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    31 October 2025, Volume 6 Issue 5
    Contents in Chinese and English
    2025, 6(5):  0. 
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    Editorial
    Innovating with synthetic biology to empower the future of agriculture
    WU Zhiqiang, DAI Junbiao, LIN Min, HUANG Sanwen
    2025, 6(5):  987-991.  doi:10.12211/2096-8280.2025-097
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    Comment
    Plant synthetic biology and bioproduction of human milk oligosaccharides
    YU Wenwen, LV Xueqin, LI Zhaofeng, LIU Long
    2025, 6(5):  992-997.  doi:10.12211/2096-8280.2024-089
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    Human milk oligosaccharides (HMOs) are the third largest solid component in breast milk. They have a wide range of applications due to their beneficial physiological functions such as regulating the immune system, maintaining digestive health, and promoting brain development. There is a growing interest in the development of green and efficient bioproduction of HMOs via synthetic biology technologies. Recently, Patrick M. Shih’s team from the University of California, Berkeley, has engineered the model plant Nicotiana benthamiana as a photosynthetic platform for HMOs production. Specifically, the enzymes involved in HMOs biosynthesis were heterologously expressed in the cytosol to reconstruct the metabolic pathways required for HMOs bioproduction. Furthermore, they optimized the productions of HMOs by enhancing the supply of key precursors. Finally, several HMOs were successfully produced from the cost-effective raw materials CO2. The reported study provides deeper insights into the green bioproduction of HMOs, and expands the potential applications of plant synthetic biology technologies in the green and sustainable bioproduction of other dairy-based functional nutraceuticals. From the perspective of regulatory approval and industrial application, the aforementioned technology remains at the proof-of-concept stage. In contrast, an integrated approach combining CO2 capture and conversion with microbial fermentation shows greater potential for demonstrating scalable green biomanufacturing of HMOs in the near term.

    Invited Review
    Progress and challenges of synthetic biology in agriculture
    LIU Jie, GAO Yu, MA Yongshuo, SHANG Yi
    2025, 6(5):  998-1024.  doi:10.12211/2096-8280.2025-065
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    Synthetic biology is a multidisciplinary field that has revolutionized agriculture by designing and constructing novel life systems. Due to limited arable land resources, it is inevitable that soil will become polluted with heavy metals, and that pesticide and fertilizer residues will accumulate, resulting in low crop photosynthetic efficiency. Traditional agricultural production cannot meet the challenges posed by modern food demands and climate change. Compared to traditional agricultural technologies, synthetic biology presents a promising approach by incorporating advanced technologies into agricultural systems, allowing more efficient and widespread solutions to global agrarian challenges. It represents a strategic high ground for addressing population growth, climate change, and promoting sustainable bioeconomic development. Synthetic biology has the potential to enhance crop photosynthesis, optimize nitrogen fixation mechanisms, improve biological stress tolerance, increase crop yields, and optimize nutritional quality, thereby promoting sustainable agricultural and ecological development. The advancement of biosensor components, gene circuit design, and related technologies can enhance the utilization of free nutrients, such as carbon and nitrogen in crops, while decreasing reliance on fertilizers. Additionally, by integrating microbial chassis-based cell factories, a sustainable system has been developed to convert biomass waste into safe, nutrient-rich fertilizers, enabling efficient waste-to-resource transformation. This article reviews the development history of agricultural synthetic biology and summarizes the latest research progress in synthetic biology technologies widely used in agriculture, including gene editing, metabolic engineering strategies, the development of biosensor components, gene circuit design and artificial intelligence. The core application areas of synthetic biology in agriculture are elaborated upon, including improvement in crop yield and resource utilization, enhancements in stress resistance, optimization in crop nutrition, and refinements in microbial interactions. Finally, the current challenges facing agricultural synthetic biology and its future development trends are discussed. The multidimensional application of synthetic biology in agricultural will facilitate the circular utilization of energy and resources, effectively ensuring food security and promoting the sustainable development of agriculture in the future.

