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Fermentation
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Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition
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Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition

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

Deadline for manuscript submissions: 30 August 2025 | Viewed by 5346

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 microbiol 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 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 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.

Published Papers (6 papers)

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Research

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17 pages, 4633 KiB  
Article
High-Level Extracellular Expression of Collagenase ColH in Bacillus subtilis for Adipose-Derived Cells Extraction
by Ling-Feng Xu, Dai Xue, Nuo Chen, Chang Su, Jin-Song Gong, Jian-Ying Qian, Zhen-Zhen Wang, Xu-Dong Ma, Nan Xie, Zheng-Hong Xu and Jin-Song Shi
Fermentation 2025, 11(5), 242; https://doi.org/10.3390/fermentation11050242 - 24 Apr 2025
Viewed by 165
Abstract
Collagenase has a wide range of applications in the medicine, cosmetic, and food industries. Inefficient expression of collagenase impedes its industrial production and commercial applications. In this study, a secretory expression system for collagenase ColH from Clostridium histolyticum was constructed in Bacillus subtilis [...] Read more.
Collagenase has a wide range of applications in the medicine, cosmetic, and food industries. Inefficient expression of collagenase impedes its industrial production and commercial applications. In this study, a secretory expression system for collagenase ColH from Clostridium histolyticum was constructed in Bacillus subtilis. Signal peptide optimization effectively solved the secretion problem of large collagenase with a molecular weight of about 116 kDa, doubling the extracellular enzyme activity. Then, promoter optimization further improved the enzyme activity to 264 U/mL. By the co-optimization of the nitrogen sources and carbon sources, and employing a fed-batch fermentation strategy, the enzyme activity could reach 669 U/mL, which is, currently, the highest level reported in the industry. The recombinant collagenase ColH was purified through a purification process suitable for industrial production with a specific activity of 565.25 U/mg. Based on the purified collagenase, cells were successfully prepared from adipose tissue, indicating its potential use in cell therapy. This study provides a promising candidate for the industrial production of collagenase and highlights its potential application to extract cells from tissues. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)
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17 pages, 3434 KiB  
Article
Two-Step Bio-Based Production of Heme: In Vivo Cell Cultivation Followed by In Vitro Enzymatic Conversion
by Bahareh Arab, Murray Moo-Young, Yilan Liu and Chih-Hsiung Perry Chou
Fermentation 2025, 11(4), 198; https://doi.org/10.3390/fermentation11040198 - 8 Apr 2025
Viewed by 337
Abstract
Heme is a chemical compound crucial for various biological processes and industrial applications. However, the microbial production of heme is often limited by its intracellular accumulation and associated toxicity. To address this, we employed a two-step approach involving in vivo cell cultivation for [...] Read more.
Heme is a chemical compound crucial for various biological processes and industrial applications. However, the microbial production of heme is often limited by its intracellular accumulation and associated toxicity. To address this, we employed a two-step approach involving in vivo cell cultivation for the production of a heme precursor (coproporphyrin III or coproheme) followed by its in vitro conversion(s) to heme. For the first step, we engineered Escherichia coli strains by implementing the coproporphyrin-dependent (CPD) pathway for bacterial cell cultivation, extracellularly producing up to 251 mg/L coproporphyrin III and 85 mg/L coproheme, respectively. For the second step, we cloned the hemH and hemQ genes for expression in E. coli, and the expressed gene products, i.e., coproheme decarboxylase (ChdC/HemH) and heme synthase (HemQ), were purified. Using the purified enzymes with modulated reaction conditions, we achieved up to a 77.2% yield to convert coproporphyrin III to coproheme and a 45.8% yield to convert coproheme to heme. This in vitro approach not only bypassed the intracellular toxicity constraint associated with in vivo cell cultivation but also enabled precise reaction control, leading to a higher efficiency and yield for heme (and coproheme) production. By applying novel strategies in strain engineering and bioprocessing to overcome inherent bioprocess challenges, this study paves the way for industrial biotechnology for the sustainable, efficient, and even large-scale bio-based production of heme. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)
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15 pages, 4227 KiB  
Article
Biofermentation of Wheat Bran by Monascus anka and Production of High Value-Added Dietary Fiber
by Xuefeng Wu, Siqi He, Hongyi Xu, Hui Zhang, Jing Cai, Min Zhang, Dongdong Mu, Zhenhong Li, Xingjiang Li and Lanhua Liu
Fermentation 2025, 11(3), 157; https://doi.org/10.3390/fermentation11030157 - 20 Mar 2025
Viewed by 354
Abstract
In this study, wheat bran was used to prepare dietary fiber by Monascus anka in liquid fermentation. The structural and functional characteristics of wheat bran dietary fiber were analyzed. Scanning electron microscopy and X-ray diffraction analysis indicated that the insoluble dietary fiber matrix [...] Read more.
