Robustness and design principles of synthetic microbial communities for application

Qi Panqing; Liu Xuewen; Wu Mengdi; Hou Qihui; Nie Yong; Wu Xiaolei; Ma Anzhou

doi:10.12211/2096-8280.2026-043

您当前的位置：

首页 >

文章列表页 >

Robustness and design principles of synthetic microbial communities for application

更新时间：2026-08-04

- Robustness and design principles of synthetic microbial communities for application
- 面向应用的合成微生物群落鲁棒性及设计原则
- Synthetic Biology Journal Pages: 1-16(2026)
- 作者机构：
  
  1.中国科学院生态环境研究中心，北京 100085
  2.中国科学院大学，资源与环境学院，北京 100049
  3.北京大学，力学与工程科学学院，北京 100871
  4.香港中文大学，物理系，香港 999077
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2026-043
  CLC： T-012
- Received：14 May 2026，
  
  Revised：2026-07-31，
  
  Online First：04 August 2026，
- 稿件说明：
移动端阅览
齐泮晴，刘学文，吴梦迪，侯启会，聂勇，吴晓磊，马安周. 面向应用的合成微生物群落鲁棒性及设计原则［J］. 合成生物学， 2026， 7. DOI： 10.12211/2096-8280.2026-043

Qi Panqing， Liu Xuewen， Wu Mengdi， Hou Qihui， Nie Yong， Wu Xiaolei， Ma Anzhou. Robustness and design principles of synthetic microbial communities for application［J］. Synthetic Biology Journal， 2026， 7. DOI： 10.12211/2096-8280.2026-043
齐泮晴，刘学文，吴梦迪，侯启会，聂勇，吴晓磊，马安周. 面向应用的合成微生物群落鲁棒性及设计原则［J］. 合成生物学， 2026， 7. DOI： 10.12211/2096-8280.2026-043 DOI：

Qi Panqing， Liu Xuewen， Wu Mengdi， Hou Qihui， Nie Yong， Wu Xiaolei， Ma Anzhou. Robustness and design principles of synthetic microbial communities for application［J］. Synthetic Biology Journal， 2026， 7. DOI： 10.12211/2096-8280.2026-043 DOI：

摘要

合成微生物群落（Synthetic microbial communities， SynComs）作为合成生物学从单细胞工厂向多细胞群体协作范式转变的核心载体，是实现复杂工程化功能的重要策略。然而，当合成微生物群落从可控的实验室环境转移至复杂、异质的开放生境时，其群落组成与功能的维持能力（即鲁棒性/稳健性，Robustness）往往显著降低。本文首先从环境适配性、功能稳定性、定植稳定性及尺度扩展性四个维度，系统解构了应用场景下合成微生物群落鲁棒性的多维内涵。为应对开放环境的复杂性，并规避低复杂度合成微生物群落（通常含20个以下物种）涌现特性固有的局限性，本文以能够模拟自然生境复杂性的大规模合成微生物群落（含20个以上物种）为研究模型，通过逆向工程解析其在波动压力下维持鲁棒性的深层机制。分析表明，大规模合成微生物群落的鲁棒性源于非线性耦合所产生的涌现特性：在系统发育维度，高丰度物种间的多样性冗余构筑了严密的生态位屏障，显著增强入侵防御能力；在代谢维度，群落成员构建了高效的负反馈回路，关键物种的代谢汇功能有效缓解了有害中间产物的毒性积累；在环境响应维度，群落与宿主调控及生境波动表现出强相关性。值得注意的是，现有研究还表明定植能力与功能表现之间存在解耦现象，即合成微生物群落的功能鲁棒性可在不依赖永久性生态位占据的前提下，以瞬时、即时性的效应形式呈现。基于上述认识，本文提出了面向合成微生物群落应用的四项理性设计原则：1）系统发育维度的生态位饱和原则——通过在目标场景中最大化谱系饱和度以增强入侵抗性；2）代谢负反馈原则——利用关键代谢汇物种消除代谢毒性；3）宿主维度的环境耦合原则——实现合成微生物群落与土著环境因子的稳态匹配；4）功能需求驱动的效应权衡原则——作为顶层约束，该原则主张依据具体应用场景（如即时干预型与长期维持型）动态调整其他原则的设计逻辑。本综述为合成微生物群落跨越实验室至开放生境的尺度障碍提供了关键的方法学指引，同时为强化"设计-构建-测试-学习"（DBTL）循环的底层约束及理性构建高性能、高稳定性合成微生物群落指明了可供参考的优化路径。

