Journal of Microbiology

Editor’s Choice articles are curated by our senior editors, who represent each section, to highlight research published in 2025 that they consider particularly interesting to our readers and/or important within the respective research area.

editor_pick

Evolutionary Microbiology and Systematics
Microbial Ecology and Environmental Microbiology
Microbial Physiology and Biochemistry
Microbial Genetics, Genomics
and Molecular Biology (Prokaryote)
Microbial Genetics, Genomics
and Molecular Biology (Eukaryote)
Microbial Pathogenesis
and Host-Microbe Interaction
Synthetic Microbiology and Biotechnology
Virology

Synthetic Microbiology and Biotechnology

Journal of Microbiology is pleased to present the Synthetic Microbiology and Biotechnology Editors’ Choice 2025, highlighting ten outstanding papers published in 2025 that exemplify recent advances in synthetic biology, systems metabolic engineering, and microbial biotechnology. This curated collection showcases innovative approaches for understanding, engineering, and harnessing microorganisms to address challenges in sustainable biomanufacturing, human health, and environmental applications.

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Review

CRISPR-Cas technologies: Emerging tools from research to clinical application: Hana Hyeon, Soonhye Hwang, Yongyang Luo, Eunkyoung Shin, Ji-Hyun Yeom, Hong-Man Kim, Minkyung Ryu, Kangseok Lee; J. Microbiol. 2025;63(8):e2504012. Published online August 31, 2025; DOI: https://doi.org/10.71150/jm.2504012

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Abstract PDF

CRISPR-Cas technologies have emerged as powerful and versatile tools in gene therapy. In addition to the widely used SpCas9 system, alternative platforms including modified amino acid sequences, size-optimized variants, and other Cas enzymes from diverse bacterial species have been developed to apply this technology in various genetic contexts. In addition, base editors and prime editors for precise gene editing, the Cas13 system targeting RNA, and CRISPRa/i systems have enabled diverse and adaptable approaches for genome and RNA editing, as well as for regulating gene expression. Typically, CRISPR-Cas components are transported to the target in the form of DNA, RNA, or ribonucleoprotein complexes using various delivery methods, such as electroporation, adeno-associated viruses, and lipid nanoparticles. To amplify therapeutic efficiency, continued developments in targeted delivery technologies are required, with increased safety and stability of therapeutic biomolecules. CRISPR-based therapeutics hold an inexhaustible potential for the treatment of many diseases, including rare congenital diseases, by making permanent corrections at the genomic DNA level. In this review, we present various CRISPR-based tools, their delivery systems, and clinical progress in the CRISPR-Cas technology, highlighting its innovative prospects for gene therapy.

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CRISPR: a precise genome editing strategy for the treatment of hepatocellular carcinoma
Subhrojyoti Mukherjee, Manish Kumar
Expert Review of Anticancer Therapy.2026; 26(5): 599. CrossRef
Targeted gene editing of PCCA pseudoexon using CRISPR-Cas12a for potential therapy in propionic acidemia
Mar Álvarez, José V. del Álamo, Eva Richard, Lourdes R. Desviat
Molecular Therapy Nucleic Acids.2026; 37(3): 102990. CrossRef
Mechanotransduction in Marfan Syndrome and Related Aortic Disorders: Insights from Transcriptomic Analyses
Anna Cantalupo, Jason R. Cook, Jens Hansen, Samia Lasaad, Lisa M. Satlin, Ravi Iyengar
Genes.2026; 17(7): 770. CrossRef
Precision medicine in asthma: endotype stratification, biomarker-guided biologics, and emerging therapeutic strategies
Swapnil S. Sanap, Krishna R. Gupta, Uma D. Kabra, Milind J. Umekar
Molecular Biology Reports.2026;[Epub] CrossRef

Review

A review on computational models for predicting protein solubility: Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na; J. Microbiol. 2025;63(1):e.2408001. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2408001

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Abstract PDF

Protein solubility is a critical factor in the production of recombinant proteins, which are widely used in various industries, including pharmaceuticals, diagnostics, and biotechnology. Predicting protein solubility remains a challenging task due to the complexity of protein structures and the multitude of factors influencing solubility. Recent advances in computational methods, particularly those based on machine learning, have provided powerful tools for predicting protein solubility, thereby reducing the need for extensive experimental trials. This review provides an overview of current computational approaches to predict protein solubility. We discuss the datasets, features, and algorithms employed in these models. The review aims to bridge the gap between computational predictions and experimental validations, fostering the development of more accurate and reliable solubility prediction models that can significantly enhance recombinant protein production.