In this study, wheat bran was used to prepare dietary fiber by Monascus anka in liquid fermentation. The structural and functional characteristics of wheat bran dietary fiber were analyzed. Scanning electron microscopy and X-ray diffraction analysis indicated that the insoluble dietary fiber matrix was disrupted during the liquid fermentation. Infrared spectroscopy and differential scanning calorimetry analysis demonstrated that intramolecular hydrogen bonds were broken and the oligosaccharides increased. The soluble dietary fiber content increased from 10.7 g/100 g to 16.5 g/100 g, which contributed to improvements in the water-holding capacity, oil-holding capacity, and swelling capacity of wheat bran dietary fiber. UV–Vis spectroscopy analysis demonstrated that the M. anka wheat bran fermentation broth (MWFB) mainly contained yellow pigments (236.6 μ mL−1). HPLC-MS spectrometry further showed MWFB contained three known Monascus pigments: monasine (observed. m/z 359.1853 [M+H]+), ankaflavin (observed. m/z 387.2151 [M+H]+), and monascorubrin (observed. m/z 382.2007 [M+H]+). In conclusion, M. anka can make the most use of wheat bran and improve the structure and function of dietary fiber, thereby expanding its application potential in functional food additives, gut microbiota modulation, and low-calorie baked goods. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)
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14 pages, 3725 KiB  
Article
Metagenomic Insights into the Bacterial Diversity of Balinese Fermented Sausage (Urutan) from the Household Industry
by Ida Bagus Agung Yogeswara, Ni Wayan Nursini, I Gusti Ayu Wita Kusumawati and Purwaningtyas Kusumaningsih
Fermentation 2024, 10(12), 629; https://doi.org/10.3390/fermentation10120629 - 10 Dec 2024
Viewed by 1042
Abstract
Fermented urutan is a dry fermented sausage made from a mixture of pork and Balinese spices, traditionally prepared using conventional methods. However, variations in spices and raw materials may affect the bacterial diversity of urutan. This study aimed to reveal the bacterial [...] Read more.
Fermented urutan is a dry fermented sausage made from a mixture of pork and Balinese spices, traditionally prepared using conventional methods. However, variations in spices and raw materials may affect the bacterial diversity of urutan. This study aimed to reveal the bacterial diversity of urutan from household industries using a metagenomic approach. A bacterial diversity analysis was conducted using Nanopore Sequencing Technology (ONT). Samples were collected from household industries in two regencies: Tabanan and Gianyar. The results show that Bacillota (98%) had the highest abundance in all samples at the phylum level. At the genus level, variations in bacterial composition were observed, with Staphylococcus (8–89%), Weissella (5–32%), and Lactococcus (3–39%) being the most abundant. The richness and diversity of bacterial species were greater in the KH group (Gianyar regency) than in the BRT group (Tabanan regency). A correlation analysis revealed that five genera—Staphylococcus, Lactococcus, Mammalicoccus, Macrococcoides, and Citrobacter—showed a strong correlation with the pH, water activity (aW), and acidity of fermented urutan. These findings provide insights into the bacterial community and could aid in the development of starter cultures to improve the consistency and quality of traditional fermented foods. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)
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17 pages, 8122 KiB  
Article
Enhanced Production of Acid Phosphatase in Bacillus subtilis: From Heterologous Expression to Optimized Fermentation Strategy
by Yang Liu, Wenjing Shuai, Zheng Xu, Xiao Yu, Zhong Yao, Ping Wei, Fang Ni and Yang Sun
Fermentation 2024, 10(12), 594; https://doi.org/10.3390/fermentation10120594 - 21 Nov 2024
Viewed by 1133
Abstract
Acid phosphatases (ACPase, EC 3.1.3.2) are hydrolytic enzymes widely distributed in both plant and animal tissues. Despite their ubiquitous presence, the production and specific activity of ACPase in these sources remain suboptimal. Consequently, the development of microbial cell factories for large-scale ACPase production [...] Read more.
Acid phosphatases (ACPase, EC 3.1.3.2) are hydrolytic enzymes widely distributed in both plant and animal tissues. Despite their ubiquitous presence, the production and specific activity of ACPase in these sources remain suboptimal. Consequently, the development of microbial cell factories for large-scale ACPase production has emerged as a significant research focus. In this study, we successfully expressed the phosphatase PAP2 family protein (acid phosphatase) from Acinetobacter nosocomialis 1905 in Bacillus subtilis 168. The specific activity of the crude enzyme solution was 59.60 U/mg. After purification, the enzyme activity increased to 86.62 U/mL, with a specific activity of 129.60 U/mg. Characterization of the enzyme revealed optimal activity at 45 °C and a pH of 6.0. The Km value was determined to be 0.25 mmol/L using p-nitrophenylphosphoric acid disodium salt as the substrate. Additionally, the enzyme activity was found to be enhanced by the presence of Ni2+. Dissolved oxygen and medium were subsequently optimized during fermentation on the basis of a commercially available 5 L bioreactor. The recombinant strain B. subtilis 168/pMA5-Acp achieved maximal volumetric enzyme activity of 136.9 U/mL after 12 h of fermentation under optimized conditions: an aeration rate of 1.142 VVM (4 lpm), an agitation speed of 350 rpm, and an optimal ratio of lactose to fish powder (7.5 g/L:12.5 g/L). These optimizations resulted in a 5.9-fold increase in volumetric enzyme activity, a 4.9-fold increase in enzyme synthesis per unit cell volume, and a 48.6% increase in biomass concentration. This study establishes a comprehensive technological framework for prokaryotic fermentation-based ACPase production, potentially addressing the bottleneck in industrial-scale applications. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)
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Review