Abstract

Synthetic microbial communities (SynComs)

serving as the core vehicle for the paradigm shift in synthetic biology from monoculture cell factories to multicellular consortia

represent a pivotal strategy for achieving complex functionalities. However

a significant robustness gap persists when transitioning SynComs from controlled laboratory settings to complex

heterogeneous open environments. This review first systematically deconstructs the multidimensional connotations of robustness of SynComs for application across four key dimensions: environmental fitness

functional stability

colonization persistence

and scale-up adaptability. To address the complexity of open environments and circumvent the inherent limitations of emergent properties in low-complexity SynComs (typically comprising fewer than 20 species)

this review employs high-complexity

large-scale SynComs (comprising more than 20 species)

designed for high-fidelity emulation of complex natural habitats

as research models. Through reverse engineering

we characterize the underlying ecological mechanisms that maintain robustness under fluctuating pressures. Our analysis reveals that the robustness of large-scale SynComs originates from emergent properties generated by nonlinear coupling. In the phylogenetic dimension

diversity redundancy among high-abundance species forms a rigorous niche barrier

significantly enhancing invasive defense. In the metabolic dimension

members of SynComs construct efficient negative feedback loops

where the metabolic sink function of key species effectively alleviates the toxic accumulation of hazardous intermediates. In the environmental response dimension

the consortia exhibit strong correlations with host regulation and habitat fluctuations. Crucially

existing studies have indicated a decoupling between colonization and function

demonstrating that the functional robustness of SynComs can manifest as transient and immediate effects

rather than relying on permanent niche occupation. Based on these insights

we propose four rational design principles for the application of SynComs: 1) Phylogenetic niche saturation

enhancing invasion resistance by maximizing lineage saturation in target scenarios; 2) Metabolic negative feedback regulation

utilizing key metabolic sink species to eliminate metabolic toxicity; 3) Host-environment coupling

achieving steady-state alignment between artificial consortia and indigenous environmental factors; and 4) Functional demand-driven effect trade-offs. Functioning as a top-level constraint

this principle advocates for the dynamic adjustment of design logic across the other principles based on specific application scenarios (e.g.

immediate intervention vs. long-term maintenance). This review provides systematic methodological guidance for the application of SynComs to overcome scale barriers when transitioning from the laboratory to open environments. Furthermore

it offers robust theoretical support for strengthening the underlying constraints of the "Design-Build-Test-Learn" (DBTL) cycle and for the rational construction of high-performance

stable SynComs.

关键词

Keywords

references

周文娟 , 付刚 , 齐显尼 , 等 . 发酵工业菌种的迭代创制 [J ] . 生物工程学报 , 2022 , 38 ( 11 ): 4200 - 4218 .

ZHOU Wenjuan , FU Gang , QI Xianni , et al . Upgrading microbial strains for fermentation industry [J ] . Chinese Journal of Biotechnology , 2022 , 38 ( 11 ): 4200 - 4218 .

Liu Y , Xue B , Liu H , et al . Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform [J ] . Biotechnology Advances , 2024 , 72 : 108348 .

高聪 , 陈城虎 , 陈修来 , 等 . 代谢工程改造微生物合成生物基单体的进展与挑战 [J ] . 化工进展 , 2023 , 42 ( 08 ): 4123 - 4135 .

GAO Cong , CHEN Chenghu , CHEN Xiulai , et al . Progress and challenges of engineering microorganisms to produce biobased monomers [J ] . ChemicalIndustry and Engineering Progress , 2023 , 42 ( 8 ): 4123 - 4135 .

朱华伟 , 李寅 . 合成生物制造2026 [J ] . 生物工程学报 , 2026 , 42 ( 03 ): 991 - 1026 .

ZHU Huawei , LI Yin . Biomanufacturing driven by engineered organisms (2026) [J ] . Chinese Journal of Biotechnology , 2026 , 42 ( 3 ): 991 - 1026 .