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MPRL: Multi-perspective representation learning for accurate and generalizable protein solubility prediction
Xiongyan Yang, Shouyong Jiang, Yong Wang, Jinsong Gong
Expert Systems with Applications.2026; 308: 131142. CrossRef
Artificial Intelligence in Chemical Engineering: Protein Design from First Principles to Structural Prediction
Joseph S. Bailey, Søren C. Spina, Andrew Hu, Nathan Phan, Rachel B. Getman, Blaise R. Kimmel
ACS Engineering Au.2026; 6(2): 249. CrossRef
Pro4S: Prediction of protein solubility by fusing sequence, structure, and surface
Jie Qian, Lin Yang, Renxiao Wang, Yifei Qi
Protein Science.2026;[Epub] CrossRef

Review

Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data: Sungwon Jung; J. Microbiol. 2025;63(1):e.2411006. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2411006

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Abstract PDF

This review explores current advancements in microbiome functional analysis enabled by next-generation sequencing technologies, which have transformed our understanding of microbial communities from mere taxonomic composition to their functional potential. We examine approaches that move beyond species identification to characterize microbial activities, interactions, and their roles in host health and disease. Genome-scale metabolic models allow for in-depth simulations of metabolic networks, enabling researchers to predict microbial metabolism, growth, and interspecies interactions in diverse environments. Additionally, computational methods for predicting metabolite profiles offer indirect insights into microbial metabolic outputs, which is crucial for identifying biomarkers and potential therapeutic targets. Functional pathway analysis tools further reveal microbial contributions to metabolic pathways, highlighting alterations in response to environmental changes and disease states. Together, these methods offer a powerful framework for understanding the complex metabolic interactions within microbial communities and their impact on host physiology. While significant progress has been made, challenges remain in the accuracy of predictive models and the completeness of reference databases, which limit the applicability of these methods in under-characterized ecosystems. The integration of these computational tools with multi-omic data holds promise for personalized approaches in precision medicine, allowing for targeted interventions that modulate the microbiome to improve health outcomes. This review highlights recent advances in microbiome functional analysis, providing a roadmap for future research and translational applications in human health and environmental microbiology.

