白洋
研究领域：微生物组与宿主互作
通讯地址：北京大学金光楼620房间
电子邮件：ybai@pku.edu.cn
研究方向
白洋实验室致力于研究微生物组与宿主的良性互作机制，重点关注非模式微生物。这些非模式微生物在微生物组中占据绝大多数，与宿主形成良性互作关系，对宿主的生长与健康至关重要。然而，我们对他们的了解非常有限。实验室的研究方向主要包括：
研究方向一：运用微生物组学数据分析、微生物高通量培养和分子遗传学技术，探索根际微生物组对水稻、拟南芥等植物生长与健康所起的作用，以及其潜在的分子机制。
研究方向二：基于微生物基因组和宏基因组资源，高效挖掘微生物中尚未被发现的暗物质，探索全新的生物学过程及其在实际应用中的潜力。
研究方向三：结合微生物分子遗传学和生物信息学等方法，开发推动微生物组领域发展的关键技术。
代表性论文
1. Jingying Zhang, Weidong Liu, Binglei Wang, Qianhang Zhai, Yang Bai*. (2026). Plant microbiome regulation for sustainable agriculture. Current Opinion in Biotechnology, 98: 103444.
2. Nannan Li#*, Guoliang Li#, Xiaofang Huang#, Lige Ma#, Danning Wang#, Yu Luo#, Xulv Cao, Yantao Zhu, Jianxin Mu, Ran An, Jianhua Zhao, Yongfeng Wang, Cuiling Yang, Hao Chen, Ying Xu, Lixi Jiang, Meng Luo, Xiaodan Li, Yachen Dong, Xinping Chen, Frank Hochholdinger, Yong Jiang, Jochen C. Reif, Daojie Wang*, Yanfeng Zhang*, Yang Bai*, Peng Yu*. (2026). Large-scale multi-omics unveils host microbiome interactions driving root development and nitrogen acquisition. Nature Plants, 12: 319-336.
3. Jingying Zhang#, Bing Wang#, Haoran Xu#, Weidong Liu#, Jingwei Yu#, Qiuxia Wang#, Hong Yu#, Jinwei Wei#, Rui Dai, Jinghang Zhou, Yuhang He, Di Zou, Jinhua Yang, Xinwei Ban, Qingliang Hu, Xiangbing Meng, Bin Hu, Mingyu Wang, Peiyong Xin, Jinfang Chu, Changsheng Li, Ruben Garrido-Oter, Peng Yu, Aalt Dirk Jan van Dijk, Lemeng Dong, Harro Bouwmeester, Song Gao*, Ancheng Huang*, Chengcai Chu*, Jiayang Li*, Yang Bai*. (2025). Root Microbiota Regulates Tiller Number in Rice. Cell, 188:2521-2539.
4. Rui Dai#, Jingying Zhang#, Fang Liu#, Haoran Xu, Jing-Mei Qian, Shani Cheskis, Weidong Liu, Binglei Wang, Honghui Zhu, Lotte J. U. Pronk, Marnix H. Medema, Ronnie de Jonge, Corné M.J. Pieterse, Asaf Levy, Klaus Schlaeppi, Yang Bai*. (2025). Crop root bacterial and viral genomes unveil unexplored species and microbiome patterns. Cell,188:3152-3166.
5. Jing-Mei Qian, Kangping Li, Weidong Liu, Jingyi Zhang, Allan Wylie, Brian Arnall, Mark J. Krzmarzick, Ertao Wang, Giles E. D. Oldroyd, Yang Bai*, Feng Feng*, Jingying Zhang*. (2025). Chitooligosaccharide receptors modulate root microbiota to enhance symbiosis and growth in Medicago. Current Biology, 35: 3930-3942.
6. Haoran Xu, Weidong Liu, Yuhang He, Di Zou, Jinghang Zhou, Jingying Zhang*, Yang Bai*. (2025). Plant-root microbiota interactions in nutrient utilization. Frontiers of Agricultural Science and Engineering, 12: 16-26.
7. Shouyue Zhang#, Ao Sun#, Jing-Mei Qian#, Shuo Lin, Wenjing Xing, Yun Yang, Han-Zhou Zhu, Xin-Yi Zhou, Yan-Shuo Guo, Yun Liu, Yu Meng, Shu-Lin Jin, Wenhao Song, Cheng-Ping Li, Zhaofu Li, Shuai Jin, Jian-Hua Wang, Meng-Qiu Dong, Caixia Gao, Chunlai Chen*, Yang Bai*, Jun-Jie Gogo Liu*. (2024). Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Nature, 630: 484-492.
8. Qin Han, Guanghui Zhu, Hongmei Qiu, Mingbo Li, Jiaming Zhang, Xinying Wu, Renhao Xiao, Yan Zhang, Wei Yang, Bing Tian, Lanxi Xu, Jiayang Zhou, Yutong Li, Yueqiang Wang*, Yang Bai*, Xia Li*. (2024). Quality traits drive the enrichment of Massilia in the rhizosphere to improve soybean oil content. Microbiome, 12: 244.
9. Limeng Liu#*, Xusheng Hao#, Yang Bai*, Ye Tian*. (2024). The soil Mycobacterium sp. promotes health and longevity through different bacteria-derived molecules in Caenorhabditis elegans. Aging Cell, 00, e14416.
