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Fermentation
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Applied Microorganisms and Industrial/Food Enzymes, 3rd Edition
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Applied Microorganisms and Industrial/Food Enzymes, 3rd Edition

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: 15 May 2026 | Viewed by 2972

Special Issue Editor

Prof. Dr. Xian Zhang

E-Mail Website
Guest Editor
School of Biotechnology, Jiangnan University, Wuxi 214122, China
Interests: cell metabolism; enzymaticization; protein engineering; fermentation process; fermentation control
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms are widely applied in producing value-added compounds, improving food flavor, maintaining soil fertility, and protecting the environment. They have been successfully applied to produce antibiotics, biofuels, vitamins, and food flavors after genetic modification.

With the continuous development of genome editing technology, omics technology, and the expansion of biological information databases, the application scope of microorganisms has been further expanded. These changes have had a far-reaching impact, which has promoted the technological upgrading of traditional industries and also had great potential economic benefits.

In addition, with the boom of structural biology and AI technology, it is more feasible to understand the relationship between protein structure and function. Thus, protein engineering has become more reliable in endowing proteins such as industrial/food enzymes with new properties and functions. Therefore, it provides the possibility to design and reconstruct novel synthetic pathways in engineered microbial cell factories.

The goal of this Special Issue is to publish both recent innovative research results and review papers on applied microorganisms and industrial/food enzymes.

Prof. Dr. Xian Zhang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-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 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • applied microorganisms
  • industrial/food enzymes
  • fermentation optimization
  • metabolic engineering
  • synthetic biology
  • protein engineering
  • transcriptional regulation
  • host cells
  • protein expression
  • high-throughput screening

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Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Published Papers (3 papers)

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Research

15 pages, 1994 KB  
Article
Enzymatic Production of Phosphatidylserine Using a Phospholipase D Immobilized via a Composite Polysaccharide Strategy
by Mengyao Li, Zequn Zhang, Jingyu Chen, Hui Sun, Fuping Lu, Yihao Liu and Yihan Liu
Fermentation 2026, 12(3), 156; https://doi.org/10.3390/fermentation12030156 - 16 Mar 2026
Viewed by 617
Abstract
Phosphatidylserine (PS), a valuable phospholipid, is widely used in food, pharmaceutical and cosmetic industries. Its enzymatic synthesis, catalyzed by phospholipase D (PLD) via transphosphatidylation under mild conditions, has drawn considerable attention. However, the industrial use of free PLD is limited by poor stability, [...] Read more.
Phosphatidylserine (PS), a valuable phospholipid, is widely used in food, pharmaceutical and cosmetic industries. Its enzymatic synthesis, catalyzed by phospholipase D (PLD) via transphosphatidylation under mild conditions, has drawn considerable attention. However, the industrial use of free PLD is limited by poor stability, difficult recovery, and high cost. To address these challenges, a ternary composite carrier—integrating the flexibility of chitosan, the stability of cellulose, and the macroporosity of agarose—was constructed for immobilizing the PLD from Streptomyces antibioticus (saPLD). The resulting saPLD@chitosan–cellulose–agarose biocatalyst demonstrated enhanced immobilization efficiency, catalytic performance, and stability across varying pH and temperatures. After eight consecutive batches of usage, the PS yield of saPLD@chitosan–cellulose–agarose reached over 60% of that from the first batch. Thus, this study established a new method for preparing immobilized saPLD, and developed a robust and promising platform for the efficient and sustainable production of PS. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 3rd Edition)
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19 pages, 2404 KB  
Article
Metabolic Flux Analysis of Escherichia coli Based on Kinetic Model and Genome-Scale Metabolic Network Model
by Zhiren Gan, Jingyan Jiang, Mengxuan Zhou, Qihang Tao, Jinpeng Yang, Renquan Guo, Xueliang Li, Jian Ding and Zhenggang Xie
Fermentation 2026, 12(3), 134; https://doi.org/10.3390/fermentation12030134 - 4 Mar 2026
Viewed by 753
Abstract
The application of Genome-Scale Metabolic Network Models (GSMM) in fermentation optimization is hampered by challenges in differentiating viable from dead cells and parameter distortion induced by conventional detection methods. Using E. coli BL21(DE3) as the model organism, this study developed a flux analysis [...] Read more.
The application of Genome-Scale Metabolic Network Models (GSMM) in fermentation optimization is hampered by challenges in differentiating viable from dead cells and parameter distortion induced by conventional detection methods. Using E. coli BL21(DE3) as the model organism, this study developed a flux analysis strategy that couples cell kinetics with GSMM. Key parameters were estimated using the gradient descent algorithm, thereby enabling precise prediction of viable cell concentration and glucose consumption dynamics. Integrating this with the Quadratic Programming-based parsimonious Flux Balance Analysis (QP-pFBA) algorithm, intracellular metabolic reaction fluxes were quantified. Results demonstrated that the model can effectively differentiate viable from dead cells; Batch D, adopting the gradient-increasing feeding strategy, achieved the maximum specific growth rate (μmax) of 0.6457, the highest among the four batches. Moreover, key metabolic reaction fluxes were highly correlated with the feeding strategy. This framework forgoes specialized, high-cost equipment and offers robust cross-strain/process adaptability, thereby greatly advancing GSMM utility. It provides a powerful tool for precise fermentation control and accelerates the shift toward data-driven biomanufacturing. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 3rd Edition)
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20 pages, 2313 KB  
Article
Evolutionary Engineering and Molecular Characterization of a Sulfur Dioxide-Stress-Resistant Saccharomyces cerevisiae Strain
by Halil İbrahim Kısakesen, Zeynep Başak Canbay, Aziz Kaan Korkmaz, Alican Topaloğlu, Ömer Esen, Mevlüt Arslan, Can Holyavkin and Zeynep Petek Çakar
Fermentation 2025, 11(11), 652; https://doi.org/10.3390/fermentation11110652 - 19 Nov 2025
Cited by 2 | Viewed by 1280
Abstract
Sulfiting agents are common preservatives in the food and beverage industry to inhibit spoilage microorganisms. Sulfite produced by the dissolution of sulfur dioxide (SO2) in water is used as a microbial inhibitor and antioxidant during winemaking. Thus, sulfite resistance is a [...] Read more.
Sulfiting agents are common preservatives in the food and beverage industry to inhibit spoilage microorganisms. Sulfite produced by the dissolution of sulfur dioxide (SO2) in water is used as a microbial inhibitor and antioxidant during winemaking. Thus, sulfite resistance is a desirable trait for wine yeasts. However, consumer health concerns regarding SO2 exposure require a better understanding of the molecular basis of sulfite resistance/response. In this study, we have developed a highly SO2-stress-resistant Saccharomyces cerevisiae strain (F3) using evolutionary engineering by repeated batch selection at gradually increased potassium metabisulfite (K2S2O5) levels. F3 was resistant to 1.1 mM K2S2O5 stress, which was strongly inhibitory to the reference strain, and cross-resistant to oxidative, heat, and freeze–thaw stresses. F3 also had enhanced cell wall integrity and altered carbon metabolism, indicating its potential for industrial applications, including winemaking. Comparative whole genome sequencing revealed point mutations in SSU1 and FZF1 that are related to SO2 transport; ATG14, related to autophagy; and other genes involved in vacuolar protein sorting. Comparative transcriptomic analysis showed significant upregulation of SSU1 and differential expression of genes related to transport and carbohydrate metabolism. These findings may shed light on the molecular mechanisms contributing to SO2 resistance and industrial robustness in S. cerevisiae. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 3rd Edition)
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