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Next‐Generation Eco‐Omics: Integrating Microbial Function Into Predictive Ecosystem Models
Kulmani Mehar, Kamakshi Priya K, Amit Prakash Sen, Ravi Kumar Paliwal, Bhavan Kumar M., Aravindan Munusamy Kalidhas, Tapas Kumar Mohapatra, Aseel Samrat, Ravikumar Jayabal
Biotechnology and Applied Biochemistry.2026; 73(3): 1667. CrossRef
The Role of Genitourinary Microbiome in Male Cancer Etiology and Progression: Insights from Next-Generation Sequencing and Meta-Omics
Pooja Tiwary, Krishil Oswal, Ryan Varghese
Société Internationale d’Urologie Journal.2026; 7(1): 9. CrossRef
Bioinformatics in Antifungal Design: Strategies To Overcome Resistance from a Proteomic Perspective
Diego Romário-Silva, Edja Maria Melo de Brito Costa, Joanilda Paolla Raimundo Silva, Letícia Targino Campos, Vitória Marina Abrantes Batista, Camila Vital de Araújo, Sonaly Lima Albino, Arthur Gabriel Corrêa de Farias, Igor José dos Santos Nascimento, Ric
Current Fungal Infection Reports.2026;[Epub] CrossRef
16S-Pipeline: A comprehensive web-based platform for end-to-end 16S rRNA amplicon sequencing analysis
Tatsuya Unno
Journal of Microbiology.2026; 64(5): e2603014. CrossRef
Advances in Enzymatic Production of Prebiotic Oligosaccharides from Agro-Industrial Waste: A Critical Review and Industrial Framework
Slim Smaoui
Foods.2026; 15(12): 2156. CrossRef
Activity-guided discovery of antibiotic-transforming bacteria from environmental microbiomes using D-amino acid–assisted fluorescence-activated cell sorting
Yi Liu, Kai-Li Wang, Yu-Qi Hong, Ye Yuan, Hua Wang, Yi-Qun Chen, Sheng-Song Yu, Zi-Xuan Lu, Yuan Pan, Ting-Ting Zhu
Environmental Pollution.2026; 405: 128591. CrossRef
An inferential ceiling in nanomaterial-assisted phytoremediation studies: Insights from a semi-systematic review of functional evidence in soil microbial communities
Ottavia Pinto, Marco Contin, Luca Marchiol
Applied Soil Ecology.2026; 225: 107199. CrossRef
Microbiome–metabolite signaling networks in gastrointestinal disease: systems biology, network rewiring, and precision therapeutics
Yahya A. Almutawif, Hamza M. A. Eid
Archives of Microbiology.2026;[Epub] CrossRef
Naringenin: From sustainable biosynthesis to gut microbiota-mediated bioactivation and systemic health outcomes
Shutong Liu, Tian Gong, Chenxu Zhao, Chaoqun Zhang, Yanhui Han, Hang Xiao, Yonghong Meng
Trends in Food Science & Technology.2026; 176: 105914. CrossRef
Microbiota, chronic inflammation, and health: The promise of inflammatome and inflammatomics for precision medicine and health care
Huan Zhang, Bing Jun Yang Lee, Tong Wang, Xuesong Xiang, Yafang Tan, Yanping Han, Yujing Bi, Fachao Zhi, Xin Wang, Fang He, Seppo J. Salminen, Baoli Zhu, Ruifu Yang
hLife.2025; 3(7): 307. CrossRef
Study on the Rhizosphere Soil Microbial Diversity of Five Common Orchidaceae Species in the Transitional Zone Between Warm Temperate and Subtropical Regions
Jingjing Du, Shengqian Guo, Xiaohang Li, Zhonghu Geng, Zhiliang Yuan, Xiqiang Song
Diversity.2025; 17(9): 605. CrossRef
Bioengineered Skin Microbiome: The Next Frontier in Personalized Cosmetics
Cherelle Atallah, Ayline El Abiad, Marita El Abiad, Mantoura Nakad, Jean Claude Assaf
Cosmetics.2025; 12(5): 205. CrossRef
Computational Metagenomics: State of the Art
Marco Antonio Pita-Galeana, Martin Ruhle, Lucía López-Vázquez, Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus
International Journal of Molecular Sciences.2025; 26(18): 9206. CrossRef
Rotation of Corydalis yanhusuo with different crops enhances its quality and soil nutrients: a multi-dimensional analysis of rhizosphere microecology
Jia Liu, Qiang Yuan, Kejie Zhang, Xiaoxiao Sheng, Zixuan Zhu, Ning Sui, Hui Wang
BMC Plant Biology.2025;[Epub] CrossRef

Review

Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation: Jun Ren, So Hee Oh, Dokyun Na; J. Microbiol. 2025;63(3):e2501033. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501033

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Abstract PDF

Precise and tunable gene expression is crucial for various biotechnological applications, including protein overexpression, fine-tuned metabolic pathway engineering, and dynamic gene regulation. Untranslated regions (UTRs) of mRNAs have emerged as key regulatory elements that modulate transcription and translation. In this review, we explore recent advances in UTR engineering strategies for bacterial gene expression optimization. We discuss approaches for enhancing protein expression through AU-rich elements, RG4 structures, and synthetic dual UTRs, as well as ProQC systems that improve translation fidelity. Additionally, we examine strategies for fine-tuning gene expression using UTR libraries and synthetic terminators that balance metabolic flux. Finally, we highlight riboswitches and toehold switches, which enable dynamic gene regulation in response to environmental or metabolic cues. The integration of these UTR-based regulatory tools provides a versatile and modular framework for optimizing bacterial gene expression, enhancing metabolic engineering, and advancing synthetic biology applications.