    Strategies and prospects of synthetic biology in crop photosynthesis
    SUN Yang, CHEN Lichao, SHI Yanyun, WANG Ke, LV Dandan, XU Xiumei, ZHANG Lixin
    2025, 6(5):  1025-1040.  doi:10.12211/2096-8280.2024-094
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    Photosynthesis is the primary source of energy and materials for nearly all life activities on Earth, and its efficiency directly impacts crop growth and yield. With the rapid development of synthetic biology, researchers have begun to explore engineering approaches to optimize the fundamental processes of photosynthesis at various levels, including light energy utilization, carbon fixation, photorespiration, and stress adaptation. This review summarizes recent advances in improving photosynthetic efficiency, with a focus on the synthetic biological strategies that can be implemented in crops. To achieve efficient light absorption and electron transport, novel light energy conversion models have been developed, involving the engineering of light-harvesting antennae to minimize energy loss and the development of orthogonal electron transport chains to enhance quantum yield. Multi-level optimization strategies have been developed for carbon assimilation pathways, including directed evolution and activity modification of Rubisco, optimization of key enzymes in the Calvin-Benson-Bassham cycle, and the introduction of CO2 concentrating mechanisms into C3 plants. Furthermore, novel photorespiratory bypasses have been engineered through synthetic biology approaches, which optimize glycolate metabolism to effectively reduce photorespiratory carbon loss while enhancing photosynthetic efficiency in crops. Additionally, various engineering strategies have been developed to optimize photosynthetic performance under adverse conditions, such as the enhancement of non-photochemical quenching components to tolerate high light and the application of stress-responsive elements to adapt to temperature fluctuations. By employing synthetic biology techniques, significant improvements in plant photosynthetic efficiency and stress resistance have been achieved. This has led to enhanced biomass and crop yields, thereby providing new solutions to address global food security challenges. In the future, strategies based on synthetic biology, combined with a deeper understanding of the molecular mechanisms of photosynthesis and emerging technologies like artificial intelligence, will offer more effective methods and pathways for the engineering of photosynthesis, resulting in a substantial enhancement of crop photosynthetic efficiency.

    Research advances in nitrogen fixation synthetic biology
    LI Chao, ZHANG Huan, YANG Jun, WANG Ertao
    2025, 6(5):  1041-1057.  doi:10.12211/2096-8280.2025-081
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    Nitrogen is an essential element for plant growth and development. Legume plants form symbiotic relationships with rhizobia, which facilitates the biological fixation of atmospheric nitrogen (N2) into ammonia (NH3) that is directly usable by the plants through the action of rhizobial nitrogenase. This process reduces the need for chemical nitrogen fertilizers. However, under the pressure of continuously increasing food demand driven by a growing global population, the major non-leguminous food crops for humans, such as maize, rice and wheat, lack the ability to form nodules and establish symbiosis with rhizobia. This results in a heavy dependence on chemical nitrogen fertilizer to maintain high and stable yields. However, the overuse of chemical nitrogen fertilizers has caused serious environmental problems, including soil compaction and acidification, greenhouse gas emissions, and water eutrophication, all of which threaten agricultural sustainability and global food security. To achieve green and sustainable agricultural development and reduce the use of chemical fertilizers, nitrogen-fixing synthetic biology utilizes tools of synthetic biology to modify, optimize, and even de novo design biological nitrogen fixation systems. These engineered systems are applied across agricultural production, environmental protection, and industrial biotechnology, addressing global challenges such as excessive dependence on chemical nitrogen fertilizers, high energy consumption, and environmental pollution. The innovative strategies for bioengineering biological nitrogen fixation in non-leguminous crops can be categorized into the following four aspects. These strategies include engineering rhizobial nitrogen-fixing bacteria to increase nitrogen supply to the host, engineering crops to enhance the ability of plants to recruit nitrogen-fixing microbes in the rhizosphere to improve nitrogen use efficiency, forming nodule-like structures for symbiotic nitrogen fixation, and transferring functional nitrogenase components into plant cells to create self-fertilizing crops. Significant advances have been achieved in all these approaches in recent years, demonstrating their potential to boost yields while reducing fertilizers. This review provides a comprehensive overview of recent breakthroughs in nitrogen-fixing synthetic biology. We also discuss the current challenges and future prospects, offering theoretical insights and technical guidance to support further research and the practical application of biological nitrogen fixation in sustainable agriculture and environmental protection.

