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Fermentation
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Microbial Production of Industrial Enzymes
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Microbial Production of Industrial Enzymes

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Industrial Fermentation".

Deadline for manuscript submissions: closed (30 October 2025) | Viewed by 9918

Special Issue Editor

Prof. Dr. Yihan Liu

E-Mail Website
Guest Editor
College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
Interests: biocatalysis; enzyme engineering; fermentation engineering; industrial microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes are highly efficient biocatalysts extensively researched for industrial-scale catalysis due to several distinct advantages, including their ability to operate under milder reaction conditions, their exceptional product selectivity, and their lower environmental and physiological toxicities. Today, microbial enzymes are widely used across various industries, including food, pharmaceuticals, feed, detergents, textiles, paper, and leather; however, not all industrial enzymes meet the critical requirements for industrial applications, partly due to their low activity, insufficient stability, and limited yield, which restrict their use in various industries. In recent decades, numerous strategies have been employed to overcome the challenges posed by the limitations of enzymes in the various industry.

The aim of this Special Issue is to publish both innovative research findings and review articles on the microbial production of industrial enzymes. Contributions focusing on the development of novel enzymes are also welcome.

Prof. Dr. Yihan Liu
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

  • mining and evolution of enzymes
  • high-level expression of industrial enzymes
  • fermentation process control of enzymes
  • production of industrial enzymes
  • modification of host strains

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Published Papers (6 papers)

