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Microorganisms
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Industrial Microbiology
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Industrial Microbiology

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: 28 February 2026 | Viewed by 6020

Special Issue Editor

Dr. Liang Dong

E-Mail Website
Guest Editor
School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
Interests: brewing; fermentation; food chemistry; food analysis

Special Issue Information

Dear Colleagues,

Industrial microbiology refers to the microorganisms utilized in industrial production processes, which include bacteria, fungi, yeasts, algae, and more. These microorganisms, under specific growth conditions, are capable of producing products beneficial to humans through their metabolic activities. The variety of industrial microorganisms is extensive, encompassing extremophiles such as thermophiles and halophiles, as well as microorganisms from common environments. They possess a high reproductive rate, capable of generating a large number of offspring in a short period. Additionally, the genetic material of industrial microorganisms is relatively simple, making it easier to modify through genetic engineering. Moreover, they have diverse metabolic pathways that can produce a wide array of compounds. Therefore, industrial microorganisms play a significant role in numerous fields such as food, pharmaceuticals, chemical engineering, and environmental protection.This Special Issue invites the submission of original research articles, reviews, and perspectives that encompass various aspects of industrial microbiology, including but not limited to the following topics:

  1. Fermentation Engineering: Utilizing the metabolic capabilities of microorganisms to produce products such as alcohol, organic acids, antibiotics, and enzyme preparations through fermentation.
  2. Genetic Engineering: Modifying the genetic traits of microorganisms through gene editing techniques to enhance their production efficiency or endow them with new functions.
  3. Biotransformation: Using microorganisms or enzymes to convert one type of compound into another that is more useful.
  4. Biosynthesis: Producing drugs, fine chemicals, and more through microbial biosynthetic pathways.
  5. Bioremediation: Employing microorganisms to degrade pollutants in the environment for environmental remediation.

Dr. Liang Dong
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. Microorganisms 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 2700 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

  • microorganisms
  • fermentation
  • synthesis
  • transformation
  • genetic modification
  • omics
  • environmental protection

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

Published Papers (4 papers)

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Research

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23 pages, 2293 KB  
Article
Bioconversion of a Dairy By-Product (Scotta) into Mannitol-Stabilized Violacein via Janthinobacterium lividum Fermentation
by Mario Trupo, Rosaria Alessandra Magarelli, Salvatore Palazzo, Vincenzo Larocca, Maria Martino, Anna Spagnoletta and Alfredo Ambrico
Microorganisms 2025, 13(9), 2125; https://doi.org/10.3390/microorganisms13092125 - 11 Sep 2025
Viewed by 676
Abstract
Violacein is a natural pigment with a wide range of biological activities, including antimicrobial, antitumor, and immunostimulatory properties. However, its industrial-scale production is hindered by low yields from microbial fermentation. This study investigated the use of scotta, a low-value by-product of the [...] Read more.
Violacein is a natural pigment with a wide range of biological activities, including antimicrobial, antitumor, and immunostimulatory properties. However, its industrial-scale production is hindered by low yields from microbial fermentation. This study investigated the use of scotta, a low-value by-product of the dairy industry, as an alternative and cost-effective substrate for violacein biosynthesis using Janthinobacterium lividum DSM1522. Different types of scotta, including one derived from lactose-free cheese production, were characterized and tested in flask cultures and a 2 L bioreactor. The results demonstrated that both medium dilution and increased oxygen-transfer coefficient (kLa) significantly enhanced violacein production. In the bioreactor, a final yield of 58.72 mg of violacein for each litre of diluted scotta was achieved. The pigment was then stabilized through a spray-drying process using mannitol as a carrier, resulting in a water-soluble powder that retained antibacterial activity against Bacillus subtilis. The drying process also improved pigment solubility in water, suggesting its potential application in formulations to control Gram-positive bacteria. Overall, this study highlights the potential of scotta as a sustainable fermentation substrate and presents a promising encapsulation approach for violacein stabilization. However, further investigations are needed to optimize the spray-drying process, specifically, to characterize the microgranules and to determine their storage stability. Full article
(This article belongs to the Special Issue Industrial Microbiology)
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18 pages, 5832 KB  
Article
Exploring the Skin Benefits of Extremophilic Postbiotics from Exiguobacterium artemiae: A New Frontier in Thermal Protection
by Haeun Lee, Dayeon Roo, Dong-Geol Lee, Seunghyun Kang, Jinwoo Min, Heecheol Kang, Young Mok Heo and Kyung Eun Lee
Microorganisms 2025, 13(7), 1569; https://doi.org/10.3390/microorganisms13071569 - 3 Jul 2025
Viewed by 659
Abstract
Rising global temperatures increase skin exposure to heat stress, which can impair skin structure and function. While several cosmetic ingredients have been developed to mitigate heat-induced damage, most primarily aim to enhance hydration or suppress inflammation, lacking mechanistic insights into their action under [...] Read more.
Rising global temperatures increase skin exposure to heat stress, which can impair skin structure and function. While several cosmetic ingredients have been developed to mitigate heat-induced damage, most primarily aim to enhance hydration or suppress inflammation, lacking mechanistic insights into their action under heat stress. This study assessed E. artemiae-derived SUPER-T and its exosome form, Thermasome, in heat-stressed human skin fibroblasts. Transcriptomic profiling revealed that heat stress upregulated heat-related thermal receptors and downregulated key extracellular matrix (ECM)-related genes. Notably, treatment with SUPER-T upregulated expression of these genes, suggesting a reparative role as a barrier to alleviate heat stress at the dermal–epidermal junction. For its application in a field of cosmetics, SUPER-T encapsulated in exosomes (Thermasome) enhanced the heat resilience, suggesting its better transdermal and heat protective effects. Thermasome further improved skin heat resilience and enhanced ECM gene expression including collagen genes. Our findings provide a mechanistic basis for the development of functional cosmetical materials that target ECM remodeling under heat-stressed conditions. Full article
(This article belongs to the Special Issue Industrial Microbiology)
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Review

