Fermentation: 10th Anniversary

A special issue of Fermentation (ISSN 2311-5637).

Deadline for manuscript submissions: 31 December 2025 | Viewed by 10146

Special Issue Editor


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Guest Editor
Retired, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL, USA
Interests: microbial physiology and metabolism; aerobic and anaerobic fermentation; strain improvement; scale up

Special Issue Information

Dear Colleagues,

With 2025 marking the 10th anniversary of Fermentation (ISSN 2311-5637), we are taking this opportunity to celebrate the Fermentation journal achievements over the last 10 years. This Special Issue aims to cover the latest research and developments on a broad range of topics on all aspects of fermentation, such as microbial metabolism, food fermentation, process improvements and automation, next-generation strain developments, process modeling, control, unconventional feedstocks, downstream processing, efficient product recovery, waste fermentation, and probiotic strains and fermentation. We warmly invite you to contribute original research papers or comprehensive review articles for a peer review and possible publication in this Special Issue.

Fully comprehensive in its scope, this project includes:

  • Fermentation process and product development;
  • Strain improvement;
  • Bioprocess and metabolic engineering;
  • Fermentation food and beverages;
  • Scale-up of fermentation processes;
  • Downstream processing of fermentation products;
  • Microbial physiology and metabolism;
  • Applied genetics and molecular biotechnology;
  • Genomics, proteomics, metabolomics and systems biology;
  • Bioinformatics;
  • Bioreactor design, monitoring, biosensors and instrumentation;
  • Biosafety and biosecurity;
  • Biopharmaceuticals and biotech drugs;
  • Probiotics.

Dr. Badal C. Saha
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial metabolism
  • fermentation process
  • strain improvement
  • bioprocesses
  • bioreactor design
  • scale-up
  • beverages
  • fermented food
  • bioconversion
  • biofuels
  • commodity chemicals
  • pharmaceuticals
  • bioproducts
  • probiotics
  • gut microbiota

Published Papers (9 papers)