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Research

18 pages, 1563 KB  
Article
Amylase Enzyme Production in Bacteria Associated with Marine Macroalgae: Screening, Optimization and Biofilm Inhibitory Activity
by Sathianeson Satheesh and Lafi Al Solami
Fermentation 2026, 12(2), 112; https://doi.org/10.3390/fermentation12020112 - 13 Feb 2026
Viewed by 1082
Abstract
Bacteria associated with marine macroalgae are considered a promising source for secondary metabolites and industrially significant enzymes. Amylases, which are commercially important enzymes mainly isolated from microorganisms, exhibit antibacterial, anti-inflammatory, anti-viral and antibiofilm activities. In this study, bacteria associated with the green macroalga [...] Read more.
Bacteria associated with marine macroalgae are considered a promising source for secondary metabolites and industrially significant enzymes. Amylases, which are commercially important enzymes mainly isolated from microorganisms, exhibit antibacterial, anti-inflammatory, anti-viral and antibiofilm activities. In this study, bacteria associated with the green macroalga Ulva fasciata were explored for amylase enzyme production, optimization and antibiofilm activity against marine biofilm-forming bacteria. A total of 12 amylase-producing bacterial strains were obtained from the alga. Among the strains, strain MD02 showed higher amylase activity (138.2 U mL−1) and strong biofilm inhibitory activity (89.5% inhibition). Molecular identification of strain MD02 showed similarity with Bacillus sp. The parameters influencing amylase production were initially tested using the traditional approach (one factor) followed by a two-level full factorial design and central composite design combined with response surface methodology. Results of statistical optimization showed a higher amylase yield (307.1 U mg−1) at pH 7.5, 0.75% inoculum and 0.7% glucose. This study advances our knowledge of the significance of Ulva-associated marine bacteria as a source of amylase enzymes and an effective biofilm control agent. Overall, this study highlights the potential significance of marine-algae-associated bacteria for enzyme production and demonstrates the feasibility of cost-effective amylase enzyme production using low-cost substrates. Full article
(This article belongs to the Special Issue Microbial Production of Industrial Enzymes)
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25 pages, 321 KB  
Article
Upcycling of Chinese Nong-Flavor Baijiu Distiller’s Grains Through Solid-State Fermentation by Microbial-Enzyme Synergy
by Lin Qiao, Kai Wang, Xu Xin, Weiwei Wang, Yongwei Wang, Junxun Li, Qingming Cao, Kuanbo Liu and Aike Li
Fermentation 2026, 12(1), 13; https://doi.org/10.3390/fermentation12010013 - 25 Dec 2025
Viewed by 790
Abstract
Chinese Baijiu distiller’s grains are by-products of the Chinese Baijiu brewing process, characterized by high water content, high acidity, and high fiber content, which make them unsuitable for animal feed, especially for monogastric animals. This study investigated the possibility of increasing the feed [...] Read more.
Chinese Baijiu distiller’s grains are by-products of the Chinese Baijiu brewing process, characterized by high water content, high acidity, and high fiber content, which make them unsuitable for animal feed, especially for monogastric animals. This study investigated the possibility of increasing the feed value of Nong-flavor Baijiu distiller’s grains (NFBDGs) for monogastric animals via solid-state fermentation by microbial-enzyme synergy. Experiments evaluated microbial growth, pH variation, improvement of crude protein (CP), true protein (TP), and acid-soluble protein (ASP), degradation of crude fiber (CF), acid detergent fiber (ADF), and neutral detergent fiber (NDF). The results indicated that Ligilactobacillus salivarius CRS23, Bacillus subtilis YLZ7, Saccharomyces cerevisiae CJM26, and xylanase were identified for the fermentation of NFBDGs. When the initial moisture content of NFBDGs was 60% and the initial pH was 3.4, under the conditions of aerobic fermentation at 37 °C for 4 days, the pH of NFBDGs increased from 3.49 to 6.04, the contents of CP and TP increased by 33.59% and 31.21%,,, respectively, while the contents of CF, ADF, and NDF decrease by 35.44%, 20.53%, and 25.02% respectively. The nutritional value of NFBDGs was significantly improved after microbial-enzyme synergistic fermentation, providing a new approach for their application as feed. Full article
(This article belongs to the Special Issue Microbial Production of Industrial Enzymes)
13 pages, 1612 KB  
Article
An Engineered Multi-Enzyme Cascade with Low-Cost ATP Regeneration for Efficient D-Allulose Production from D-Fructose
by Yutong Lu, Huayang Tang, Dexun Fan, Qingzhu Wang and Shuangyan Han
Fermentation 2025, 11(12), 667; https://doi.org/10.3390/fermentation11120667 - 28 Nov 2025
Viewed by 1247
Abstract
D-Allulose is a promising low-calorie rare sugar with significant health benefits. However, its industrial production is hindered by the low catalytic efficiency (≤33% conversion) and unfavorable equilibrium of the key enzyme, D-allulose 3-epimerase (DAE). To overcome this thermodynamic bottleneck, an in vitro synthetic [...] Read more.
D-Allulose is a promising low-calorie rare sugar with significant health benefits. However, its industrial production is hindered by the low catalytic efficiency (≤33% conversion) and unfavorable equilibrium of the key enzyme, D-allulose 3-epimerase (DAE). To overcome this thermodynamic bottleneck, an in vitro synthetic enzymatic cascade based on a phosphorylation–dephosphorylation strategy was constructed. This engineered system comprises four synergistically operating enzymes: D-allulose-3-epimerase (DAE), L-rhamnulose kinase (RhaB), polyphosphate kinase (PPK), and acid phosphatase (AP). Through rational design and systematic optimization, the cascade achieved an exceptional 84.5% conversion yield from 50 mM D-fructose. Importantly, the system also maintained high conversion rates of 64.4% and 61.1% at high D-fructose loadings (50–100 g L−1). This performance, together with the integration of a low-cost PolyP6–PPK ATP regeneration module, underscores the potential industrial applicability of the proposed cascade strategy. Full article
(This article belongs to the Special Issue Microbial Production of Industrial Enzymes)
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17 pages, 5197 KB  
Article
Growth Kinetics and Extracellular Enzyme Secretion of Aureobasidium pullulans m11-2 as an Alternative Source of Polysaccharidases for Winemaking
