Resource Utilization of Microorganisms: Fermentation and Biosynthesis

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 532

Special Issue Editor


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Guest Editor
The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214000, China
Interests: bioprocess; fermentation; bioleaching; extremophiles; physiological and metabolic mechanisms; acidophiles
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Special Issue Information

Dear Colleagues,

Microorganisms serve as pivotal biocatalysts in sustainable biomanufacturing, driving innovations in resource efficiency and economic viability. This Special Issue explores cutting-edge advances in microbial resource utilization, fermentation optimization, synthetic biology, and sustainability utilization to enhance biosynthesis pathways for high-value products. This Special Issue focuses on maximizing the resource potential of industrial microorganisms through integrated approaches in fermentation and biosynthesis. Studies on fermentation process engineering, covering nutrient formulation, bioreactor operations, and environmental control will be featured. Additionally, we seek papers exploring advances in strain improvement using synthetic biology tools for producing enzymes, therapeutics, and natural compounds, including metabolic engineering, chassis cell design, heterologous expression systems, and cell-free biosynthesis. Research on circular bioeconomy strategies, such as microbial waste recycling and clean production technologies, is also welcomed. 

This Special Issue is dedicated to all aspects of “Resource Utilization of Microorganisms: Fermentation and Biosynthesis” research, with special emphasis on the following topics:

  1. Fermentation Process Optimization
  • Engineering of nutrient regimes, bioreactor design, environmental parameters, and scale-up strategies for yield enhancement. 
  1. Molecular-Level Strain Improvement
  • Metabolic engineering, synthetic biology, and heterologous expression systems (enzymes/proteins/natural products); chassis cell design; directed evolution; and cell-free biosynthesis. 
  1. Sustainability utilization
  • Microbial recycling of industrial effluents/residues via circular fermentation and clean production technologies. 

Prof. Dr. Shoushuai Feng
Guest Editor

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Keywords

  • industrial microorganisms resources
  • microbial physiological traits
  • fermentation optimization
  • synthetic biology
  • sustainability application

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Published Papers (1 paper)

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Research

28 pages, 9356 KiB  
Article
Integrated Microbiome–Metabolome Analysis and Functional Strain Validation Reveal Key Biochemical Transformations During Pu-erh Tea Pile Fermentation
by Mengkai Hu, Huimin Zhang, Leisa Han, Wenfang Zhang, Xinhui Xing, Yi Wang, Shujian Ou, Yan Liu, Xiangfei Li and Zhenglian Xue
Microorganisms 2025, 13(8), 1857; https://doi.org/10.3390/microorganisms13081857 - 8 Aug 2025
Viewed by 311
Abstract
Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria [...] Read more.
Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria, Aspergillus, Blastobotrys, Thermomyces, and Rasamsonia as dominant genera, with prokaryotic communities showing greater richness and diversity than eukaryotic ones. Beta diversity and clustering analyses revealed stable microbial structures during late fermentation stages. Non-targeted metabolomics detected 347 metabolites, including 56 significantly differential compounds enriched in caffeine metabolism and unsaturated fatty acid biosynthesis. Fermentation phases exhibited distinct metabolic patterns, with volatile aroma compounds (2-acetyl-1-pyrroline, 2,5-dimethylpyrazine) and health-beneficial fatty acids (linoleic acid, arachidonic acid) accumulating in later stages. OPLS-DA and KEGG PATHWAY analyses confirmed significant shifts in metabolite profiles relevant to flavor and biofunctionality. RDA revealed strong correlations between microbial taxa, environmental parameters, and representative metabolites. To functionally verify microbial contributions, 17 bacterial and 10 fungal strains were isolated. Six representative strains, mainly Bacillus and Aspergillus, exhibited high enzymatic activity on macromolecules, confirming their roles in polysaccharide and protein degradation. This integrative multi-omics investigation provides mechanistic insights into Pu-erh tea fermentation and offers a scientific basis for microbial community optimization in tea processing. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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