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Microbial Fermentation: Advances in Synthetic Biology, Metabolic Engineering, and Biomanufacturing

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 453

Special Issue Editor

1. Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
2. Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
Interests: synthetic biology; metabolic engineering; cellular agriculture; precision fermentation; industrial microbiology; microbial cell factory; fermentation engineering

Special Issue Information

Dear Colleagues,

Microbial fermentation, as a cornerstone of industrial biotechnology, has long been a driving force in transforming raw biological materials into valuable products. In recent years, the convergence of synthetic biology, metabolic engineering, and advanced biomanufacturing techniques has revolutionized this field, unlocking unprecedented potential for generating new quality productive forces across various industries. Leveraging molecular-level advancements, such as DNA/protein engineering (e.g., CRISPR-based genome editing, enzyme design) or metabolic pathway regulation (e.g., genetic biosensors, cofactor engineering), researchers are now able to produce a wide range of high-value compounds—from foods and pharmaceuticals to sustainable chemicals and novel materials—with enhanced efficiency, sustainability, and scalability.

This Special Issue aims to showcase cutting-edge research at the intersection of synthetic biology, metabolic engineering, and microbial fermentation. We welcome original research articles and critical reviews that explore innovative strategies for chassis engineering (e.g., model/non-model microorganisms, extremophiles), advanced metabolic regulation techniques (e.g., dynamic pathway control, multi-omics integration), and sustainable biomanufacturing approaches (e.g., co-culture systems, waste valorization). Studies focusing on the molecular mechanisms underlying microbial productivity, as well as computational tools and high-throughput platforms for accelerating the design–build–test–learn (DBTL) cycle, are also encouraged.

Dr. Yaokang Wu
Guest Editor

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Keywords

  • microbial fermentation
  • synthetic biology
  • metabolic engineering
  • biomanufacturing
  • industrial biotechnology

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Published Papers (1 paper)

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Research

19 pages, 3786 KB  
Article
Metabolic Characterization of Two Flor Yeasts During Second Fermentation in the Bottle for Sparkling Wine Production
by Juan Carlos García-García, María Trinidad Alcalá-Jiménez, Juan Carlos Mauricio, Cristina Campos-Vázquez, Inés M. Santos-Dueñas, Juan Moreno and Teresa García-Martínez
Int. J. Mol. Sci. 2025, 26(21), 10457; https://doi.org/10.3390/ijms262110457 - 28 Oct 2025
Viewed by 258
Abstract
The global sparkling wine market continues to grow steadily, reaching approximately 24 million hectoliters in 2023, with an annual increase of around 4% despite a general decline in overall alcoholic beverage consumption. This growth highlights the importance of employing diverse yeast strains to [...] Read more.
The global sparkling wine market continues to grow steadily, reaching approximately 24 million hectoliters in 2023, with an annual increase of around 4% despite a general decline in overall alcoholic beverage consumption. This growth highlights the importance of employing diverse yeast strains to improve product variety and quality. Flor yeasts are specialized strains of Saccharomyces cerevisiae that develop a biofilm on the surface of certain wines during biological ageing. They possess unique physiological properties, including high ethanol tolerance and the capacity to adhere, which supports wine clarification. They also have the ability to contribute unique volatile compounds and aroma profiles, making them promising candidates for sparkling wine production. This study evaluated two flor yeast strains (G1 and N62), which were isolated from the Pérez Barquero winery during the second fermentation process using the traditional method. Sparkling wines were produced by inoculating base wine (BW) with each strain, and the wines were monitored at 3 bar CO2 pressure and after 9 months of ageing on lees. Comprehensive metabolomic analysis was performed using GC-MS for volatile compounds and HPLC for nitrogen compounds, with statistical analysis including PCA, ANOVA, Fisher’s LSD, and correction FDR tests. Strain N62 demonstrated faster fermentation kinetics and higher cellular concentration, reaching 3 bar pressure in 27 days compared to 52 days for strain G1. Both strains achieved similar final pressures, 5.1–5.4 bars. Metabolomic profiling revealed significant differences in the profiles of volatile and nitrogen compounds between the two strains. G1 produced higher concentrations of 3-methyl-1-butanol, 2-methyl-1-butanol, and acetaldehyde, while N62 generated elevated levels of glycerol, ethyl esters, and amino acids, including glutamic acid, aspartic acid, and alanine. These findings demonstrate that both flor yeast strains successfully complete sparkling wine fermentation while producing distinct metabolic signatures that could contribute to unique sensory characteristics. This supports their potential as alternatives to conventional sparkling wine yeasts for enhanced product diversification. Full article
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