine how hydraulic retention time (HRT) influences biohydrogen generation and the formation of end-products during the co-digestion of olive mill wastewater (OMW), cheese whey (CW), and sewage sludge (SS) mixed in a 40:40:20 (v/ [...] Read more.

The purpose of this study was to examine how hydraulic retention time (HRT) influences biohydrogen generation and the formation of end-products during the co-digestion of olive mill wastewater (OMW), cheese whey (CW), and sewage sludge (SS) mixed in a 40:40:20 (v/v/v) ratio. The relationship between the substrates, resulting metabolites, and microbial communities was also explored. Continuous fermentation trials were carried out under both mesophilic (37 °C) and thermophilic conditions using HRTs of 12, 24 and 48 h. Acetic, propionic, and butyric acids were identified as the main end-products. The highest hydrogen production rate (4.4 ± 0.5 L H₂/L_reactor/day) occurred under thermophilic conditions at an HRT of 24 h, whereas under mesophilic operation at the same HRT the hydrogen production reached 3.0 ± 0.3 L H₂/L_reactor/day. In contrast, the greatest accumulation of volatile fatty acids (VFAs) was observed under mesophilic conditions (10.02 g/L), while thermophilic operation at 24 h HRT resulted in 5.54 g/L of total VFAs. The improved performance under thermophilic fermentation is likely linked to the suppression of hydrogen-consuming bacteria at elevated temperatures, which favors rapid hydrogen producers. Microbial community analysis indicated dominance of Firmicutes and persistent Lactobacillus prevalence across conditions. Shorter HRT at 37 °C promoted community diversification with genera such as Olsenella, Dialister, and Prevotella increasing in relative contribution. Under thermophilic operation, consortia remained Lactobacillus-dominant but showed significant temporal restructuring. The predominance of acetic acid (~2.80 g/L) and butyric acid (~2.60 g/L) indicates that hydrogen generation mainly followed the acetic and butyric pathways. This study reveals how targeted control of HRT and temperature can steer microbial communities toward highly hydrogen-productive consortia in the continuous dark fermentation of mixed agro-industrial wastes. Full article

(This article belongs to the Special Issue Women’s Special Issue Series: Fermentation)

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18 pages, 4137 KB

Open AccessArticle

Qualitative Assessment and Interrelation of Organic Carbon Transport and Bioactivity Characteristics During Natural Composting and Vermicomposting: Various Pig Manure/Straw Pellets Ratios

by Yong Zhou, Mengting Huang, Wenqiang Li, Zuhong Zheng, Wanping Chen, Lang Hu and Huankai Li

Fermentation 2026, 12(2), 98; https://doi.org/10.3390/fermentation12020098 - 9 Feb 2026

Abstract

The transformation pathways of organic carbon (OC) fractions and their interrelationship with microbial activity during natural composting (NC) and vermicomposting (VC) remain poorly understood across pig manure (PM)/straw pellets (SP) ratios. Therefore, the objective of this study was to elucidate the regulatory mechanisms [...] Read more.

The transformation pathways of organic carbon (OC) fractions and their interrelationship with microbial activity during natural composting (NC) and vermicomposting (VC) remain poorly understood across pig manure (PM)/straw pellets (SP) ratios. Therefore, the objective of this study was to elucidate the regulatory mechanisms of substrate mixing ratios on carbon fraction transformation and microbial functional networks during these processes. To achieve this, five PM/SP ratios [100:0 (T1), 75:25 (T2), 50:50 (T3), 25:75 (T4), and 0:100 (T5)] were composted with or without earthworms, revealing the T2 (75:25) ratio had most efficient composting performance within 60 days due to the suitable initial C/N ratio (31.65 ± 0.99). Consequently, the T2 treatment reached the highest organic degradation, including TOC reduction (58.6%), TN accumulation (63.9%), and C/N decline (74.8%) in the VC. Vermicomposting markedly stimulated functional microbial groups—nitrogen-fixing, phosphate-solubilizing, and potassium-solubilizing bacteria—thereby enhancing nutrient (N, P, K) bioavailability. The prominence of the optimal C/N ratio across multiple hydrolytic and oxidative enzymes in the VC-T2 further proved that this ratio provided an optimal nutrient and structural balance for both earthworms and microbial consortia. Strong correlations between bacterial abundance and enzyme activities (r ≥ 0.98), lignin and dissolved OC (r ≈ −0.81), and particulate organic carbon and mineral-associated carbon (r > 0.9) highlighted microbially mediated carbon stabilization through enzymatic mineralization, aggregation, and redistribution of carbon from active pools toward mineral-associated OC. This work identifies the critical PM-SP ratio for waste valorization and mechanistically links earthworm–bacteria interactions to carbon sequestration pathways. Full article

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16 pages, 1239 KB

Open AccessArticle

Enhancing Sustainability and Productivity in Komagataella phaffii Fermentation: A Techno-Economic Comparison of Fed-Batch and Continuous Cultivation with Mixed Induction Strategies

by Almir Yamanie, Salomé de Sá Magalhães, Acep Riza Wijayadikusumah, Neni Nurainy and Eli Keshavarz-Moore

Fermentation 2026, 12(2), 97; https://doi.org/10.3390/fermentation12020097 - 9 Feb 2026

Abstract

The increasing demand for recombinant proteins has driven innovation in bioprocessing strategies using Komagataella phaffii as a host organism. Conventional fed-batch cultivation with pure methanol induction remains widely used but presents challenges including high methanol consumption, extended downtime, and elevated operational costs. This [...] Read more.