Wu G , Yan Q , Jones J A , et al . Metabolic burden: Cornerstones in synthetic biology and metabolic engineering applications [J ] . Trends in Biotechnology , 2016 , 34 ( 8 ): 652 - 664 .

Li B , Liu W . Engineering microbial consortia for biosynthesis: Construction, regulation, and applications [J ] . Biotechnology Advances , 2026 , 88 : 108846 .

Qiu C , Zhang T , Liang G , et al . Regulating cellular activity to enhance microbial cell factory efficiency [J ] . Biotechnology Advances , 2026 , 86 : 108745 .

Bittihn P , Din M O , Tsimring L S , et al . Rational engineering of synthetic microbial systems: from single cells to consortia [J ] . Current Opinion in Microbiology , 2018 , 45 : 92 - 99 .

McCarty N S , Ledesma-Amaro R . Synthetic biology tools to engineer microbial communities for biotechnology [J ] . Trends in Biotechnology , 2019 , 37 ( 2 ): 181 - 197 .

徐昭勇 , 胡海洋 , 许平 , 等 . 人工合成微生物组的构建与应用 [J ] . 合成生物学 , 2021 , 2 ( 2 ): 181 - 193 .

XU Zhaoyong , HU Haiyang , XU Ping , et al . Development and application of synthetic microbiome [J ] . Synthetic Biology Journal , 2021 , 2 ( 2 ): 181 - 193 .

Großkopf T , Soyer O S . Synthetic microbial communities [J ] . Current Opinion in Microbiology , 2014 , 18 : 72 - 77 .

朱彤 , 吴边 . 合成微生物组:当"合成生物学"遇见"微生物组学" [J ] . 科学通报 , 2019 , 64 ( 17 ): 1791 - 1798 .

ZHU Tong , WU Bian . Synthetic microbiome: When "synthetic biology" meets "microbiomics" (in Chinese) . Chin Sci Bull , 2019 , 64 : 1791 - 1798 .

周静茹 , 刘鹏 , 夏建业 , 等 . 基于约束的基因组规模代谢网络模型构建方法研究进展 [J ] . 生物工程学报 , 2021 , 37 ( 5 ): 1526 - 1540 .

ZHOU Jingru , LIU Peng , XIA JianYe , et al . Advances in the development of constraint-based genome-scale metabolic network models . Chin JBiotech , 2021 , 37 ( 5 ): 1526 - 1540 .

Wang W , Xia Y , Zhang P , et al . Narrow-spectrum resource-utilizing bacteria drive the stability of synthetic communities through enhancing metabolic interactions [J ] . Nature Communications , 2025 , 16 ( 1 ): 6088 .

Schäfer M , Pacheco A R , Künzler R , et al . Metabolic interaction models recapitulate leaf microbiota ecology [J ] . Science , 2023 , 381 ( 6653 ): eadf5121 .

Egidi E , Nielsen U N . Predator-microbe dynamics inform strategies for robust synthetic community assembly [J ] . Environmental Microbiology , 2026 , 28 ( 6 ): e70336 .

Madsen C S , Kimbrel J A , Diep P , et al . Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia [J ] . The ISME Journal , 2025 , 19 ( 1 ).

Zhang Y , Jing M , Lyu L , et al . Principles for rigorous design and application of synthetic microbial communities [J ] . Advanced Science , 2026 , 13 ( 10 ): e14750 .

Wang Z , Wang S , He Q , et al . Ecological design of high-performance synthetic microbial communities: from theoretical foundations to functional optimization [J ] . ISME communications , 2025 , 5 ( 1 ).

Lawson C E , Harcombe W R , Hatzenpichler R , et al . Common principles and best practices for engineering microbiomes [J ] . Nature Reviews Microbiology , 2019 , 17 ( 12 ): 725 - 741 .

Fonseca-García C , Pettinga D , Wilson A , et al . Defined synthetic microbial communities colonize and benefit field-grown sorghum [J ] . The ISME Journal , 2024 , 18 ( 1 ).

Li Z , Bai X , Jiao S , et al . A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance [J ] . Microbiome , 2021 , 9 ( 1 ): 217 .

Gao C-H , Cao H , Cai P , et al . The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity [J ] . The ISME Journal , 2020 , 15 ( 1 ): 29 - 40 .