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Research

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14 pages, 1763 KiB  
Article
Characterisation of Low Molecular Weight Compounds of Strawberry Tree (Arbutus unedo L.) Fruit Spirit Aged with Oak Wood
by Ofélia Anjos, Carlos A. L. Antunes, Sheila Oliveira-Alves, Sara Canas and Ilda Caldeira
Fermentation 2024, 10(5), 253; https://doi.org/10.3390/fermentation10050253 - 13 May 2024
Viewed by 377
Abstract
There is a trend towards the commercialisation of strawberry tree fruit spirit (AUS) with wood ageing, motivated by its favourable sensory characteristics. Additionally, further studies are necessary to elucidate the optimal conditions regarding ageing time and toasting level. This study evaluated the changes [...] Read more.
There is a trend towards the commercialisation of strawberry tree fruit spirit (AUS) with wood ageing, motivated by its favourable sensory characteristics. Additionally, further studies are necessary to elucidate the optimal conditions regarding ageing time and toasting level. This study evaluated the changes in colour and low molecular weight compounds (LMWC) of AUS aged for three and six months using oak wood (Quercus robur L.) with light, medium and medium plus toasting levels. For this purpose, phenolic acids (gallic, ellagic, ferulic and syringic acids), phenolic aldehydes (vanillin, syringaldehyde, coniferaldehyde and sinapaldehyde) and furanic aldehydes (furfural, 5-hydroxymethylfurfural and 5-methylfurfural) were quantified using the HPLC method. Chromatic characteristics, colour sensory analysis and total polyphenol index were also analysed. Fourier transform near-infrared spectroscopy (FT-NIR) was used to discriminate between samples. The results emphasized the favourable effect of oak wood contact on enhancing the colour and enriching AUS with low molecular weight compounds (LMWC). AUS aged in medium toasted wood exhibits high levels of total phenolic index, 5-hydroxymethylfurfural, furfural, coniferaldehyde, sinapaldehyde, sum LMWC and chromatic characteristics b* and C. Concentrations of syringaldehyde, ellagic acid, vanillin and syringic acid and a lighter colour (a* chromaticity coordinates) are higher in AUS aged with slightly more toasted wood. Nearly all analysed parameters showed an increase with ageing time. The FT-NIR technique allowed for the differentiation of aged AUS, focusing more on ageing time than on toasting level. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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14 pages, 5937 KiB  
Article
Enhancing Xylanase Production from Aspergillus tamarii Kita and Its Application in the Bioconversion of Agro-Industrial Residues into Fermentable Sugars Using Factorial Design
by Jose Carlos Santos Salgado, Paulo Ricardo Heinen, Josana Maria Messias, Lummy Maria Oliveira-Monteiro, Mariana Cereia, Carem Gledes Vargas Rechia, Alexandre Maller, Marina Kimiko Kadowaki, Richard John Ward and Maria de Lourdes Teixeira de Moraes Polizeli
Fermentation 2024, 10(5), 241; https://doi.org/10.3390/fermentation10050241 - 30 Apr 2024
Viewed by 617
Abstract
The endo-1,4-β-xylanases (EC 3.2.1.8) are the largest group of hydrolytic enzymes that degrade xylan, the major component of hemicelluloses, by catalyzing the hydrolysis of glycosidic bonds β-1,4 in this polymer, releasing xylooligosaccharides of different sizes. Xylanases have considerable potential in producing bread, animal [...] Read more.
The endo-1,4-β-xylanases (EC 3.2.1.8) are the largest group of hydrolytic enzymes that degrade xylan, the major component of hemicelluloses, by catalyzing the hydrolysis of glycosidic bonds β-1,4 in this polymer, releasing xylooligosaccharides of different sizes. Xylanases have considerable potential in producing bread, animal feed, food, beverages, xylitol, and bioethanol. The fungus Aspergillus tamarii Kita produced xylanases in Adams’ media supplemented with barley bagasse (brewer’s spent grains), a by-product from brewery industries. The culture extract exhibited two xylanase activities in the zymogram, identified by mass spectrometry as glycosyl hydrolase (GH) families 10 and 11 (GH 10 and GH 11). The central composite design (CCD) showed excellent predictive capacity for xylanase production (23.083 U mL−1). Additionally, other enzyme activities took place during the submerged fermentation. Moreover, enzymatic saccharification based on a mixture design (MD) of three different lignocellulosic residues was helpful in the production of fermentable sugars by the A. tamarii Kita crude extract. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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13 pages, 310 KiB  
Article
Effect of Chemical and Microbial Additives on Fermentation Profile, Chemical Composition, and Microbial Populations of Whole-Plant Soybean Silage
by Jefferson Rodrigues Gandra, Caio Seiti Takiya, Tiago Antonio Del Valle, Cibeli de Almeida Pedrini, Erika Rosendo de Sena Gandra, Giovani Antônio, Euclides Reuter de Oliveira, Igor Kieling Severo and Francisco Palma Rennó
Fermentation 2024, 10(4), 204; https://doi.org/10.3390/fermentation10040204 - 10 Apr 2024
Viewed by 777
Abstract
This study evaluated the effects of two chemical additives or a microbial inoculant on chemical composition and DM losses in whole-plant soybean silage. One-hundred and twenty mini-silos were used in a completely randomized design experiment with the following treatments: water without chloride (control, [...] Read more.