The increasing demand for recombinant proteins has driven innovation in bioprocessing strategies using Komagataella phaffii as a host organism. Conventional fed-batch cultivation with pure methanol induction remains widely used but presents challenges including high methanol consumption, extended downtime, and elevated operational costs. This study evaluates alternative strategies combining mixed induction (methanol/sorbitol) with continuous cultivation to enhance productivity, sustainability, and improved economic outcome. Using KEX2 protease as a model industrial recombinant protein, we compared four cultivation modes: fed-batch with methanol (benchmark), fed-batch with mixed induction, continuous with methanol, and continuous with mixed induction. Cell growth, volumetric yield, and specific productivity were evaluated at 5L scale and then modelled to simulate industrial scales (40 L and 400 L). Results demonstrate that continuous cultivation with mixed induction significantly improves yield up to 9-fold compared to conventional fed-batch and reduces methanol usage and oxygen demand. Techno-economic simulations reveal that a 40 L continuous process can match or exceed the output of two 400 L fed-batch runs, while lowering capital and operating costs and minimizing environmental footprint. This integrated strategy offers a scalable, low-cost, and safer method for recombinant protein production, supporting compact and sustainable manufacturing solutions. Full article

(This article belongs to the Special Issue Scale-Up Challenges in Microbial Fermentation)

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15 pages, 1215 KB

Open AccessArticle

Functional Valorization and Bioactivity Enhancement of Spent Coffee Grounds Through Lactic Acid Fermentation

by Mihye Park and Kwang-ok Kim

Fermentation 2026, 12(2), 96; https://doi.org/10.3390/fermentation12020096 - 8 Feb 2026

Abstract

Spent coffee grounds are an abundant agro-industrial by-product with considerable potential as a functional food ingredient. This study investigated the effects of lactic acid fermentation on the antioxidant and anti-inflammatory activities of spent coffee grounds, as evaluated using their extracts, with a focus [...] Read more.

Spent coffee grounds are an abundant agro-industrial by-product with considerable potential as a functional food ingredient. This study investigated the effects of lactic acid fermentation on the antioxidant and anti-inflammatory activities of spent coffee grounds, as evaluated using their extracts, with a focus on fermentation-induced remodeling of phenolic compounds and the functional implications. Fermentation was conducted using Lactobacillus plantarum, and changes in microbial growth, pH, reducing sugar content, phenolic composition, antioxidant capacity, and anti-inflammatory activity were evaluated. During fermentation, viable cell counts increased from 6.73 log colony-forming units (CFU)/mL at 0 h to 9.27 log CFU/mL at 48 h, accompanied by a decrease in pH and an increase in reducing sugar content, indicating active microbial metabolism. Total polyphenol content increased markedly, reaching 97.44 mg gallic acid equivalents (GAE)/100 g in water extracts fermented for 48 h compared with 62.96 mg GAE/100 g in non-fermented controls. High-performance liquid chromatography analysis revealed significant enrichment of phenolic acids, including caffeic, ferulic, and protocatechuic acids. Correspondingly, fermented extracts exhibited enhanced antioxidant activities, as determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP), superoxide dismutase (SOD-like, and catalase assays. In addition, fermented extracts showed improved cellular compatibility and significantly inhibited nitric oxide production (approximately 50–60% at 200–300 μg/mL) and pro-inflammatory cytokine production, with interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) inhibition rates exceeding 60% at 200–300 μg/mL in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. These biological effects were closely linked to fermentation-induced qualitative and quantitative changes in phenolic composition, providing mechanistic insight beyond simple activity enhancement. Overall, lactic acid fermentation enhances the functional properties of spent coffee grounds, highlighting their potential as upcycled, value-added ingredients for functional food and nutraceutical applications. Full article

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

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16 pages, 2191 KB

Open AccessArticle

A Co-Fermentation Strategy from Corncob Hydrolysate to Enhance Simultaneous Co-Production of Lactic Acid and Ethanol

by Xiaona Wang, Yongsheng Li, Yuanchun Zhang, Yuanyuan Ren, Hongzhi Ma, Jianguo Liu and Qunhui Wang

Fermentation 2026, 12(2), 95; https://doi.org/10.3390/fermentation12020095 - 7 Feb 2026

Abstract

Efficient co-utilization of mixed sugars from lignocellulosic hydrolysates is often hindered by carbon catabolite repression and pretreatment-derived inhibitors. In this study, a co-fermentation strategy using Saccharomyces cerevisiae (S. cerevisiae) and Enterococcus mundtii (E. mundtii) was developed to simultaneously produce [...] Read more.