    Engineering rhizosphere synthetic microbial communities to enhance crop nutrient use efficiency
    ZHENG Lei, ZHENG Qiteng, ZHANG Tianjiao, DUAN Kun, ZHANG Ruifu
    2025, 6(5):  1058-1071.  doi:10.12211/2096-8280.2025-075
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    Modern agriculture confronts the dual challenge of suboptimal nutrient use efficiency (NUE) and the escalating chain of environmental burdens. These include increased greenhouse gas emissions, widespread soil degradation, and rising water eutrophication due to excessive fertilizer runoff. In this context, the rhizosphere microbiome, an indispensable symbiotic partner to plants throughout their life cycle, has been shown to critically regulate the transformation, mobilization, and supply of key soil nutrients. This occurs through core ecological mechanisms such as associative nitrogen fixation (e.g., performed by genera including Azospirillum), organic acid secretion-mediated dissolution of insoluble phosphorus (as commonly observed in Pseudomonas), and siderophore-chelated iron mobilization, which enhance nutrient accessibility for plant uptake. Recent breakthroughs in synthetic biology have significantly advanced the engineering of stable and efficient Synthetic Microbial Communities (SynComs), propelling this approach into a burgeoning frontier of agricultural biotechnology. SynComs integrate functionally diverse microbial strains to overcome well-documented limitations of single-strain inoculants, such as inconsistent performance and low resilience under field conditions. These designed communities form more stable and robust functional modules within the rhizosphere, leading to improved nutrient cycling and root system health. Beyond their application as agronomic biofertilizers, SynComs also serve as a powerful toolset for deciphering complex microbe-microbe interactions and elucidating synergistic mechanisms between microorganisms and host plants. Despite the considerable promise of SynComs technology, several critical barriers impede its real-world deployment. These include poor colonization stability of artificially constructed communities, limited environmental adaptability across varying agroecosystems with divergent soil properties and climatic conditions, and an insufficient mechanistic understanding of multi-trophic plant-microbe interactions. Additionally, commercialization faces further challenges due to prohibitive costs linked to large-scale production, formulation, and field application, as well as undefined long-term ecological risks such as potential disruption of native microbial communities or horizontal gene transfer. To realize the full potential of SynComs, coordinated multidisciplinary efforts are essential. Research should focus on engineering adaptively intelligent consortia capable of responding to dynamic environmental conditions, creating field-applicable tools for real-time monitoring and precision regulation, advancing scalable deployment strategies amenable to existing farming systems, and establishing rigorous ecological risk assessment protocols. An in-depth understanding of rhizosphere microbiome functions, coupled with the active development of SynCom technologies, represents a pivotal opportunity to address pressing agricultural nutrient management challenges. Such advances can significantly reduce inputs of synthetic fertilizers while enhancing nutrient use efficiency, ultimately promoting a transition toward resource-efficient and ecologically sustainable agricultural systems. Collectively, these efforts posses theoretical value and substantial industrial potential.

    Plant artificial chromosomes: current research progress and future application perspectives
    PU Ya, JIAO Yuling
    2025, 6(5):  1072-1092.  doi:10.12211/2096-8280.2025-089
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    Continuous and remarkable innovation in biology and biotechnology has increasingly exposed the limitations of traditional genetic engineering, including random integration of transgenes and challenges in regulating multiple genes, in both basic research and practical applications. With the rapid advancement of synthetic biology, which emphasizes the design and construction of novel biological systems with predefined functions, plant artificial chromosomes (PACs) have emerged as a pivotal development. PACs not only deepen our understanding of chromosome structure and function at the molecular level but also serve as precisely engineered chromosomal vectors. These constructs effectively avoid position effects and linkage drag, providing a robust platform for the co-expression of multiple genes, stacking of complex traits, and engineering of metabolic pathways.This review summarizes the history, progress, and current status of PACs research, highlighting various construction strategies. This includes truncating and modifying endogenous chromosomes, assembling chromosomal elements, such as telomeres, centromeres, and replication origins, to construct PACs, as well as de novo designing and synthesizing chromosomal fragments for genome rewriting. The latter approach involves creating entirely new DNA sequences tailored to specific research or application needs. In addition, the review also addresses the critical challenges of constructing functional centromeres, which are essential for accurate chromosome segregation during cell division, and explores techniques for delivering large DNA fragments into plant cells — a crucial step for the efficient introduction of PACs. Furthermore, this paper highlights persistent challenges in the field, such as difficulties in synthesizing centromere, technical bottlenecks in delivering large DNA fragments, and the instability of artificial chromosomes. Finally, it highlights the extensive application potential of PACs in basic chromosome research, synthetic biotechnology, and agricultural genetic engineering. By integrating emerging technologies such as gene editing and AI-driven design, PACs are poised to become core tools for elucidating chromosomal mechanisms, enabling precise crop improvement, and advancing green biomanufacturing. This integration will drive sustainable agricultural development and breakthroughs in plant science.