This study evaluated the effects of two chemical additives or a microbial inoculant on chemical composition and DM losses in whole-plant soybean silage. One-hundred and twenty mini-silos were used in a completely randomized design experiment with the following treatments: water without chloride (control, CON); a microbial inoculant (INO); a chemical additive containing 35–45% formic acid (FA type); and another chemical additive containing 50–60% propionic acid (PA type). Data were analyzed using mixed models of SAS, and treatment differences were evaluated by the following orthogonal contrasts: C1 = CON vs. additives (INO + FA type + PA type); C2 = INO vs. chemical additives (FA type + PA type); and C3 = PA type vs. FA type. Silage pH and ammonia nitrogen concentration were decreased, and concentrations of lactic acid and acetic acid were increased with additives. Counts of lactic acid bacteria were higher in silages with INO than with chemical additives. DM recovery increased with FA type and PA type. Additives increased DM and CP concentrations. Silage A-fraction proportion was greater with additives. Additives, particularly FA type and PA type, improved chemical composition and fermentative profile and reduced undigestible proportions of protein in whole-plant soybean silage. Chemical additives were more effective in reducing silage DM losses than INO. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
13 pages, 3162 KiB  
Article
Investigation of Crypthecodinium cohnii High-Cell-Density Fed-Batch Cultivations
by Konstantins Dubencovs, Arturs Suleiko, Anastasija Suleiko, Elina Didrihsone, Mara Grube, Karlis Shvirksts and Juris Vanags
Fermentation 2024, 10(4), 203; https://doi.org/10.3390/fermentation10040203 - 10 Apr 2024
Viewed by 832
Abstract
Crypthecodinium cohnii is a marine microalga that can accumulate high amounts of polyunsaturated fatty acids (PUFAs) and thus replace conventional routes of fish oil production. They are associated with the destruction of marine resources and multiple downstream/purification complications. The major drawbacks of using [...] Read more.
Crypthecodinium cohnii is a marine microalga that can accumulate high amounts of polyunsaturated fatty acids (PUFAs) and thus replace conventional routes of fish oil production. They are associated with the destruction of marine resources and multiple downstream/purification complications. The major drawbacks of using C. cohnii for industrial-scale production are associated with low PUFA productivity. One of the means of increasing the PUFA synthesis rate is to maintain the medium component concentrations at optimal values throughout cultivation, thus increasing PUFA production efficiency, which can result in the successful transfer of the process to pilot and/or industrial scale. The goal of the present research was to develop techniques for increasing the efficiency of PUFA production via C. cohnii cultivation. Multiple experiments were carried out to test and fine-tune the cultivation medium composition and oxygen transfer factors. The biomass yields from individual components, yeast extract, sea salts, and glucose amounted to 5.5, 0.65, and 0.61 g·g−1, respectively. C. cohnii cell susceptibility to mechanical damage was experimentally evaluated. Power inputs of <276.5 W/m3 did not seem to promote cell destruction when Pitched-blade impellers were used. The obtained cultivation conditions were shown to be efficient in terms of increasing the biomass productivity and the omega-3 fatty acid content in C. cohnii. By using the applied methods, the maximal biomass productivity reached 8.0 g·L−1·day−1, while the highest obtained biomass concentration reached 110 g·L−1. A steady increase in the concentration of PUFAs during cultivation was observed from the FTIR data. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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16 pages, 1748 KiB  
Article
Valorization of Sugarcane Vinasse and Crude Glycerol for Single-Cell Oils Production by Rhodotorula glutinis R4: A Preliminary Approach to the Integration of Biofuels Industries for Sustainable Biodiesel Feedstock
by D. Daniela Maza, Julio Maximiliano Barros, José Manuel Guillamón, Manuel J. Aybar and Silvana C. Viñarta
Fermentation 2024, 10(4), 178; https://doi.org/10.3390/fermentation10040178 - 23 Mar 2024
Viewed by 1050
Abstract
Single-cell oils (SCOs) offer a promising alternative to conventional biodiesel feedstocks. The main objective of this work was to obtain SCOs suitable for biodiesel production from the oleaginous yeast Rhodotorula glutinis R4 using sugarcane vinasse from a local sugar-derived alcohol industry as the [...] Read more.
Single-cell oils (SCOs) offer a promising alternative to conventional biodiesel feedstocks. The main objective of this work was to obtain SCOs suitable for biodiesel production from the oleaginous yeast Rhodotorula glutinis R4 using sugarcane vinasse from a local sugar-derived alcohol industry as the substrate. Additionally, crude glycerol from the local biodiesel industry was evaluated as a low-cost carbon source to replace expensive glucose and as a strategy for integrating the bioethanol and biodiesel industries for the valorization of both agro-industrial wastes. R4 achieved a high lipid accumulation of 88% and 60% (w/w) in vinasse-based culture media, containing 10% and 25% vinasse with glucose (40 g L−1), respectively. When glucose was replaced with crude glycerol, R4 showed remarkable lipid accumulation (40%) and growth (12.58 g L−1). The fatty acids profile of SCOs showed a prevalence of oleic acid (C18:1), making them suitable for biodiesel synthesis. Biodiesel derived from R4 oils exhibits favorable characteristics, including a high cetane number (CN = 55) and high oxidative stability (OS = 13 h), meeting international biodiesel standards (ASTMD6751 and EN14214) and ensuring its compatibility with diesel engines. R. glutinis R4 produces SCOs from vinasse and crude glycerol, contributing to the circular economy for sustainable biodiesel production. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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11 pages, 1545 KiB  
Article
The Biosynthesis of the Monoterpene Tricyclene in E. coli through the Appropriate Truncation of Plant Transit Peptides
by Meijia Zhao, Shaoheng Bao, Jiajia Liu, Fuli Wang, Ge Yao, Penggang Han, Xiukun Wan, Chang Chen, Hui Jiang, Xinghua Zhang and Wenchao Zhu
Fermentation 2024, 10(3), 173; https://doi.org/10.3390/fermentation10030173 - 20 Mar 2024
Viewed by 1115
Abstract