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Rhodo-Box: A Synthetic Biology Toolbox to Facilitate Metabolic Engineering of Rhodobacter sphaeroides
Matic Kostanjšek, Antoine Raynal, George Dimopoulos, Gerrich Behrendt, Vitor A. P. Martins dos Santos, Jules Beekwilder, Christos Batianis, Ruud A. Weusthuis, Enrique Asin-Garcia, Markus M. M. Bisschops
ACS Synthetic Biology.2026; 15(4): 1400. CrossRef
Production of the recombinant spider silk MaSp2 protein using the marine purple photosynthetic nonsulfur bacterium Rhodovulum sulfidophilum under autotrophic conditions
Miki Suzuki, Keiji Numata
NPG Asia Materials.2026;[Epub] CrossRef
Plant-associated microbes as a reservoir for next-generation antimicrobials: Ecology, bioactivity, biotechnological advances, and translational prospects
Akram B. Sultan, Mohamed Abdel-Haleem
Physiological and Molecular Plant Pathology.2026; 145: 103398. CrossRef
Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef
Recombinase-Mediated Cassette Exchange-Based CRISPR Activation Screening Identifies Hyperosmotic Stress-Resistant Genes in Chinese Hamster Ovary Cells
Minhye Baek, Seokchan Kweon, Yujin Kim, Nathan E. Lewis, Jae Seong Lee, Gyun Min Lee
ACS Synthetic Biology.2025; 14(8): 3116. CrossRef

Review

Recent advances in the Design-Build-Test-Learn (DBTL) cycle for systems metabolic engineering of Corynebacterium glutamicum: Subeen Jeon, Yu Jung Sohn, Haeyoung Lee, Ji Young Park, Dojin Kim, Eun Seo Lee, Si Jae Park; J. Microbiol. 2025;63(3):e2501021. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501021

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Abstract PDF

Existing microbial engineering strategies—encompassing metabolic engineering, systems biology, and systems metabolic engineering—have significantly enhanced the potential of microbial cell factories as sustainable alternatives to the petrochemical industry by optimizing metabolic pathways. Recently, systems metabolic engineering, which integrates tools from synthetic biology, enzyme engineering, omics technology, and evolutionary engineering, has been successfully developed. By leveraging modern engineering strategies within the Design-Build-Test-Learn (DBTL) cycle framework, these advancements have revolutionized the biosynthesis of valuable compounds. This review highlights recent progress in the metabolic engineering of Corynebacterium glutamicum, a versatile microbial platform, achieved through various approaches from traditional metabolic engineering to advanced systems metabolic engineering, all within the DBTL cycle. A particular focus is placed C5 platform chemicals derived from L-lysine, one of the key amino acid production pathways of C. glutamicum. The development of DBTL cycle-based metabolic engineering strategies for this process is discussed.