    Construction and application of plant artificial chromosomes
    WEI Jiaxiu, JI Peiyun, JIE Qingyu, HUANG Qiuyan, YE Hao, DAI Junbiao
    2025, 6(5):  1093-1106.  doi:10.12211/2096-8280.2025-086
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    Plant artificial chromosomes (PACs) are human-designed chromosomes that can independently replicate and are stably inherited in plant cells, offering significant potential for genetic engineering. A key advantage of PACs lies in their capacity to accommodate large genetic cassettes while functioning independently of the host genome, establishing PACs as a versatile platform for stable and biosafe genetic manipulation. This review systematically outlines current strategies for PAC construction, methodologies, and future application prospects from a synthetic biology perspective. Current strategies for PAC construction are broadly categorized into top-down and bottom-up approaches. The top-down strategy utilizes endogenous chromosomal elements through techniques such as telomere-mediated chromosomal truncation (TMCT) to generate minichromosomes. In contrast, the bottom-up strategy focuses on the de novo assembly of functional elements, such as centromeres, telomeres, and autonomous replication sequences to synthesize novel chromosomes. Significant progress has also been made in developing extra-nuclear PACs based on plastid or mitochondrial genomes, which benefits from prokaryotic-like transcription and translation systems and offer higher transgene containment. However, the efficient delivery of large PAC constructs into plant cells remains a major technical hurdle. This review evaluates various delivery methodologies to address this challenge. By enabling high-capacity, chromosome-scale engineering, PACs significantly expand the scope of synthetic biology, supporting not only large-scale genomic modifications in existing species but also the de novo design of synthetic gene networks and metabolic pathways. Delivering large PAC constructs into plant cells remains a major bottleneck, and the review evaluates various methods. By enabling chromosomal-level engineering, PACs expand the scope of synthetic biology. Beyond supporting large-scale modifications in existing plants, PACs also allow the de novo assembly of novel gene networks and metabolic pathways, paving the way for engineering plant systems with novel, non-native traits and functions. To fully unleash this potential, several technical challenges must be addressed, including efficient synthesis and delivery of large DNA fragments, enhancement of genetic stability, and the integration of artificial intelligence (AI) with synthetic biology for precise design and functional optimization of PACs. Through iterative design-build-test-learn (DBTL) cycles, PACs can be developed into predictable and stable biological systems. The convergence of these approaches is expected to drive transformative applications across agriculture, pharmaceuticals, and ecology.

    Plant synthetic biology: new opportunities for large-scale culture of plant cells
    YAN Zhaotao, ZHOU Pengfei, WANG Yangzhong, ZHANG Xin, XIE Wenyan, TIAN Chenfei, WANG Yong
    2025, 6(5):  1107-1125.  doi:10.12211/2096-8280.2024-095
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    Plant Cell Culture (PCC) has emerged as a highly promising chassis for synthetic biology, offering a range of advantages such as short growth cycles, cost-effectiveness, absence of pathogenic risks, and abundant secondary metabolites. These features make PCC an attractive alternative for applications in medicine, food, and health. However, insufficient production efficiency due to difficulties in genetic transformation, complex regulatory networks, cell aggregation, and poor genetic stability remains a major obstacle that limits the commercialization of PCC. Synthetic biology, with its bottom-up engineering design approach, provides a powerful toolkit to address these challenges. By enabling the precise design and modification of native plant cells, synthetic biology offers innovative strategies to develop efficient and economically viable plant cell factories. In this paper, we first review the current status of PCC in synthesizing high-value compounds, particularly recombinant proteins and secondary metabolites. Recent advancements have demonstrated the potential of PCC to produce therapeutic proteins, vaccines, industrial enzymes and bioactive compounds such as alkaloids, flavonoids, and terpenoids. These successes underscore the versatility of PCC as a bioproduction platform. We then explore the role of synthetic biology in advancing PCC industrialization. Key developments include the creation of high-quality plant cell lines through genome editing tools like CRISPR/Cas9, enhancing genetic stability and metabolic efficiency. Additionally, synthetic biology has improved genetic transformation systems, overcoming a critical bottleneck in PCC. Enhanced expression systems, incorporating synthetic promoters and regulatory elements, have significantly boosted target compound yields. Furthermore, synthetic biology has expanded PCC applications by enabling the biosynthesis of heterologous compounds beyond their native metabolic pathways. Finally, we discuss future prospects, emphasizing the potential of synthetic biology to overcome current technical challenges. Emerging technologies including multi-omics integration, machine learning, and synthetic organelle development are anticipated to further enhance PCC’s scalability and efficiency. By addressing these challenges, synthetic biology will pave the way for large-scale plant cell cultivation, thereby facilitating its widespread adoption in industrial bioproduction. The convergence of PCC and synthetic biology holds immense potential for the sustainable, cost-effective, and scalable production of high-value compounds.