Zhou K , Qiao K , Edgar S , et al . Distributing a metabolic pathway among a microbial consortium enhances production of natural products [J ] . Nature Biotechnology , 2015 , 33 ( 4 ): 377 - 383 .

Jing J , Garbeva P , Raaijmakers J M , et al . Strategies for tailoring functional microbial synthetic communities [J ] . The ISME Journal , 2024 , 18 ( 1 ).

张理 , 李凯旋 , 马志远 , 等 . 合成微生物组在农田土壤健康调控中的研究进展 [J ] . 生物技术通报 , 2026 , 42 ( 05 ): 16 - 26 .

ZHANG Li , LI Kaixuan , MA Zhiyuan , et al . Research progress of synthetic microbiome in the regulation ofagricultural soil health [J ] . Biotechnology Bulletin , 2026 , 42 ( 05 ): 16 - 26 .

Henry L P , Bergelson J . Applying ecological principles to microbiome engineering [J ] . Nature Microbiology , 2025 , 10 ( 9 ): 2111 - 2121 .

Bernstein H C , Carlson R P . Microbial consortia engineering for cellular factories: In vitro to in silico systems [J ] . Computational and Structural Biotechnology Journal , 2012 , 3 ( 4 ): e201210017 .

Kumar C , Esposito A , Bertani I , et al . Sorghum rhizosphere bacteriome studies and generation of multistrain beneficial bacterial consortia [J ] . Microbiological Research , 2025 , 292 : 128036 .

Yin C , Hagerty C H , Paulitz T C . Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen [J ] . Frontiers in Microbiology , 2022 , 13 : 908981 .

Hao X , Wang X , Wang X , et al . Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enha nces wheat drought tolerance [J ] . Microbiome , 2026 , 14 ( 1 ): 76 .

Cheng A G , Ho P-Y , Aranda-Díaz A , et al . Design, construction, and in vivo augmentation of a complex gut microbiome [J ] . Cell , 2022 , 185 ( 19 ): 3617 - 3636.e19 .

Bai X , Li Z , Chen B , et al . High bacterial diversity drives the suppression of a soilborne plant disease [J ] . Proceedings of the National Academy of Sciences , 2026 , 123 ( 10 ): e2509303123 .

Lindemann S R , Bernstein H C , Song H-S , et al . Engineering microbial consortia for controllable outputs [J ] . The ISME Journal , 2016 , 10 ( 9 ): 2077 - 2084 .

Ceballos Rodriguez-Conde F , Zhu S , Dikicioglu D . Harnessing microbial division of labor for biomanufacturing: a review of laboratory and formal modeling approaches [J ] . Critical Reviews in Biotechnology , 2025 , 45 ( 6 ): 1249 - 1267 .

Roell G W , Zha J , Carr R R , et al . Engineering microbial consortia by division of labor [J ] . Microbial Cell Factories , 2019 , 18 ( 1 ): 35 .

Xu X , Dinesen C , Pioppi A , et al . Composing a microbial symphony: synthetic communities for promoting plant growth [J ] . Trends in Microbiology , 2025 , 33 ( 7 ): 738 - 751 .

Gallardo-Navarro O , Aguilar-Salinas B , Rocha J , et al . Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology [J ] . Heliyon , 2024 , 10 ( 14 ): e33896 .

Kamrad S , Aulakh S K , Mozzachiodi S , et al . Interspecies interactions drive bacterial proteome reorganization and emergent metabolism [J ] . Nature Ecology & Evolution , 2026 , 10 , 1127 - 1144 .

高春辉 , 杨宁 , 王创 , 等 . 有涌现性功能的合成菌群在作物育种上的应用前景 [J ] . 合成生物学 , 2024 , 5 ( 1 ): 144 - 153 .

GAO Chunhui , YANG Ning , WANG Chuang , et al . Application prospects ofsynthetic bacterial communities with emergent functions in crop breeding [J ] . Synthetic Biology Journal , 2024 , 5 ( 1 ): 144 - 153 .

Moran J , Graham L C , Tikhonov M . Emergent predictability in microbial ecosystems [J ] . Science , 2026 , 392 ( 6794 ): eadr1440 .