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21 pages, 2335 KiB  
Review
Research and Prospects of Enzymatic Hydrolysis and Microbial Fermentation Technologies in Protein Raw Materials for Aquatic Feed
by Qiang Wang, Zhitao Qi, Weilai Fu, Mingzhu Pan, Xidong Ren, Xian Zhang and Zhiming Rao
Fermentation 2024, 10(12), 648; https://doi.org/10.3390/fermentation10120648 - 16 Dec 2024
Cited by 1 | Viewed by 2203
Abstract
Aquaculture relies heavily on formulated feed, with feed costs accounting for approximately 50% of the total production expenses. High-protein feed is expensive, and some raw materials are dependent on imports. Organic waste, primarily from food scraps and agricultural residues, can be considered feed [...] Read more.
Aquaculture relies heavily on formulated feed, with feed costs accounting for approximately 50% of the total production expenses. High-protein feed is expensive, and some raw materials are dependent on imports. Organic waste, primarily from food scraps and agricultural residues, can be considered feed ingredients to reduce costs. Through fermentation, the nutritional value of these feeds can be enhanced, promoting the growth of aquatic animals, such as fish, and reducing overall costs. Enzymatic hydrolysis and microbial fermentation are commonly used bioprocessing methods, particularly suitable for unconventional feed sources. These methods not only enhance the nutritional value of the feed but also reduce the content of anti-nutritional factors, improving feed digestibility. Enzymatic hydrolysis is often combined with microbial fermentation to produce more efficient novel biofeeds. This synergistic approach enhances microbial fermentation efficiency and the degradation of macromolecules, further improving the nutritional value of the feed, promoting intestinal digestion and absorption, and enhancing animal production performance. Compared to treatments with single strains or enzymes, the synergistic fermentation of feed with microorganisms and enzymes shows more significant effects. This review summarizes the fermentation mechanisms and classifications of enzymatic hydrolysis and microbial fermentation in producing novel biofeeds. It also outlines the advantages of this synergistic process and its progress in aquatic animal production, providing a scientific basis for its broader application in aquaculture. Full article
(This article belongs to the Special Issue Applied Microorganisms and Industrial/Food Enzymes, 2nd Edition)
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