    Research progress and development trends in the biosynthesis of neutral core human milk oligosaccharides
    LIU Dan, WANG Jianyu, JIANG Zhengqiang
    2025, 6(5):  1126-1144.  doi:10.12211/2096-8280.2025-083
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    Human milk oligosaccharides (HMOs) are essentially functional and nutritional components found in human milk. They can be primarily classified into fucosylated, neutral core, and sialylated HMOs. Lacto-N-triose Ⅱ (LNT Ⅱ), lacto-N-neotetraose (LNnT), and lacto-N-tetraose (LNT) are common neutral core human milk oligosaccharides (ncHMOs), which can be extended to form longer-chain HMOs and play important roles in intestinal health. In recent years, the biosynthesis of ncHMOs has developed rapidly, and industrial-scale production is from theoretical possibility to practical reality. The synthesis approaches for ncHMOs include chemical synthesis, enzymatic synthesis, and microbial cell synthesis. As the rapid development in biotechnology, enzymatic and microbial cell synthesis have emerged as prominent methods in ncHMOs biosynthesis. Enzymatic synthesis is highly efficient, regioselective, and stereoselective. Currently, glycosyltransferases and glycoside hydrolases represent the two major types of enzymes used for biosynthesizing ncHMOs. Glycosidase-based enzymatic synthesis has demonstrated high conversion rates for LNT Ⅱ and LNnT production. However, the enzymatic synthesis of LNT is less efficient and requires further improvement. Notably, the production of LNnT and LNT typically relies on LNT Ⅱ as a key precursor, requiring a multi-step synthetic strategy. Microbial cell synthesis employs metabolic engineering to construct continuously synthetic pathways in microbial cells such as Escherichia coli and Bacillus subtilis. Knocking out genes in competitive pathway, optimizing genes expression, regenerating cofactors have significantly enhanced the yields of ncHMOs. The biosynthesis of ncHMOs faces several critical challenges, including the low activity and poor substrate specificity of key glycosyltransferases, such as β-1,3-N-acetylglucosaminyltransferase and β-1,3-galactosyltransferase. Additionally, the transporters of LNT Ⅱ and LNnT are not clear in microbial cell. Furthermore, the yields of LNT Ⅱ should be substantially improved for industrial-scale production. Thus, it is important to overcome the interconnected limitations in enzyme engineering (particularly glycosyltransferase specificity and activity), microbial cell modification (focusing on metabolic compatibility and pathway design), and bioprocess optimization (through rational pathway redesign) via an integrated synthetic biology and fermentation engineering approach in the future. These strategies are essential for achieving efficient, cost-effective biosynthesis of ncHMO at industrial scale.

    Agricultural synthetic biology driving innovation in animal nutrition: advances and prospects
    LI Yicheng, LUO Huiying, YAO Bin, TU Tao
    2025, 6(5):  1145-1166.  doi:10.12211/2096-8280.2025-082
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    Animal nutrition is the cornerstone of sustainable animal husbandry development, with its overall efficiency directly influencing resource utilization, environmental carrying capacity, and global food security. Recent rapid advances in agricultural synthetic biology have enabled researchers to engineer animal nutrient utilization systems through innovative strategies. These primarily encompass feed ingredient optimization, the production of synthetic feed additive and the enhancement of gastrointestinal nutrient conversion efficiency. This review systematically examines recent progress in this field, focusing on the application of agricultural synthetic biology strategies for advancing animal nutrition. In the realm of feed ingredient quality improvement, gene editing technologies have significantly enhanced the nutritional value of key crops. For example, the specific knockout of the GhPGF gene in cotton has resulted in cottonseed detoxification, while targeted modifications to the sorghum kafirin gene family has enhanced protein digestibility and quality. To decrease reliance on soybean meal, various strategies have been developed to utilize microbial protein resources. These include overcoming production bottlenecks in methylotrophic yeast, precisely tuning carbon metabolism pathways in Clostridiumautoethanogenum, and developing cell wall disruption techniques for microalgae to enhance protein bioavailability. Synthetic biology approaches have also revolutionized the production of feed additive. Key strategies encompass metabolic pathway engineering to enhance precursor supply, cofactor optimization to boost metabolic flux, gene editing to reduce competition from alternative pathways, and protein engineering to improve the activity of rate-limiting enzymes. Furthermore, emerging tools in synthetic biology show great promise for regulating gastrointestinal function. These include biotechnology-optoelectronic integration for advanced sensing systems, novel gene editing tools for precise modulation of gut microbiota, and intelligent synthetic microbial consortia for targeted regulation of the gastrointestinal microenvironment. Agricultural synthetic biology holds immense potential for enhancing feed conversion efficiency, safeguarding animal health, and driving the green transformation of animal husbandry. This review further discusses current challenges in the field, including technological bottlenecks and scalability issues, and outlines future development trends, emphasizing the critical role of synthetic biology in shaping next-generation animal nutrition systems.