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Designing prokaryotic gene expression regulatory elements: From genomic mining to artificial intelligence-driven generation
Xuan Zhou, Wenyan Cao, Chao Huang, Xiaojuan Zhang, Shenghu Zhou, Yu Deng
Biotechnology Advances.2026; 87: 108781. CrossRef
Green bioconversion of insoluble chitin: chitinase development pathways via multi-strategy synergy
Zhi-Ping Sai, Yi-Rui Yin, Li-Quan Yang, Jia-Hui Wang, Xin-Yi Yang, Fu-Xian Liu, Xin Jing, Yi Zhang, Yu-Da Li, Peng Sang, Zheng-Feng Yang
Bioresources and Bioprocessing.2026;[Epub] CrossRef
Transformer‐Based Prediction of Sec‐ and Tat‐Type Signal Peptides for Enhanced Bacterial Protein Secretion
Seongmo Kang, Seong Min Lee, Ryu Hong Park, Gunhyeong Lee, Je Hyeon Lee, Ki Jun Jeong, Hyun Uk Kim
Biotechnology Journal.2026;[Epub] CrossRef
Engineering of Corynebacterium glutamicum for the enhanced production of optically pure (meso)-2,3-butanediol
Eun Seo Song, Kyeong Ho Kim, Joon Young Lee, Ki Jun Jeong
Bioresources and Bioprocessing.2026;[Epub] CrossRef
Synthetic biology development of microbial strains for liquid biofuel production
Kun Li, Jinsong Xuan, Yingang Feng
Biotechnology Advances.2026; 90: 108891. CrossRef
Fungal factories for feeding the future: mycoproteins as a sustainable protein source at the interface of food, health, and biotechnology innovation
Cristina Firincă, Mariana Constantin, Iuliana Răut, Lucian-Gabriel Zamfir, Maria-Luiza Jecu, Mihaela Doni, Ana-Maria Gurban
Sustainable Food Technology.2026; 4(4): 3493. CrossRef
Systematic metabolic engineering of Corynebacterium glutamicum for enhancing L-isoleucine production
Zhi-Han Gong, Ya-Ru Zhang, Jian-Zhong Xu
Systems Microbiology and Biomanufacturing.2026;[Epub] CrossRef
Genome-scale reconstruction of lignin-derived aromatic catabolism across Pseudomonas enables a modular chassis design for lignin bioconversion
Hafiz Rameez Khalid, Ayesha Muqadass, Huda Ahmad Alghamdi, Muhammad Zohaib Nawaz, Daochen Zhu
Green Chemistry.2026; 28(21): 8694. CrossRef
Systems metabolic engineering: an integrated approach for future environmental biotechnology
Eleftheria Panagiotidou, Eleni Theodosiou
Biotechnology for the Environment.2026;[Epub] CrossRef
Regulatory architecture of high-altitude adaptation in Artemisia: from signal perception to specialized metabolism
Bushra Quyoom, Tariq Bashir Rather, Bilal Ahmad Mir, Latif Ahmad Peer
Plant Cell Reports.2026;[Epub] CrossRef
Pathway engineering for sustainable biomanufacturing: integrating AI, systems biology, enzyme engineering, and dynamic control
Yuki Ogawa, Tomokazu Shirai
Current Opinion in Biotechnology.2026; 100: 103553. CrossRef
Recent advances in bacterial polyhydroxyalkanoates (PHAs) production: strategies for yield enhancement
Shruti S. Raut, Arpit Sharma, Abha Mishra
European Polymer Journal.2026; 256: 115010. CrossRef
SBOL converter: enabling backward compatibility for biological designs
Metehan Ünal, Chris J. Myers, Ihsan Tolga Medeni, Jacob Beal, Prashant Vaidyanathan, Lukas Buecherl, Felipe Buson, Georgie Hau Sørensen, Gonzalo Vidal, Carolus Vitalis, Erik Kubaczka, Roberto Galizi, Göksel Mısırlı
Journal of Integrative Bioinformatics.2026;[Epub] CrossRef
Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef
Time-Series Metabolome and Transcriptome Analyses Reveal the Genetic Basis of Vanillin Biosynthesis in Vanilla
Zeyu Dong, Shaoguan Zhao, Yizhang Xing, Fan Su, Fei Xu, Lei Fang, Zhiyuan Zhang, Qingyun Zhao, Fenglin Gu
Plants.2025; 14(13): 1922. CrossRef
Systems and Synthetic Biology Approaches for Optimizing Microbial Cell Factories
Jongoh Shin, Myung Hyun Noh, Seung-Ho Baek, Jonghyeok Shin, Jung Ho Ahn, Sung Sun Yim, Sungho Jang, Hyun Gyu Lim
KSBB Journal.2025; 40(3): 214. CrossRef
Digital to Biological Translation: How the Algorithmic Data-Driven Design Reshapes Synthetic Biology
Abdul Manan, Nabila Qayyum, Rajath Ramachandran, Naila Qayyum, Sidra Ilyas
SynBio.2025; 3(4): 17. CrossRef