Tricyclene, a tricyclic monoterpene naturally occurring in plant essential oils, holds potential for the development of medicinal and fuel applications. In this study, we successfully synthesized tricyclene in E. coli by introducing the heterologous mevalonate (MVA) pathway along with Abies grandis geranyl diphosphate [...] Read more.
Tricyclene, a tricyclic monoterpene naturally occurring in plant essential oils, holds potential for the development of medicinal and fuel applications. In this study, we successfully synthesized tricyclene in E. coli by introducing the heterologous mevalonate (MVA) pathway along with Abies grandis geranyl diphosphate synthase (GPPS) and Nicotiana sylvestris tricyclene synthase (TS) XP_009791411. Initially, the shake-flask fermentation at 30 C yielded a tricyclene titer of 0.060 mg/L. By increasing the copy number of the TS-coding gene, we achieved a titer of 0.103 mg/L. To further enhance tricyclene production, optimal truncation in the N-terminal region of TS XP_009791411 resulted in an impressive highest titer of 47.671 mg/L, approximately a 794.5-fold improvement compared to its wild-type counterpart. To the best of our knowledge, this is the highest titer of the heterologous synthesis of tricyclene in E. coli. The SDS-PAGE analysis revealed that lowering induction temperature and truncating the random coil N-terminal region effectively improved TS solubility, which was closely associated with tricyclene production levels. Furthermore, by truncating other TSs, the titers of tricyclene were improved to different degrees. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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19 pages, 2530 KiB  
Article
Effects of Fermented Goat Milk on Adiposity and Gut Microbiota in a Diet-Induced Obesity Murine Model
by Antonela Marquez, Matías Russo, Carlos Tomei, Patricia Castellano, Edoardo Puglisi, Roxana Medina and Paola Gauffin-Cano
Fermentation 2024, 10(3), 155; https://doi.org/10.3390/fermentation10030155 - 7 Mar 2024
Viewed by 1227
Abstract
The administration of goat milk fermented (FGM) with Lactobacillus delbrueckii subsp. indicus CRL1447 and supplemented with different mixes of lactobacilli strains (Mix1: Limosilactobacillus fermentum CRL1446 + Lactiplantibacillus paraplantarum CRL1449 + Lactiplantibacillus paraplantarum CRL1472; Mix2: CRL1446 + CRL1449; Mix3: CRL1446 + CRL1472; and Mix4: [...] Read more.
The administration of goat milk fermented (FGM) with Lactobacillus delbrueckii subsp. indicus CRL1447 and supplemented with different mixes of lactobacilli strains (Mix1: Limosilactobacillus fermentum CRL1446 + Lactiplantibacillus paraplantarum CRL1449 + Lactiplantibacillus paraplantarum CRL1472; Mix2: CRL1446 + CRL1449; Mix3: CRL1446 + CRL1472; and Mix4: CRL1449 + CRL1472) was investigated regarding body weight, metabolic and inflammatory parameters, and gut microbiota (GM) composition in mice fed a high-fat diet (HFD). Body weight gain, adipocyte size, fasting blood glucose, serum triglyceride, and leptin levels were significantly reduced in the group fed FGM+Mix3 compared with the obese mice fed FGM. FGM+Mix2 and FGM+Mix3 modified the GM composition, reversing the dysbiosis caused by the HFD. Although there were no significant changes at the phylum level, the GM composition was significantly changed at the family and genus levels. Results suggest that the administration of FGM+Mix3 improves metabolic and immune profiles in obese mice while positively modulating the GM, therefore attenuating the risk factors associated with obesity. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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15 pages, 4130 KiB  
Article
Enhanced Anti-Inflammatory and Non-Alcoholic Fatty Liver Disease (NAFLD) Improvement Effects of Bacillus subtilis-Fermented Fagopyrum tataricum Gaertner
by Chan-Hwi Park, Hyun Kang and Sung-Gyu Lee
Fermentation 2024, 10(3), 116; https://doi.org/10.3390/fermentation10030116 - 20 Feb 2024
Viewed by 1305
Abstract
In this study, we investigated the enhanced anti-inflammatory activity and the effects on non-alcoholic fatty liver disease (NAFLD) of fermented Fagopyrum tataricum (F. tataricum) Gaertner extract (FFT) through in vitro analysis. We utilized high-performance liquid chromatography (HPLC) to analyze the non-fermented [...] Read more.
In this study, we investigated the enhanced anti-inflammatory activity and the effects on non-alcoholic fatty liver disease (NAFLD) of fermented Fagopyrum tataricum (F. tataricum) Gaertner extract (FFT) through in vitro analysis. We utilized high-performance liquid chromatography (HPLC) to analyze the non-fermented F. tataricum Gaertner extract (NFT) and the marker components, rutin and quercetin in FFT, to confirm changes in composition due to fermentation. The anti-inflammatory activity of NFT and FFT was evaluated using a lipopolysaccharide (LPS)-induced RAW 264.7 cell inflammation model. Simultaneously, the NAFLD improvement effects were measured by evaluating lipid accumulation and the expression of lipid synthesis regulators in free fatty acid (FFA)-induced HepG2 cells. HPLC analysis confirmed an increase in rutin content after the fermentation of F. tataricum Gaertner. Upon treatment with NFT and FFT at a concentration of 400 μg/mL, LPS-induced nitric oxide (NO) production values in RAW 264.7 cells were reduced to 16.12 μM and 2.09 μM, respectively, indicating enhanced significant inhibition (p < 0.05) of NO production through fermentation. FFT demonstrated the significant inhibition (p < 0.05) of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2) protein, and inflammatory cytokine mRNA expression through the nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) pathways in LPS-induced RAW 264.7 cells. In FFA-induced HepG2 cells, FFT significant suppressed (p < 0.05) lipid accumulation and the expression of sterol regulatory element binding protein (SREBP)-1c, CCAAT/enhancer binding protein (C/EBP)α proteins, and acetyl-CoA carboxylase (ACC) mRNA. The results of this study suggest the potential utilization of FFT as a material for improving NAFLD. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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Review