    Biosynthesis and manufacture of microbial oils and vegetable oils
    SU Juanjuan, ZHENG Jiawen, MIAO Runze, HAN Peng, WANG Shi’an, LI Fuli
    2025, 6(5):  1167-1183.  doi:10.12211/2096-8280.2024-093
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    Oils and fatty acid derivatives are essential raw materials across various industries, including food, bioenergy, functional materials, and pharmaceutical chemicals, with significant global demand. Currently, China heavily relies on imported oilseed crops, and the cultivation of oil crops is constrained by limited arable land, making it difficult to meet the growing demand for oils. The development of synthetic biology offers a promising solution, particularly through the microbial oil synthesis technology, which utilizes renewable resources to produce oils, presenting a strategic alternative to traditional oil production methods. The work provides a comprehensive overview of the current research progress in the biosynthesis and biomanufacturing of microbial oils and vegetable oils. It highlights the commercial demonstration cases of microbial synthesis for high-value oils, including arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). It also presents the industrial demonstration cases of bulk oil synthesis, such as biorefining technology that utilizes lignocellulosic materials. The economic differences between vegetable oils and microbial oils are analyzed, emphasizing the challenges and opportunities in cost reduction and scalability. Additionally, the review summarizes the technologies for oil separation, extraction, and detection, which are critical for improving the efficiency and quality of oil production. Looking ahead, high-value oils are expected to undergo rapid development in the short term, driven by their applications in health, nutrition, and specialty chemicals. In the medium to long term, microbial bulk oils hold great potential, especially through the utilization of non-food feedstocks such as lignocellulosic biomass and industrial waste, enabling the transition to a circular economy in the oil industry. The integration of synthetic biology tools, including genetic engineering, metabolic pathway optimization, and high-throughput screening, will be essential for constructing efficient microbial cell factories capable of producing oils with high yields and tailored compositions. Furthermore, the development of low-cost, full-chain biorefining technologies will be crucial for overcoming the economic barriers to large-scale microbial oil production. By addressing these challenges, microbial oils have the potential to revolutionize traditional oil production methods, offering sustainable and environmentally friendly alternatives to meet the increasing global demand for oils. This review underscores the importance of continued research and innovation in synthetic biology and biomanufacturing to unlock the full potential of microbial and plant oils in various industrial applications.

    Construction of microbial cell factories for aspartate-family feed amino acids
    ZHAO Xinyu, SHENG Qi, LIU Kaifang, LIU Jia, LIU Liming
    2025, 6(5):  1184-1202.  doi:10.12211/2096-8280.2025-032
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    Amino acids are essential components of animal feed, playing key roles in improving digestive function in livestock, enhancing meat quality, increasing protein conversion efficiency, and reducing reliance on soybean meal. Driven by global population growth and dietary changes, the increasing demand for animal protein has strained the livestock industry. This industry traditionally relies heavily on soybean meal as its primary protein source, a method that results in low nitrogen utilization and exacerbates environmental pollution from nitrogen emissions. Aspartate-family amino acids, including L-lysine, L-methionine, L-threonine, and L-isoleucine, represent the most significant category of feed amino acids, accounting for nearly 90% of global consumption. They address current challenges by balancing feed nutrition according to the ideal protein standard and enabling a low-carbon transition in animal husbandry. The primary method for producing these four amino acids is through microbial fermentation, with Escherichia coli and Corynebacterium glutamicum serving as the primary host organisms. Rapid advances in systems biology, synthetic biology, metabolic engineering, and evolutionary engineering have facilitated the construction and optimization of high-yield amino acid-producing strains. This has significantly enhanced production efficiency and substantially reduced costs. Based on an analysis of the aspartate-family amino acid biosynthetic pathways, this paper details strain modification methods and strategies. These encompass four key aspects: metabolic pathway reconstruction, metabolic pathway optimization, cofactor supply enhancement, and improved product efflux. These approaches have enabled the industrial-scale production of strains achieving high titers and yields. Finally, future research directions are discussed, focusing on three fronts: enhancing strain stress resistance in industrial environments, expanding the range of utilizable substrates, and optimizing dynamic regulatory systems. These advancements are intended to offer theoretical guidance and technical support for the development of high-performance amino acid-producing strains. The ultimate objective is to facilitate the global shift towards efficient and environmentally sustainable feed amino acid production, thereby alleviating pressures on protein resources.

    Advances in small-molecule biopesticides and their biosynthesis
    SONG Kainan, ZHANG Liwen, WANG Chao, TIAN Pingfang, LI Guangyue, PAN Guohui, XU Yuquan
    2025, 6(5):  1203-1223.  doi:10.12211/2096-8280.2024-078
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    Small-molecule biopesticides, in contrast to chemically synthesized pesticides, demonstrate superior degradability in the natural environment and exert a lesser adverse impact on non-target organisms and the overall ecosystem. Consequently, the evolution of small-molecule biopesticides represents a pivotal shift for the pesticide industry towards more sustainable and environmentally benign practices, with their significance projected to escalate in the realm of agricultural production in the years ahead. Despite their potential, these pesticides are currently constrained by a limited variety and suboptimal production yields, primarily attributable to the intricate research and manufacturing processes that demand substantial time and resource investments. Moreover, the biosynthetic pathways of the majority of these small molecules remain enigmatic, posing a significant challenge to their industrial application. However, the advent of synthetic biology and metabolic engineering offers promising solutions to these impediments. This progress is not merely instrumental in deepening our understanding of the intricate synthetic mechanisms of these bioactive compounds within biological systems, but it also paves the way for augmenting their production yields. By employing microbial cell factories, these technologies enable an efficient and targeted biosynthesis of specific biopesticides, thereby overcoming the limitations associated with traditional extraction and purification methods from natural sources. Microbial cell factories not only facilitate the cost-effective and environmentally friendly large-scale production of small-molecule biopesticides but also foster the innovation of novel biopesticide varieties. This review aims to summarize the small-molecule biopesticides and some semi-synthetic pesticides derived from natural products that were registered in China from January 2000 to December 2024, including eight polyketides, twelve terpenes, four alkaloids, and five other small-molecule biopesticides. Depending on their specific uses in agricultural practices, they can be classified into insecticides, microbicide, plant growth regulators, and so on. Furthermore, this review provides a succinct overview of the representative biosynthetic pathways and the corresponding microbial cell factories that are pivotal to the production of these biopesticides. We expect that an in-depth understanding of the biosynthesis of small-molecule biopesticides will pave solid ways for further elucidation of biosynthesis pathways, yield improvement, and the discovery and application of novel biopesticides.