Article

Exploring the biosynthetic potential of Korean Actinobacteria for antibacterial metabolite discovery: Sehong Park, Hyun-Woo Je, Yujin Cha, Boncheol Gu, Yeojeong Cho, Jin-Il Kim, Ji Won Seo, Seung Bum Kim, Jino Son, Moonsuk Hur, Changmin Sung, Min-Kyu Oh, Hahk-Soo Kang; J. Microbiol. 2025;63(9):e2504002. Published online September 30, 2025; DOI: https://doi.org/10.71150/jm.2504002

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Abstract PDF Supplementary Material: Actinobacteria, a phylum of Gram-positive bacteria, are renowned for their remarkable ability to produce antibacterial natural products. The National Institute of Biological Resources (NIBR) of Korea maintains a collection of Korean native actinobacteria. In this study, we explored the phylogenetic and biosynthetic diversity of the NIBR actinobacteria collection to assess its potential as a source of new antibacterial natural products. A 16S rDNA-based phylogenetic analysis revealed a high level of genetic diversity within the collection, with a predominance of Streptomyces, along with rare actinobacterial genera such as Kitasatospora and Micromonospora. Additionally, genetic network analysis of biosynthetic gene clusters (BGCs) from 15 sequenced NIBR actinobacterial strains demonstrated extensive BGC diversity, with many clusters identified as cryptic. Screening of culture extracts for antibacterial activity, followed by dereplication of active extracts, suggested the presence of potentially novel antibacterial natural products. Activity-guided isolation and whole-genome sequencing of the active strain KU57 led to the isolation of one new and three known svetamycin congeners along with their BGC. Overall, our findings highlight the NIBR actinobacteria collection as a valuable source for the discovery of new antibacterial natural products.

Review

Advancements in the production of value-added products via methane biotransformation by methanotrophs: Current status and future perspectives: Ok Kyung Lee, Jong Seok Lee, Yoonyong Yang, Moonsuk Hur, Kyung Jin Lee, Eun Yeol Lee; J. Microbiol. 2025;63(3):e2412024. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2412024

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Abstract PDF

Methane gas is recognized as a promising carbon substrate for the biosynthesis of value-added products due to its abundance and low price. Methanotrophs utilized methane as their sole source of carbon and energy, thus they can serve as efficient biocatalysts for methane bioconversion. Methanotrophs-catalyzed microbial bioconversion offer numerous advantages, compared to chemical processes. Current indirect chemical conversions of methane suffer from their energy-intensive processes and high capital expenditure. Methanotrophs can be cell factories capable of synthesizing various value-added products from methane such as methanol, organic acids, ectoine, polyhydroxyalkanoates, etc. However, the large-scale commercial implementation using methanotrophs remains a formidable challenge, primarily due to limitations in gas-liquid mass transfer and low metabolic capacity. This review explores recent advancements in methanotroph research, providing insights into their potential for enabling methane bioconversion.

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Biodegradable Plastic Production from Waste C1 Carbon Sources: Current Trends and Future Directions
Zeeshan Mustafa, Eun Yeol Lee
ChemCatChem.2026;[Epub] CrossRef
Exploring the potential of nanobubble technology integration with natural polymer κ-carrageenan-immobilized Methylosinus trichosporium OB3b: A review of methane-to-methanol conversion
Muhammad Nauman Zulfiqar, Tingting Hou, Imran Pasha, Pengfei Li, Hui Sun, Liang Liu, Chao He, Gang Li, Youzhou Jiao
Renewable and Sustainable Energy Reviews.2026; 231: 116777. CrossRef
Advances in biotechnological methods for genetic and metabolic engineering in Methylomonas sp. DH-1
Thi Duc Thai, Jun Ren, So Hee Oh, Dokyun Na
Journal of Biological Engineering.2026;[Epub] CrossRef
Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Review