Northen T R , Kleiner M , Torres M , et al . Community standards and future opportunities for synthetic communities in plant-microbiota research [J ] . Nature Microbiology , 2024 , 9 ( 11 ): 2774 - 2784 .

Stenuit B , Agathos S N . Deciphering microbial community robustness through synthetic ecology and molecular systems synecology [J ] . Current Opinion in Biotechnology , 2015 , 33 : 305 - 317 .

Finkel O M , Salas-González I , Castrillo G , et al . A single bacterial genus maintains root growth in a complex microbiome [J ] . Nature , 2020 , 587 ( 7832 ): 103 - 108 .

Xu Y , Shrestha S , Sun Q , et al . Roles of microbial interactions in determining the establishment and function of synthetic consortium inoculants for soil applications [J ] . The ISME Journal , 2026 , 20 ( 1 ).

许驭丹 , 董世魁 , 李帅 , 等 . 植物群落构建的生态过滤机制研究进展 [J ] . 生态学报 , 2019 , 37 ( 7 ): 2267 - 2281 .

XU Yudan , DONG Shikui , LI Shuai , et al . Research progress on ecological filtering mechanisms for plant communityassembly [J ] . Acta Ecologica Sinica , 2019 , 37 ( 7 ): 2267 - 2281 .

Kraft N J B , Adler P B , Godoy O , et al . Community assembly, coexistence and the environmental filtering metaphor [J ] . Functional Ecology , 2015 , 29 ( 5 ): 592 - 599 .

Dooley K D , Henry L P , Bergelson J . Impact of timing on the invasion of synthetic bacterial communities [J ] . The ISME Journal , 2024 , 18 ( 1 ).

Kim J K , Chen Y , Hirning A J , et al . Long-range temporal coordination of gene expression in synthetic microbial consortia [J ] . Nature Chemical Biology , 2019 , 15 ( 11 ): 1102 - 1109 .

de Scally S Z , McDonald M J . Evolution of one species increases resistance to invasion in a simple synthetic community [J ] . Microbial Ecology , 2025 , 88 ( 1 ): 110 .

Garza Elizondo A M , del Valle Kessra I , Prates E T , et al . Building an expanded bio-based economy through synthetic biology [J ] . Biotechnology Advances , 2026 , 87 : 108775 .

曲泽鹏 , 陈沫先 , 曹朝辉 , 等 . 合成微生物群落研究进展 [J ] . 合成生物学 , 2020 , 1 ( 6 ): 621 - 634 .

QU Zepeng , CHEN Moxian , CAO Zhaohui , et al . Research advances in synthetic microbial communities [J ] . SyntheticBiology Journal , 2020 , 1 ( 6 ): 621 - 634 .

谭家霖 , 李丹宁 , 姜庚博 , 等 . 合成微生物组的理性设计与构建范式演进 [J ] . 微生物学报 , 2026 , 66 ( 04 ): 1533 - 1553 .

TAN Jialin , LI Danning , JIANG Gengbo , et al . Rational design and paradigmshifts in synthetic microbiomes [J ] . Acta Microbiologica Sinica , 2026 , 66 ( 4 ): 1533 - 1553 .

郑雷 , 郑棋腾 , 张天骄 , 等 . 构建根际合成微生物菌群促进作物养分高效吸收利用 [J ] . 合成生物学 , 2025 , 6 ( 5 ): 1058 - 1071 .

ZHENG Lei , ZHENG Qiteng , ZHANG Tianjiao , et al . Engineering rhizosphere synthetic microbial communities to enhance cropnutrient use efficiency [J ] . Synthetic Biology Journal , 2025 , 6 ( 5 ): 1058 - 1071 .

Geerdes N , de Lorimier P , Howe A , et al . Synthetic microbial communities: Bridging research and application in second-generation bioenergy feedstock microbiomes [J ] . Plant and Soil , 2025 , 517 ( 2 ): 1533 - 1561 .

Li C , Han Y , Zou X , et al . A systematic discussion and comparison of the construction methods of synthetic microbial community [J ] . Synthetic and Systems Biotechnology , 2024 , 9 ( 4 ): 775 - 783 .

Garza D R , Liu B , van de Velde C , et al . Emergence of alternative states in a synthetic human gut microbial community [J ] . Nature Communications , 2025 , 17 ( 1 ): 326 .