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21 pages, 1544 KB  
Review
Key Technologies of Synthetic Biology in Industrial Microbiology
by Xinyue Jiang, Jiayi Ji, Qi Yang, Yao Dou, Yujue Li, Xiaoyu Yang, Chunying Liu, Shaohua Dou and Liang Dong
Microorganisms 2025, 13(10), 2343; https://doi.org/10.3390/microorganisms13102343 - 13 Oct 2025
Viewed by 737
Abstract
Industrial microorganisms have a wide range of applications in biomanufacturing, energy production, environmental protectionpharmaceutical development, etc. Synthetic biology has revolutionised the field of industrial microorganisms by designing, constructing and optimising biological systems. The aim of this study is to discuss the key technologies [...] Read more.
Industrial microorganisms have a wide range of applications in biomanufacturing, energy production, environmental protectionpharmaceutical development, etc. Synthetic biology has revolutionised the field of industrial microorganisms by designing, constructing and optimising biological systems. The aim of this study is to discuss the key technologies of synthetic biology in industrial microorganisms and their application prospects. Gene editing technology, one of the core tools of synthetic biology, enables researchers to precisely modify microbial genomes to optimise their metabolic pathways or introduce new functions. Metabolic engineering, as an important direction for the application of synthetic biology in industrial microorganisms, enables the efficient synthesis of target products by optimising and reconstructing the metabolic pathways of microorganisms. The development of high-throughput screening and automated platforms has enabled large-scale gene editing and metabolic engineering experiments. The application of synthetic genomics promises to develop microbes with highly customised functions. However, there are still many challenges in this field, and future research still requires interdisciplinary collaboration to drive the application of synthetic biology in industrial microorganisms to new heights. Full article
(This article belongs to the Special Issue Industrial Microbiology)
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30 pages, 1658 KB  
Review
Industrial Microbial Technologies for Feed Protein Production from Non-Protein Nitrogen
by Yuxin Ye, Yafan Cai, Fei Wang, Yi He, Yuxuan Yang, Zhengxiang Guo, Mengyu Liu, Huimin Ren, Shilei Wang, Dong Liu, Jingliang Xu and Zhi Wang
Microorganisms 2025, 13(4), 742; https://doi.org/10.3390/microorganisms13040742 - 25 Mar 2025
Cited by 5 | Viewed by 3380
Abstract
Due to the increasing global demand for feed protein, microbial protein has great potential of being able to feed sustainably. However, the application of microbial protein in the animal cultivation industry is still limited by its high cost and availability on scale. From [...] Read more.
Due to the increasing global demand for feed protein, microbial protein has great potential of being able to feed sustainably. However, the application of microbial protein in the animal cultivation industry is still limited by its high cost and availability on scale. From the viewpoint of industrial production, it is vital to specify the crucial processes and components for further technical exploration and process optimization. This article presents state-of-the-art industrial microbial technologies for non-protein nitrogen (NPN) assimilation in feed protein production. Nitrogen sources are one of the main cost factors in the media used for large-scale microbial protein fermentation. Therefore, the available NPN sources for microbial protein synthesis, NPN utilization mechanisms, and fermentation technologies corresponding to the strain and NPN are reviewed in this paper. Especially, the random mutagenesis and adaptive laboratory evolution (ALE) approach combined with (ultra-) throughput screening provided the main impetus for strain evolution to increase the protein yield. Despite the underlying potential and technological advances in the production of microbial protein, extensive research and development efforts are still required before large-scale commercial application of microbial protein in animal feed. Full article
(This article belongs to the Special Issue Industrial Microbiology)
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