Harnessing organelle engineering to facilitate biofuels and biochemicals production in yeast: Phuong Hoang Nguyen Tran, Taek Soon Lee; J. Microbiol. 2025;63(3):e2501006. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501006

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Abstract PDF

Microbial biosynthesis using yeast species offers numerous advantages to produce industrially relevant biofuels and biochemicals. Conventional metabolic engineering approaches in yeast focus on biosynthetic pathways in the cytoplasm, but these approaches are disturbed by various undesired factors including metabolic crosstalk, competing pathways and insufficient precursors. Given that eukaryotic cells contain subcellular organelles with distinct physicochemical properties, an emerging strategy to overcome cytosolic pathway engineering bottlenecks is through repurposing these organelles as specialized microbial cell factories for enhanced production of valuable chemicals. Here, we review recent progress and significant outcomes of harnessing organelle engineering for biofuels and biochemicals production in both conventional and non-conventional yeasts. We highlight key engineering strategies for the compartmentalization of biosynthetic pathways within specific organelles such as mitochondria, peroxisomes, and endoplasmic reticulum; involved in engineering of signal peptide, cofactor and energy enhancement, organelle biogenesis and dual subcellular engineering. Finally, we discuss the potential and challenges of organelle engineering for future studies and propose an automated pipeline to fully exploit this approach.

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Peroxisome engineering in yeast: Advances, challenges, and prospects
Cuifang Ye, Xiaoqian Li, Tao Liu, Shiyu Li, Mengyu Zhang, Yao Zhao, Jintao Cheng, Guiling Yang, Peiwu Li
Biotechnology Advances.2026; 86: 108747. CrossRef
Building an expanded bio-based economy through synthetic biology
Andrea M. Garza Elizondo, Ilenne del Valle Kessra, Erica Teixeira Prates, Evan Komp, Elise K. Phillips, Nandhini Ashok, Daniel A. Jacobson, Erin G. Webb, Yannick J. Bomble, William G. Alexander, Joanna Tannous, Chung-Jui Tsai, Wayne A. Parrott, Xiaohan Ya
Biotechnology Advances.2026; 87: 108775. CrossRef
Productive chaos and precision engineering: decoupling discovery from manufacturing to revolutionize plant-inspired therapeutics
Dexter Achu Mosoh
Frontiers in Plant Science.2026;[Epub] CrossRef
Microbial platforms for sustainable aviation fuel production: Metabolic pathways, engineering constraints, and biorefinery integration
Isabela Sfalcin, Diego Bonatto
Bioresource Technology.2026; 456: 134893. CrossRef
Metabolic engineering of Yarrowia lipolytica Po1f for efficient production of citric acid
Hao Fang, Jingjing Han, Linru Fan, Jiacheng Liang, Feng Liu, Chen Zhao
Chemical Engineering Science.2026; 336: 124512. CrossRef
Metabolic engineering strategies for astaxanthin biosynthesis in non-native microbial cell factories
Asif Hussain, Habiba Bibi, Shenghu Zhou, Yu Deng
Bioresource Technology.2026; 462: 135436. CrossRef
Mitochondrial engineering strategies in yeast cell factories
Shuo Yang, Cong Gao, Guipeng Hu, Xiaomin Li, Liming Liu
Trends in Biotechnology.2026;[Epub] CrossRef
Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef
Metabolic engineering strategies for constructing methylotrophic cell factories
Pei Zhou, Yang Sun, Yinbiao Xu, Yupeng Liu, Hua Li
Systems Microbiology and Biomanufacturing.2025; 5(4): 1371. CrossRef

Review

Synthetic biology strategies for sustainable bioplastic production by yeasts: Huong-Giang Le, Yongjae Lee, Sun-Mi Lee; J. Microbiol. 2025;63(3):e2501022. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501022