Finkel O M , Salas-González I , Castrillo G , et al . The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response [J ] . PLoS Biology , 2019 , 17 ( 11 ): e3000534 .

Chaturvedi H , Singh B , Jajoo A , et al . Shielding of photosynthetic apparatus by consortia of bacterial endophytes in tomato plants suffering from fusarium wilt [J ] . Frontiers in Agronomy , 2022 , Volume 4 - 2022.

Caballero-Flores G , Pickard J M , Fukuda S , et al . An enteric pathogen subverts colonization resistance by evading competition for amino acids in the gut [J ] . Cell Host & Microbe , 2020 , 28 ( 4 ): 526 - 533.e5 .

Horrocks V , King O G , Yip A Y G , et al . Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization [J ] . Microbiology , 2023 , 169 ( 8 ).

Pamer E G . Gut microbes fend off harmful bacteria by depriving them of nutrients [J ] . Nature , 2024 , 633 : 774 - 775 .

Sun Y, O'Riordan M X D : Chapter Three - Regulation of bacterial pathogenesis by intestinal short-chain fatty acids, Sariaslani S, Gadd G M, editor, Advances in Applied Microbiology: Academic Press , 2013 : 93 - 118 .

Jakobsson H E , Rodríguez‐Piñeiro A M , Schütte A , et al . The composition of the gut microbiota shapes the colon mucus barrier [J ] . EMBO Reports , 2015 , 16 ( 2 ): 164 - 177 .

Hooper L V , Littman D R , Macpherson A J . Interactions between the microbiota and the immune system [J ] . Science , 2012 , 336 ( 6086 ): 1268 - 1273 .

Zheng D , Liwinski T , Elinav E . Interaction between microbiota and immunity in health and disease [J ] . Cell Research , 2020 , 30 ( 6 ): 492 - 506 .

Huot B , Yao J , Montgomery B L , et al . Growth-defense tradeoffs in plants: A balancing act to optimize fitness [J ] . Molecular Plant , 2014 , 7 ( 8 ): 1267 - 1287 .

Sonkoly J , Kelemen A , Valkó O , et al . Both mass ratio effects and community diversity drive biomass production in a grassland experiment [J ] . Scientific Reports , 2019 , 9 ( 1 ): 1848 .

Gao W-Q , Lei X-D , Gao D-L , et al . Mass-ratio and complementarity effects simultaneously drive aboveground biomass in temperate Quercus forests through stand structure [J ] . Ecology and Evolution , 2021 , 11 ( 23 ): 16806 - 16816 .

Afzal M , Khan S , Iqbal S , et al . Inoculation method affects colonization and activity of Burkholderia phytofirmans PsJN during phytoremediation of diesel-contaminated soil [J ] . International Biodeterioration & Biodegradation , 2013 , 85 : 331 - 336 .

Suman A , Govindasamy V , Ramakrishnan B , et al . Microbial community and function-based synthetic bioinoculants: A perspective for sustainable agriculture [J ] . Frontiers in Microbiology , 2022 , Volume 12 - 2021 .

O'Callaghan M , Ballard R A , Wright D . Soil microbial inoculants for sustainable agriculture: Limitations and opportunities [J ] . Soil Use and Management , 2022 , 38 ( 3 ): 1340 - 1369 .

Bongirwar R , Shukla P . Metabolic sink engineering in cyanobacteria: Perspectives and applications [J ] . Bioresource Technology , 2023 , 379 : 128974 .

Dolfing J , Jiang B , Henstra A M , et al . Syntrophic growth on formate: a new microbial niche in anoxic environments [J ] . Applied and Environmental Microbiology , 2008 , 74 ( 19 ): 6126 - 6131 .

Hillesland K L , Stahl D A . Rapid evolution of stability and productivity at the origin of a microbial mutualism [J ] . Proceedings of the National Academy of Sciences , 2010 , 107 ( 5 ): 2124 - 2129 .

Chang C-Y , Bajić D , Vila J C C , et al . Emergent coexistence in multispecies microbial communities [J ] . Science , 2023 , 381 ( 6655 ): 343 - 348 .

Xie X , Müller N . Enhanced aniline degradation by Desulfatiglans anilini in a synthetic microbial community with the phototrophic purple sulfur bacterium Thiocapsa roseopersicina [J ] . Systematic and Applied Microbiology , 2019 , 42 ( 5 ): 125998 .