Efficient co-utilization of mixed sugars from lignocellulosic hydrolysates is often hindered by carbon catabolite repression and pretreatment-derived inhibitors. In this study, a co-fermentation strategy using Saccharomyces cerevisiae (S. cerevisiae) and Enterococcus mundtii (E. mundtii) was developed to simultaneously produce ethanol and lactic acid from non-detoxified corncob hydrolysate. Co-fermentation performed at 39 °C significantly improved substrate utilization compared with monoculture systems, achieving pentose and total sugar utilization percentages of 67.1% and 83.7%, respectively. S. cerevisiae preferentially consumed glucose and effectively detoxified furfural and 5-hydroxymethylfurfural (5-HMF), thereby alleviating inhibitory stress and carbon catabolite repression on E. mundtii. By optimizing the inoculation sequence, a 3 h delayed inoculation of E. mundtii significantly enhanced pentose utilization from 68.6% to 80.2% and increased total sugar utilization to 90.4%. This synergistic co-fermentation strategy provides an effective approach for improving mixed-sugar utilization and multi-product bioconversion efficiency in lignocellulosic biorefineries. Full article

(This article belongs to the Topic Separation Techniques and Circular Economy)

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11 pages, 1101 KB

Open AccessArticle

A Kinetics Study on Co-Digestion of Cattle Manure, Macroalgae and Cheese Whey

by Figen Taşcı Durgut

Fermentation 2026, 12(2), 94; https://doi.org/10.3390/fermentation12020094 - 7 Feb 2026

Abstract

In this research, cattle manure, macroalgae, and cheese whey were mixed in various proportions (cattle manure:macroalgae:cheese whey ratios of 50:30:20, 30:20:50 and 20:50:30) and subjected to co-digestion under laboratory conditions at two different digestion temperatures (30 and 45 °C). The modified Gompertz and [...] Read more.

In this research, cattle manure, macroalgae, and cheese whey were mixed in various proportions (cattle manure:macroalgae:cheese whey ratios of 50:30:20, 30:20:50 and 20:50:30) and subjected to co-digestion under laboratory conditions at two different digestion temperatures (30 and 45 °C). The modified Gompertz and first-order kinetic models were used to predict biomethane potentials. The highest experimental biochemical methane potential of 0.373 Nm³CH₄/kgVS was obtained from Mixture-2 at 45 °C, while the lowest, 0.154 Nm³CH₄/kgVS, was achieved with Mixture-1 at 30 °C. Feedstock rates in the mixture and digestion temperature significantly influenced the biochemical methane potential (p < 0.05). Cheese whey was observed to positively contribute to increasing biomethane potential. Increasing the whey ratio in the mixture from 20% to 50% resulted in a 62.5% increase in biomethane production. While R² values for the modified Gompertz model ranged from 0.993 to 0.999, those of the first-order model varied between 0.968 and 0.984. Of the two kinetic models employed for estimating biomethane potentials, the modified Gompertz model yielded values closer to the experimental biomethane potentials. Full article

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

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16 pages, 4522 KB

Open AccessArticle

Optimization of Lentilactobacillus buchneri Mediated Fermentation for Valorizing Tea By-Products into Feed: Process Parameters, Nutritional Quality Enhancement, and Bacterial Community

by Xinyan Wu, Yinying Xu, Caiyun Fan, Shuting Fu, Zirui Luo, Sana Zahra Naqvi, Zhao Zhuo and Jianbo Cheng

Fermentation 2026, 12(2), 93; https://doi.org/10.3390/fermentation12020093 - 7 Feb 2026

Abstract

The massive annual production of tea generates substantial underutilized by-products, leading to resource waste. This study aimed to develop an efficient process for converting these by-products into high-quality feed via fermentation with Lentilactobacillus buchneri (L. buchneri). Using a response surface methodology, [...] Read more.

The massive annual production of tea generates substantial underutilized by-products, leading to resource waste. This study aimed to develop an efficient process for converting these by-products into high-quality feed via fermentation with Lentilactobacillus buchneri (L. buchneri). Using a response surface methodology, the key fermentation parameters (time, temperature, inoculum size, and moisture) were optimized to target pH and crude protein (CP) content. The optimal conditions (4.5 days, 34.5 °C, 5.00 × 10⁶ CFU/g, 54% moisture) yielded a product with a pH of 3.72 and CP content of 17.96%, which was similar to the predictions. Fermentation successfully reduced ether extract (EE), tea tannin (TTN), and propionic acid (PA), while increasing lactic acid (LA) and lowering pH. This process was driven by the dominance of Lactobacillus (99.29% relative abundance), as revealed by microbial analysis. This work provides a viable and optimized strategy for valorizing tea by-products into nutritionally enhanced feed, thereby contributing to sustainable agricultural practices. Full article

(This article belongs to the Section Fermentation Process Design)

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