Advances in Synthetic Biological Approaches to Microbial Engineering

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: 15 April 2026 | Viewed by 834

Special Issue Editors


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Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkoudai-chou 1-1, Nada, Kobe 657-8501, Japan
Interests: genome biology; synthetic biology; metabolic engineering; microbial platform engineering; bioproduction and bioprocess; prion science and engineering; gene therapy and biologics development; vaccine development
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Guest Editor
Engineering Biology Research Center, Kobe University, Rokkoudai-chou 1-1, Nada, Kobe 657-8501, Japan
Interests: biotechnology

Special Issue Information

Dear Colleagues,

Synthetic biology has emerged as a transformative field in microbial engineering, offering unprecedented opportunities to design and construct biological systems with novel functionalities. This rapidly evolving discipline integrates biology, engineering, and computer science principles to create microorganisms with tailored capabilities for diverse applications. Recent advancements in synthetic biology have significantly expanded our capacity to manipulate and program microbial genomes, leading to breakthroughs in biomanufacturing, environmental remediation, biosensing, and medical therapies.

Developing sophisticated tools and techniques has been instrumental in driving progress in synthetic biology. CRISPR-based genome editing has revolutionized the field by enabling precise and efficient genetic modifications in diverse microbial species. This technology, in conjunction with advances in synthetic gene circuits and metabolic pathway optimization, has enabled researchers to engineer microorganisms with increasingly complex functions. Creating minimal genomes and synthetic chromosomes has further expanded the possibilities for customizing microbial chassis for specific purposes.

Complementary approaches, such as directed evolution and cell-free systems, have accelerated the development and testing of novel biological components and pathways. These advancements have facilitated the rapid prototyping of genetic circuits and the optimization of enzymes for enhanced performance. Furthermore, the design of synthetic microbial consortia and the incorporation of non-natural components through xenobiology extend the boundaries of engineered microorganisms’ capabilities.

As synthetic biology continues to advance, it holds the potential to revolutionize various industries and address global challenges. The ability to engineer microbes for specific tasks presents new opportunities for the sustainable production of chemicals, materials, fuels, and innovative solutions for environmental remediation and healthcare. This introduction establishes the foundation for exploring the latest developments in synthetic biology and their potential impact on science.

This Special Issue on “Advances in Synthetic Biological Approaches to Microbial Engineering” aims to convene eminent researchers to support industrial microbiology research, highlight state-of-the-art advancements, and promote practical implementations. It will comprise accepted submissions addressing genetically modified microorganisms’ creation, development, fundamental characteristics, and applications in diverse biochemical processes and biomanufacturing.

Dr. Prihardi Kahar
Dr. Gregory Guirimand
Guest Editors

Manuscript Submission Information

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Keywords

  • synthetic biology
  • metabolic engineering
  • genetic circuit design
  • genome editing
  • pathway optimization
  • microbial chassis
  • bioproduction
  • adaptive laboratory evolution (ALE)
  • omics integration
  • biofoundries

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Published Papers (1 paper)

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Research

22 pages, 4157 KB  
Article
Physiological and Metabolic Challenges of Flocculating Saccharomyces cerevisiae in D-Lactic Acid Fermentation Under High-Glucose and Inhibitory Conditions
by Dianti Rahmasari, Prihardi Kahar, Filemon Jalu Nusantara Putra and Chiaki Ogino
Processes 2025, 13(11), 3723; https://doi.org/10.3390/pr13113723 - 18 Nov 2025
Viewed by 557
Abstract
Lactic acid is an important biobased chemical widely used in the production of biodegradable plastics, food, and pharmaceuticals. However, the application of flocculant Saccharomyces cerevisiae remains limited in addressing stresses such as high-glucose and inhibitor-rich conditions derived from biomass, particularly in D-lactic acid [...] Read more.
Lactic acid is an important biobased chemical widely used in the production of biodegradable plastics, food, and pharmaceuticals. However, the application of flocculant Saccharomyces cerevisiae remains limited in addressing stresses such as high-glucose and inhibitor-rich conditions derived from biomass, particularly in D-lactic acid (D-LA) production. This study investigates two genetically engineered S. cerevisiae F118 strains, ΔCYB2::LpDLDH and ΔPDC1::LpDLDH, for D-LA production under high-glucose and inhibitor-stress conditions that mimic lignocellulosic hydrolysates in shake-flask fermentation. At 150 g/L glucose, ΔCYB2::LpDLDH produced 41 ± 0.73 g/L D-LA, whereas ΔPDC1::LpDLDH yielded 80 ± 1.78 g/L, corresponding to 27% and 53% of the theoretical yield, respectively. Calcium carbonate (CaCO3) supplementation enhanced glucose consumption and strengthened flocculation in ΔPDC1::LpDLDH. The addition of 5% inhibitory chemical compounds (ICCs) consisting of furfural, HMF, and weak acids redirected carbon flux in ΔCYB2::LpDLDH toward D-LA formation and reduced ethanol byproduct accumulation. Transcriptomic analysis revealed the upregulation of stress-response genes (HOG1, TPS1) and cell-wall remodeling genes (CRH1, SCW10) in response to high-glucose stress. The strongly flocculent F118ΔCYB2::LpDLDH strain exhibited greater tolerance to weak acids and furfural than the weakly flocculent F118ΔPDC1::LpDLDH strain. Metabolomic profiling indicated that under inhibitor stress, carbon flux was diverted from the TCA cycle toward lactate synthesis to maintain redox balance. These findings highlight the multifaceted benefits of flocculation in enhancing strain robustness and D-LA productivity under harsh fermentation environments, providing insights for developing resilient yeast platforms for lignocellulosic bioprocessing. Full article
(This article belongs to the Special Issue Advances in Synthetic Biological Approaches to Microbial Engineering)
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