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18 pages, 1878 KiB  
Review
Lactic Acid Fermentation in the Food Industry and Bio-Preservation of Food
by Yulma Lizbeth Aguirre-Garcia, Sendar Daniel Nery-Flores, Lizeth Guadalupe Campos-Muzquiz, Adriana Carolina Flores-Gallegos, Lissethe Palomo-Ligas, Juan Alberto Ascacio-Valdés, Leonardo Sepúlveda-Torres and Raúl Rodríguez-Herrera
Fermentation 2024, 10(3), 168; https://doi.org/10.3390/fermentation10030168 - 15 Mar 2024
Cited by 1 | Viewed by 1769
Abstract
Studies on fermentation by acid lactic bacteria (LAB) have confirmed the presence of strains with attributes of considerable relevance for food processing. These strains, in addition to their ability to modify the texture and flavor of foods, possess beneficial properties for human health. [...] Read more.
Studies on fermentation by acid lactic bacteria (LAB) have confirmed the presence of strains with attributes of considerable relevance for food processing. These strains, in addition to their ability to modify the texture and flavor of foods, possess beneficial properties for human health. They enhance food quality by making it more nutrient-rich and contribute to food preservation. The production of lactic acid, vitamins, exopolysaccharides, and bacteriocins, among other compounds, confers these properties to LAB. In the realm of preservation, bacteriocins play a crucial role. This is because bacteriocins act by inhibiting the growth and reproduction of unwanted microorganisms by interacting with the cell membrane, causing its rupture. This preservative effect has led LAB to have widespread use during food processing. This preservative effect has led to widespread use of LAB during food processing. This review highlights the importance of fermentation carried out by LAB in the food industry and in the bio-preservation of foods. These findings emphasize the relevance of continuing investigations and harness the properties of LAB in food production. Full article
(This article belongs to the Special Issue Fermentation: 10th Anniversary)
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