    Policy planning and industrial development of agricultural synthetic biology
    ZHANG Xuebo, ZHU Chengshu, CHEN Ruiyun, JIN Qingzi, LIU Xiao, XIONG Yan, CHEN Daming
    2025, 6(5):  1224-1242.  doi:10.12211/2096-8280.2025-066
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    Agricultural synthetic biology, an emerging interdisciplinary field, synergistically integrates fundamental principles from biology, engineering and computer science, and is dedicated to advancing agricultural production towards greater efficiency and sustainability by innovatively designing and engineering of biological systems. In recent years, governments worldwide have accelerated the development of this field through the combined efforts of policy initiatives and technological innovation. Countries and regions including the United States, the European Union, the United Kingdom, and Australia have introduced policies to explicitly support the research and application of key technologies, such as gene editing and metabolic engineering, in the agricultural field. These supportive frameworks have greatly advanced the global development of agricultural synthetic biology. In China, active efforts are being made to construct an integrated innovation ecosystem connecting industry, academia, and research institutions, with the goal of accelerating the industrialization of agricultural synthetic biology technologies. Currently, several technologies have achieved initial commercial applications in areas such as breeding, food and feed production, and biological pesticides. In crop breeding, precise genome editing enables the development of varieties with enhanced yield, improved nutritional quality, and greater resistance to biotic and abiotic stresses. In the field of food and feed, genetic engineering is employed to modify microorganisms to produce enzyme preparations that improve feed digestibility and nutritional value, as well as to develop microbial-based biopreservatives to replace chemical preservatives, or natural-source coatings that extend the shelf life of fruits and vegetables. Additionally, biological pesticides derived from natural microorganisms, plant extracts or insect pheromones can effectively reduce the impact on soil, water sources and ecosystems, while reducing the risk of residues. These products are increasingly applied in crop protection, and offer sustainable alternatives for reducing environmental pollution while safeguarding food safety. Several innovative enterprises worldwide have provided valuable experience and insights into the development and application of agricultural microbial products. These companies not only demonstrate effective pathways for translating laboratory research into practical products, but also offer business models that serve as valuable references for the broader industry. Simultaneously, a number of Chinese enterprises are actively exploring the application of synthetic biology to improve crop breeding, enhance crop resistance to stress and diseases, and develop biopesticides, biofertilizers, and new bio-based materials. Some are employing synthetic biology approaches to improve crop performance under adverse environmental conditions or to enhance soil health by optimizing microbial community structures. Despite recent breakthroughs, the continued development of agricultural synthetic biology still faces numerous challenges, including limited market acceptance, underdeveloped regulatory frameworks, insufficient capital investments, and persistent technological bottlenecks. Overcoming these challenges requires a concerted, multi-faceted approach that integrates policy guidance, technological innovation, and industrial upgrading. It is essential to foster synergistic development across key domains, including the engineering of non-food crops, the expansion of photoautotrophic microbial platforms, and the advancement of carbon capture and utilization technologies. At the same time, interdisciplinary collaboration should be strengthened to encourage more research institutions and enterprises to engage in this field. Through the combined forces of supportive policies and increased capital investment, barriers such as ecological risk assessment can be effectively addressed, thereby accelerating the commercialization of new products. Governments must act promptly to establish clear, science-based regulatory pathways that ensure the safety and efficacy of emerging agricultural biotechnologies, at the same time investors should recognize the transformative potential of this field and provide financial support for startups and research initiatives. Ultimately, the goal is to catalyze a global agricultural transformation that ensures food security for a growing population, mitigates the impacts of climate change, and promotes ecological conservation and restoration. Through collaborative efforts among all stakeholders, agricultural synthetic biology has the potential to become a driving force for advancing modern agriculture and building a greener, healthier, and more sustainable future for humanity.