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Abstract PDF

The increasing environmental concerns regarding conventional plastics have led to a growing demand for sustainable alternatives, such as biodegradable plastics. Yeast cell factories, specifically Saccharomyces cerevisiae and Yarrowia lipolytica, have emerged as promising platforms for bioplastic production due to their scalability, robustness, and ease of manipulation. This review highlights synthetic biology approaches aimed at developing yeast cell factories to produce key biodegradable plastics, including polylactic acid (PLA), polyhydroxyalkanoates (PHAs), and poly (butylene adipate-co-terephthalate) (PBAT). We explore recent advancements in engineered yeast strains that utilize various synthetic biology strategies, such as the incorporation of new genetic elements at the gene, pathway, and cellular system levels. The combined efforts of metabolic engineering, protein engineering, and adaptive evolution have enhanced strain efficiency and maximized product yields. Additionally, this review addresses the importance of integrating computational tools and machine learning into the Design-Build-Test-Learn cycle for strain development. This integration aims to facilitate strain development while minimizing effort and maximizing performance. However, challenges remain in improving strain robustness and scaling up industrial production processes. By combining advanced synthetic biology techniques with computational approaches, yeast cell factories hold significant potential for the sustainable and scalable production of bioplastics, thus contributing to a greener bioeconomy.

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Integrating Machine Learning and Transcriptomics to Enhance β-Carotene Production in Saccharomyces cerevisiae
Peerapat Khamwachirapithak, Kittapong Sae-Tang, Suriyaporn Bubphasawan, Jongrak Choompuper, Xin-Qing Zhao, Verawat Champreda, Weerawat Runguphan
ACS Omega.2026;[Epub] CrossRef
Reprogramming of Saccharomyces cerevisiae for sustainable cis, cis-muconic acid production from lignocellulosic biomass
Huong-Giang Le, Ja-Kyong Ko, Sun-Mi Lee
Biotechnology and Bioprocess Engineering.2026; 31(2): 320. CrossRef
Enzymatic and microbial routes to bioplastics: The green chemistry frontier of biopolymers
Giovanni Gallo, Emma Piccoli, Luca Bombardi, Martina Aulitto, Salvatore Fusco
FEBS Open Bio.2026; 16(4): 709. CrossRef
From organic wastes to value: yeast-based bioconversion of waste-derived feedstocks into valuable compounds
Ticiana Fernandes, Maria João Sousa, Ricardo Franco-Duarte
Food Bioscience.2026; 79: 108871. CrossRef
Assessing cancer risk from pesticide exposure in selected rural areas of Greater Noida
Runjhun Mathur, Gaurav Saini, Sheo Prasad Shukla, Abhimanyu Kumar Jha
Environmental Monitoring and Assessment.2026;[Epub] CrossRef
Microbial technologies as an ecological tool for advancing environmental sustainability
Aminat Oyiza Musa, J. M. I. Yarboe, D. A. Undie, O. O. Akinpelu, H. S. Samuel, E. E. Etim
Frontiers in Microbiology.2026;[Epub] CrossRef
Harnessing yeast for polyhydroxyalkanoates (PHAs) production: Challenges, engineering strategies, and future prospects
K. Mohanrasu, Rajendran SelvaKumar, Ian Grainge, C.M. Arun, Akila Ravindran, Logeshwaran Panneerselvan, Thava Palanisami
International Journal of Biological Macromolecules.2026; 379: 153992. CrossRef
Bioplastics for a Circular Economy: Feedstocks, Processing, Lifecycle Sustainability, and Pathways to Industrial Scale
Subin Antony Jose, Elijah Biggs, Austin Bianchi, Brandon Bajada, Carson Beers, Pradeep L. Menezes
Macromol.2026; 6(3): 63. CrossRef
Advancing microbial engineering through synthetic biology
Ki Jun Jeong
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Biorefinery-based production of biodegradable bioplastics: advances and challenges in circular bioeconomy
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Review

Progress and challenges in CRISPR/Cas applications in microalgae: Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee; J. Microbiol. 2025;63(3):e2501028. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501028

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Abstract PDF

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.

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