Liu Q , Wu S , Gong S , et al . Ecologically Informed design of synthetic microbial community enables robust degradation and engraftment for antibiotic removal in wastewater [J ] . Environmental Science & Technology , 2026 , 60 ( 12 ): 9367 - 9380 .

Mueller U G , Juenger T E , Kardish M R , et al . Artificial selection on microbiomes to breed microbiomes that confer salt tolerance to plants [J ] . mSystems , 2021 , 6 ( 6 ).

Wang J , Lin R , Gong J , et al . Engineering synthetic microbial communities in the crop rhizosphere to advance agricultural systems [J ] . Applied Soil Ecology , 2026 , 222 : 107003 .

林心雨 , 李超然 , 徐希辉 , 等 . 合成微生物组设计:从理论构建到环境生物修复的应用与挑战 [J ] . 生物工程学报 , 2025 , 41 ( 11 ): 4298 - 4320 .

LIN Xinyu , LI Chaoran , XU Xihui , et al . Synthetic microbiome design: applications and challenges from theoretical construction to environmental bioremediation [J ] . Chinese Journal of Biotechnology , 2025 , 41 ( 11 ): 4298 - 4320 .

Park Y-K , Peng H , Hapeta P , et al . Engineered cross-feeding creates inter- and intra-species synthetic yeast communities with enhanced bioproduction [J ] . Nature Communications , 2024 , 15 ( 1 ): 8924 .

Srinak N , Chiewchankaset P , Kalapanulak S , et al . Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters [J ] . PLoS Computational Biology , 2024 , 20 ( 10 ): e1012533 .

Wu S , Zhou Y , Dai L , et al . Assembly of functional microbial ecosystems: from molecular circuits to communities [J ] . FEMS Microbiology Reviews , 2024 , 48 ( 6 ).

Wang L , Zhang X , Tang C , et al . Engineering consortia by polymeric microbial swarmbots [J ] . Nature Communications , 2022 , 13 ( 1 ): 3879 .

Pan R , Liu S , Chen Y , et al . Biosynthesis of biobased products from lignocellulose using filamentous fungi-integrated microbial consortia [J ] . Biotechnology for Biofuels and Bioproducts , 2025 , 18 ( 1 ): 111 .

Zhou X , Wang J , Liu F , et al . Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease [J ] . Nature Communications , 2022 , 13 ( 1 ): 7890 .

Pan R , Yang X , Qiu M , et al . Construction of coculture system containing Escherichia coli with different microbial species for biochemical production [J ] . ACS Synthetic Biology , 2023 , 12 ( 8 ): 2208 - 2216 .

Luo L , Chen X , Liu B , et al . Strengthen or Weaken: Evolutionary directions of cross-feeding after formation [J ] . Environmental Microbiology Reports , 2025 , 17 ( 4 ): e70175 .

Shi X , Yang Y , Wang C , et al . Microbial risk assessment across multiple environments based on metagenomic absolute quantification with cellular internal standards [J ] . Nature Water , 2025 , 3 ( 4 ): 473 - 485 .

孙韬 , 宋洁 , 董姗姗 , 等 . 合成微生物的环境风险防控与检测技术研究进展 [J ] . 环境科学研究 , 2024 , 37 ( 10 ): 2247 - 2259 .

SUN Tao , SONG Jie , DONG Shanshan , et al . Advances in environmental risk prevention, control, and detectiontechnologies for synthetic microorganisms [J ] , Research of Environmental Sciences , 2024 , 37 ( 10 ): 2247 - 2259 .

Fuerte-Stone J , Mimee M . Advances in biocontainment strategies of engineered microbes for use in humans [J ] . Current Opinion in Microbiology , 2026 , 91 : 102727 .

Muzafar S , Nair R R , Andersson D I , et al . The strength of interspecies interaction in a microbial community determines its susceptibility to invasion [J ] . PLoS Biology , 2024 , 22 ( 11 ): e3002889 .

Ellabaan M M H , Munck C , Porse A , et al . Forecasting the dissemination of antibiotic resistance genes across bacterial genomes [J ] . Nature Communications , 2021 , 12 ( 1 ): 2435 .