    Design and practice of plant synthetic biology theme in the International Genetically Engineered Machine Competition
    HE Yangyu, YANG Kai, WANG Weilin, HUANG Qian, QIU Ziying, SONG Tao, HE Liushang, YAO Jinxin, GAN Lu, HE Yuchi
    2025, 6(5):  1243-1254.  doi:10.12211/2096-8280.2025-057
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    As an important branch of synthetic biology, the number of research outcomes from iGEM award-winning projects is not significant, lagging behind due to the numerous challenges posed by the complex nature of plant systems. Compared with microorganisms, the genetic operation of plants has obvious shortcomings : not only the operation cycle is long, the standardized component library available for use is very scarce, and the conversion efficiency is also at a low level. These factors are superimposed together, making the engineering transformation of plants difficult. However, even so, plant synthetic biology still occupies a non-negligible position by virtue of its unique value in many key fields such as agriculture, environment and biomedicine. Because of these unique values, it has become an important research direction in the field of synthetic biology. In recent years, with the breakthrough of a series of key technologies, plant synthetic biology has ushered in new development opportunities. Advances in gene editing technology and synthetic promoter optimization have significantly enhanced the programmability of plant chassis and the regulation efficiency of gene expression, providing a highly innovative solution to solve major problems such as food security, nutrition enhancement, and plant-derived drug production in the world. In view of the development of plant synthetic biology project, combined with the evaluation criteria of iGEM competition, there are many key links that need to be focused on. In the process of setting up the topic, it is necessary to accurately lock in scientific problems with research value and ensure the forward-looking and practical nature of the research direction; At the design level, the modular design of genetic circuits is crucial for and enhancing efficiency and reliability, allowing for the orderly regulation of complex biological functions.At the same time, the effective integration of experimental operation and mathematical modeling can provide more solid theoretical support and more accurate result prediction for research. In addition, interdisciplinary collaboration is also an important driving force for the development of plant synthetic biology projects. The cross-integration of multidisciplinary knowledge such as biology, engineering, and computer science can collide more innovative sparks. At the same time, the visual presentation of the results can make the research value and innovation points more intuitive, and further enhance the application potential of the project. The application of these strategies is expected to promote the project of plant synthetic biology to shine on the international platform and contribute more to the development of this field.

    Research on market access and regulation of global bio-manufactured feed protein materials and additives
    CHEN Wuxi, MA Longxue, YANG Yang, ZHU Zhen, ZHAI Yida, DUAN Yu, CHEN Limei, LI Demao
    2025, 6(5):  1255-1273.  doi:10.12211/2096-8280.2025-060
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    With the rapid development of biotechnology, an increasing number of bio-manufactured feed materials and additives have been successfully developed. These innovative products leverage cutting-edge biotechnologies including synthetic biology, fermentation engineering, and genetic modification to produce substances such as single-cell proteins, bioactive peptides, and probiotics. For instance, single-cell proteins derived from yeast or algae are rich in essential amino acids, vitamins, and minerals, significantly enhancing the nutritional value of feed. Moreover, bio-manufacturing often utilizes renewable resources and operates under milder conditions, reducing production costs compared to conventional chemical synthesis methods. In addition, by precisely controlling the production process, bio-manufactured additives can improve animal digestion and absorption, thereby boosting breeding efficiency and promoting sustainable livestock production. However, significant differences in production processes and quality standards between bio-manufactured and traditional feed ingredients and additives have resulted in multiple market-access challenges, hindering the rapid development of the bioeconomy. This paper systematically reviews the market access mechanisms for bio-manufactured protein feed materials and additives in the European Union, the United States, Japan, and China, including relevant regulatory frameworks, approval procedures, and standard requirements. In China, despite progress in developing of bio-manufactured feed materials and additives, there are still several issues with market access and regulation. For example, the safety evaluation system for microorganisms used in bio-manufacturing lacks specific and detailed guidelines. There have been cases where innovative bio-manufactured feed additives experienced long-term delays in the approval process due to unclear evaluation criteria. The product evaluation procedures are complex and time-consuming, involving multiple departments and repetitive reviews, which increase the cost and time for enterprises to enter the market. Additionally, the research and development of synthetic biotechnology in the feed industry lags behind that of developed countries, and the approval process for new bio-manufactured products is relatively conservative, slowing down product listing and marketing. This study proposes optimization strategies, including strengthening safety evaluation requirements for microorganisms and their products for feeding, simplifying the product evaluation procedures, and accelerating the research and development of synthetic biotechnology as well as the approval of the listing and marketing of products. The ultimate objective of this study is to provide insights that will facilitate the smoother integration and high-quality development of bio-manufacturing applications within the feed and livestock industries, supporting their sustainable evolution.