Our Interests
The central question addressed by our research group is how microorganisms interact with surrounding organisms and the environment through molecules, and how these interactions ultimately influence the health of plants, animals, and humans. Our goal is to identify the molecules that are genuinely responsible for these phenomena, elucidate their biosynthetic mechanisms and biological functions, and explore strategies to enhance their application potential through rational design and engineering.
- Identify biosynthetic elements with the potential to produce novel molecules from diverse microbial resources through genomic and multi-omics approaches.
- Elucidate the biosynthetic mechanisms and ecological functions of these molecules, with a focus on how they are generated and what roles they play in nature.
- Engineer biosynthetic gene clusters and microbial chassis to achieve the stable and efficient production of target molecules, thereby supporting the discovery, optimization, and application of bioactive compounds and natural-product lead molecules.
我们关注的核心问题：微生物如何通过化学分子与周围生物及环境发生相互作用，并进一步影响动植物和人体健康。我们希望识别这些现象背后真正发挥作用的小分子，阐明它们的生物合成机制与生物学功能，并探索通过人工设计与改造提升其应用价值。
- 利用基因组数据和多组学方法，从大量微生物中挖掘具有新分子合成潜力的生物合成元件。
- 解析这些分子的生物合成过程和生态功能，回答“这个分子是如何产生的”以及“它在自然界中发挥什么作用”这两个核心问题。
- 借助合成生物学改造基因簇和底盘菌，实现目标分子的稳定、高效表达，推动活性分子和天然先导化合物的发现、优化与应用。
Recent Publications
(*corresponding author, #equal contributions)
1. Siqiang Chen, Hao Xiang, Ying Chen, Helge B. Bode, Yi-Ming Shi*
From Known Knowns to Unknown Unknowns: Synthetic Biology Paths to Antimicrobial Discovery
Curr. Opin. Microbiol. 2026, accepted.
2. Ying Chen#, Yunsheng Chen#, Hao Xiang#, Changqi Luo, Jiaqi Duan, Kun Hu, Xiaohong Zheng, Jing Liu, Yongbo Xue*, Yi-Ming Shi*
Lipid-donor-anchored genome mining uncovers dioxanopeptins, antibacterial lipopeptides with a 1,3-dioxane functionalized polyunsaturated lipid tail.
Chem. Sci. 2026, in press.
3. Edna Bode*, Julia Büllesbach#, Kevin Bauer#, Yan-Ni Shi#, Simon Reiners#, Ziheng Cui,# Petra Happel#, Yi-Ming Shi, Kevin Hoffmann, Peter Grün, Bianca Pommerenke, Uli Kazmaier, Martin Grininger, Helge B. Bode*
Pseudotetraivprolides from Pseudomonas entomophila Provide Insights into the Biosynthesis of Detoxin/Rimosamide-Like Anti-Antibiotics.
Angew. Chem. 2026, 65, e13287.
4. Wipanee Meesil, Helge B. Bode, Christian Rückert-Reed, Yi-Ming Shi, Sacha J. Pidot, Paramaporn Muangpat, Triwit Rattanarojpong, Narisara Chantratita, Sutthirat Sitthisak, Apichat Vitta, Aunchalee Thanwisai*
Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5.
Sci. Rep. 2025, 15, 23672.
5. Lena Peters#, Moritz Drechsler#, Barbara Pees, Georgia Angelidou, Liesa Salzer, Karlis Arturs Moors, Nicole Paczia, Hinrich Schulenburg, Yi-Ming Shi, Christoph Kaleta, Michael Witting, Helge B. Bode*, Katja Dierking*
Polyketide synthase-derived sphingolipids determine microbiota-mediated protection against pathogens in C. elegans.
Nat. Commun. 2025, 16, 5151.
Press release: New insights into microbiome-mediated protection against pathogens
6. Juliana Effert#; Margaretha Westphalen#; Andrea Calderari#; Yi-Ming Shi; Isam Elamri; Soumaya Najah; Peter Grün; Yanyan Li; Arnaud Gruez; Kira J. Weissman*; Helge B Bode*
Pyrrolizwilline, a unique bacterial alkaloid assembled by a nonribosomal peptide synthetase and non-enzymatic dimerization
Angew. Chem. 2024, 63, e202411258.
7. Yuyang Wang; Yan-Ni Shi; Hao Xiang; Yi-Ming Shi*
Exploring nature’s battlefield: organismic interactions in the discovery of bioactive natural products.
Nat. Prod. Rep. 2024, 41, 1630-1651. (Cover Article)
Press release: SIAT, biotrade | 生物通, ScienceNet | 科学网, Sina | 新浪
8. Zhao Xia#; Hao Xiang#; Yi-Ming Shi*
Bacterial secondary metabolites embedded in producer cell membranes and antibiotics targeting their biosynthesis.
ChemMedChem 2024, 19, e202400469.
9. Jing, S.-X.; Fu, R.; Li, C.-H.; Hugelshofer, C. L.; Shi, Y.-M.; Luo, S.-H.; Liu, Y.-C.; Liu, Y.; Li, S.-H.*
Discovery of Unusual Sesterterpenoids from Colquhounia coccinea var. mollis and Their Metabolic Implications.
J. Nat. Prod. 2023, 86, 2468-2473.
10. Meesil, W.; Muangpat, P.; Sitthisak, S.; Rattanarojpong, T.; Chantratita, N.; Machado, R. A. R.; Shi, Y.-M.; Bode, H. B.; Vitta, A.; Thanwisai, A.*
Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria.
Sci. Rep. 2023, 13, 20764.
SyM Lab 