Feng Y , Lu X , Zhao J , et al . Regional antimicrobial resistance gene flow among the One Health sectors in China [J ] . Microbiome , 2025 , 13 ( 1 ): 3 .

Han W , Xiao L , Sun H , et al . AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining [J ] . bioRxiv , 2025 : 2025 .07. 21 . 665674 .

Ruan Z , Chen K , Cao W , et al . Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling [J ] . Nature Communications , 2024 , 15 ( 1 ): 4694 .

Zhang H , Yuan G-H , Yuan C , et al . Lingshu-Cell: A generative cellular world model for transcriptome modeling toward virtual cells [J ] . arXiv: 2603.25240 , 2026 .

Johnson J A I , Bergman D R , Rocha H L , et al . Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories [J ] . Cell , 2025 , 188 ( 17 ): 4711 - 4733.e37 .

Bunne C , Roohani Y , Rosen Y , et al . How to build the virtual cell with artificial intelligence: Priorities and opportunities [J ] . Cell , 2024 , 187 ( 25 ): 7045 - 7063 .

Mu'azzam K , Santos da Silva F V , Murtagh J , et al . A roadmap for model-based bioprocess development [J ] . Biotechnology Advances , 2024 , 73 : 108378 .

Mariam I , Rova U , Christakopoulos P , et al . Data-driven synthetic microbes for sustainable future [J ] . npj Systems Biology and Applications , 2025 , 11 ( 1 ): 74 .

Cai Y , Wang Y , Hu S . Synthetic gene circuits enable sensing in engineered living materials [J ] . Biosensors , 2025 , 15 ( 9 ): 556 .

Sarac B , Yücer S , Ciftci F . Synthetic biology-driven biosensors for healthcare applications: A roadmap toward programmable and intelligent diagnostics [J ] . Biosensors and Bioelectronics , 2026 , 291 : 118036 .

Ma Y , Budde M W , Mayalu M N , et al . Synthetic mammalian signaling circuits for robust cell population control [J ] . Cell , 2022 , 185 ( 6 ): 967 - 979.e12 .

Miano A , Liao M J , Hasty J . Inducible cell-to-cell signaling for tunable dynamics in microbial communities [J ] . Nature Communications , 2020 , 11 ( 1 ): 1193 .

Varma S , Gulati K A , Sriramakrishnan J , et al . Environment signal dependent biocontainment systems for engineered organisms: Leveraging triggered responses and combinatorial systems [J ] . Synthetic and Systems Biotechnology , 2025 , 10 ( 2 ): 356 - 364 .

Liu H , Zhang L , Wang W , et al . An intelligent synthetic bacterium for chronological toxicant detection, biodegradation, and its subsequent suicide [J ] . Advanced Science , 2023 , 10 ( 31 ): 2304318 .

Grome M W , Nguyen M T A , Moonan D W , et al . Engineering a genomically recoded organism with one stop codon [J ] . Nature , 2025 , 639 ( 8054 ): 512 - 521 .

Ruan Z , Tan J , Feng Q , et al . Potentiators empower synthetic microbiomes as silent guardians against co-contamination [J ] . Nature Communications , 2025 : 1185 .

Views

下载量

CSCD

Alert me when the article has been cited

提交

Tools

Publicity Resources

The application of biological reverse engineering in synthetic biology

From strain resource biobanks to synthetic microbial communities： rational design， engineered assembly， and applications

Electrocatalytic CO2 reduction coupled with metabolic engineering of Yarrowia lipolytica for efficient isoprene biosynthesis

Applications of functional framework materials in C1 biotransformation

Progress in hybrid systems of biological entities and materials for low-carbon biosynthesis

Related Author

CHEN Xinmao

OUYANG Qi

LIN Hui

ZHAO Xize

JIANG He

LIU Shuangjiang

Related Institution

School of Physics, Peking University

State Key Laboratory of Microbial Technology， Shandong University

State Key Laboratory of Microbial Diversity and Innovative Utilization， Institute of Microbiology， Chinese Academy of Sciences

University of Chinese Academy of Sciences

Postal code：100011
Tel：010-64519339/9292 Email：synbioj@cip.com.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备12046843号-18 京公网安备11010102004073号
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