by María Eugenia Sevillano, Vilma Inés Morata and María Carolina Martín
Fermentation 2025, 11(9), 520; https://doi.org/10.3390/fermentation11090520 - 3 Sep 2025
Viewed by 1566
Abstract
Microbial enzymes, due to their efficiency, specificity, and sustainability, are central to innovative biotechnological strategies aimed at optimizing industrial processes such as winemaking. In this study, the potential of Aureobasidium pullulans m11-2, a native dimorphic fungus from the wine ecosystem, was evaluated as [...] Read more.
Microbial enzymes, due to their efficiency, specificity, and sustainability, are central to innovative biotechnological strategies aimed at optimizing industrial processes such as winemaking. In this study, the potential of Aureobasidium pullulans m11-2, a native dimorphic fungus from the wine ecosystem, was evaluated as a source of hydrolytic enzymes capable of degrading grape cell wall polysaccharides. The strain was identified at the molecular level and characterised in terms of its morphology. To maximise enzyme production, various culture media were tested. Among the concentrations tested, the optimal levels of glucose and pectin were 1 g L−1 and 10 g L−1, respectively. The partially constitutive and inducible nature of the various polysaccharidase activities (pectinases, cellulases, and xylanases) was confirmed. The effect of grape skins (a winemaking by-product) on microbial growth and enzyme synthesis was evaluated, achieving a pectinase activity of 0.622 U mL−1 when combined with 1 g L−1 of glucose. Maximum enzyme yields were detected during the exponential growth phase in both citrus pectin and grape skin media, suggesting favorable conditions for continuous bioprocessing. These results confirm that A. pullulans m11-2 is an interesting microbial option for producing polysaccharidases that can be adapted to sustainable production systems. Full article
(This article belongs to the Special Issue Microbial Production of Industrial Enzymes)
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14 pages, 1558 KB  
Article
Biocatalytic Potential of a Raoultella terrigena-Derived Lipolytic Enzyme for High-Performance Detergents
by Mfezeko Noxhaka, Nonso E. Nnolim, Lindelwa Mpaka and Uchechukwu U. Nwodo
Fermentation 2025, 11(4), 225; https://doi.org/10.3390/fermentation11040225 - 17 Apr 2025
Viewed by 1695
Abstract
Dump sites harbour microorganisms with potential for environmentally friendly industrial applications. This study assessed the lipolytic activity of municipal dumpsite-associated bacteria and evaluated the stability of the most potent isolate’s lipolytic enzyme against laundry detergents. It also examined the crude lipase’s ability to [...] Read more.
Dump sites harbour microorganisms with potential for environmentally friendly industrial applications. This study assessed the lipolytic activity of municipal dumpsite-associated bacteria and evaluated the stability of the most potent isolate’s lipolytic enzyme against laundry detergents. It also examined the crude lipase’s ability to remove stains from cotton fabric. Among twelve bacteria isolated, five demonstrated notable halo zones on tributyrin agar plates. The diameters (mm) were MN38 (11 ± 1.4), MN1310 (8.5 ± 0.7), MN28 (6.5 ± 0.71), MN18 (7.0 ± 1.4), and MN310 (8.15 ± 0.21). Quantitative analysis revealed that MN38 exhibited the highest lipase activity (14.76 ± 0.27 U/mL), while MN1310 showed the lowest (6.40 ± 0.85 U/mL). Nucleotide sequence analysis identified the isolates as Raoultella terrigena veli18 (MN38), Stenotrophomonas maltophilia veli96 (MN1310), Viridibacillus sp. veli10 (MN28), Stenotrophomonas sp. veli19 (MN18), and Klebsiella sp. veli70 (MN310). The crude lipase from R. terrigena veli18 maintained 73.33%, 52.67%, 55.0%, and 54.0% of its original activity after 60 min of exposure to Sunlight, Surf, Maq, and Omo, respectively. Adding crude lipase to enzyme-free laundry detergents significantly enhanced their cleaning efficacy, completely removing oil stains from cotton fabric. This performance of R. terrigena veli18 crude lipase highlights its potential as an effective detergent bio-additive. Full article
(This article belongs to the Special Issue Microbial Production of Industrial Enzymes)
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16 pages, 16734 KB  
Article
Engineering a Protease K for Efficient Degradation of Wool Scale Layer Using a Substrate Pocket Modification
by Lei Zhao, Xiangyang Ma, Yunan Ding, Kaixin Zheng, Kefen Wang, Fuping Lu and Yihan Liu
Fermentation 2025, 11(2), 51; https://doi.org/10.3390/fermentation11020051 - 22 Jan 2025
Cited by 1 | Viewed by 2226
Abstract
The outermost surface of wool is covered by a scale layer, posing challenges to some steps of fabric processing. This layer, primarily composed of keratin, resists degradation by conventional proteases due to its high disulfide bond content. Protease K, an extracellular serine endo-proteinase [...] Read more.
The outermost surface of wool is covered by a scale layer, posing challenges to some steps of fabric processing. This layer, primarily composed of keratin, resists degradation by conventional proteases due to its high disulfide bond content. Protease K, an extracellular serine endo-proteinase derived from Tritirachium album Limber (tPRK), is known for its ability to digest native keratin. However, its limited activity against keratin has restricted its application in wool scale layer treatment. In this study, the substrate-binding pocket of tPRK was engineered, yielding the mutant N162A, which demonstrated an 84% increase in catalytic activity toward keratin. Additionally, the catalytic efficiency (kcat/Km) of N162A on keratin improved by 44.52%. Structural analysis indicated that modifications in the substrate-binding pocket reduced steric hindrance during substrate entry while enhancing substrate binding. Additionally, 3.3 mg/mL of amino acids were released within 6 h, which were catalyzed by N162A, with a 61% increase compared to the native tPRK. Moreover, the N162A variant effectively reduced the scale layer thickness without compromising the tensile strength of the wool, maintaining its mechanical properties. The findings provide a sustainable strategy for the wool industry while broadening the scope of biotechnological applications in the textile sector. Full article
(This article belongs to the Special Issue Microbial Production of Industrial Enzymes)
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