10. Jingying Zhang, Haoran Xu, Yang Bai*. (2024). Root microbiota: Connecting nitrogen metabolism and theanine synthesis in tea plants. Current Biology, 34: 135-137.
11. Weidong Liu, Haoran Xu, Jinghang Zhou, Yuhang He, Di Zou, Yang Bai*, Jingying Zhang*. (2024). The plant microbiota: From theoretical advances to applications.
12. Xiaochen Wang, Jingying Zhang, Xinjun Lu, Yang Bai*, Guodong Wang*. (2024). Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. Journal of Genetics and Genomics, 51: 467-478.
13. Zengwei Feng, Qiuhong Liang, Qing Yao*, Yang Bai*, Honghui Zhu*. (2024). The role of the rhizobiome recruited by root exudates in plant disease resistance: current status and future directions. Environmental Microbiome, 19:91
14. Lanxiang Wang, Yue Liu, Haoran Ni, Wenlong Zuo, Haimei Shi, Weixin Liao, Hongbin Liu, Jiajia Chen, Yang Bai, Hong Yue, Ancheng Huang, Jonathan Friedman, Tong Si, Yinggao Liu, Moxian Chen, Lei Dai*. (2024). Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid. PLoS biology, 22: e3002921.
15. Yanjun Li, Cunhu Wang, Lei Zheng, Wenjing Ma, Mingjia Li, Zilong Guo, Qingsong Zhao, Kefei Zhang, Ran Liu, Yucheng Liu, Zhixi Tian, Yang Bai, Yongjia Zhong, Hong Liao. (2023). Natural variation of GmRj2/Rfg1 determines symbiont differentiation in soybean. Current Biology, 33:2478-2490.e5.
16. Jingying Zhang, Weidong Liu, Jingshu Bu, Yanbing Lin, Yang Bai*. (2023). Host genetics regulate the plant microbiome. Current Opinion in Microbiology, 72:102268.
17. Sunde Xu#, Yong-Xin Liu#, Tomislav Cernava#, Hongkai Wang, Yaqi Zhou, Tie Xia, Shugeng Cao, Gabriele Berg, Xing-Xing Shen, Ziyue Wen, Chunshun Li, Baoyuan Qu, Hefei Ruan, Yunrong Chai, Xueping Zhou, Zhonghua Ma, Yan Shi, Yunlong Yu*, Yang Bai*, Yun Chen*. (2022). Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts. Nature Microbiology, 7: 831-843.
18. Xuhui Deng, Na Zhang, Yuchan Li, Chengzhi Zhu, Baoyuan Qu, Hongjun Liu, Rong Li*, Yang Bai, Qirong Shen, Joana Falcao Salles. (2022). Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities. New Phytologist, 235: 1558-1574.
19. Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang*, Yang Bai*. (2022). The root microbiome: Community assembly and its contributions to plant fitness. Journal of Integrative Plant Biology, 64: 230-243.
20. Kunkun Fan, Hannah Holland-Moritz, Corinne Walsh, Xisheng Guo, Daozhong Wang, Yang Bai, Yong-guan Zhu, Noah Fierer, Haiyan Chu. (2022). Identification of the rhizosphere microbes that actively consume plant-derived carbon. Soil Biology and Biochemistry, 166: 108577.
21. Jingying Zhang#, Yong-Xin Liu#, Xiaoxuan Guo, Yuan Qin, Ruben Garrido-Oter*, Paul Schulze-Lefert*, Yang Bai*. (2021). High-throughput cultivation and identification of bacteria from the plant root microbiota. Nature Protocols, 16: 988-1012.
22. Jing-Mei Qian & Yang Bai*. (2021). Stuck on you: Bacterial-auxin-mediated bacterial colonization of plant roots. Cell Host & Microbe, 29: 1471-1473.
23. Zhiyao Lv#, Rui Dai#, Haoran Xu#, Yongxin Liu, Bo Bai, Ying Meng, Haiyan Li, Xiaofeng Cao*, Yang Bai*, Xianwei Song*, Jingying Zhang*. (2021). The rice histone methylation regulates hub species of the root microbiota. Journal of Genetics and Genomics, 48: 836-843.
24. Yong-Xin Liu#*, Yuan Qin#, Tong Chen#, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai*. (2021). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell, 12: 315-330.
25. Pengfan Zhang, Stjin Spaepen, Yang Bai, Stephane Hacquard, Ruben Garrido-Oter. (2021). Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME Communications, 1: 73.
26. Baoyuan Qu, Yuan Qin, Yang Bai*. (2020). From signaling to function: how strigolactones regulate plant development. Science China Life Sciences, 63: 1768-1770.
27. Xiaoxuan Guo#, Xiaoning Zhang#, Yuan Qin#, Yong-Xin Liu, Jingying Zhang, Na Zhang, Kun Wu, Baoyuan Qu, Zishan He, Xin Wang, Xinjian Zhang, Stéphane Hacquard, Xiangdong Fu*, Yang Bai*. (2020). Host-associated quantitative abundance profiling reveals the microbial load variation of root microbiome. Plant Communications, 1: 100003.
28. Qin Han, Qun Ma, Yong Chen, Bing Tian, Lanxi Xu, Yang Bai*, Wenfeng Chen*, Xia Li*. (2020). Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. The ISME Journal, 14: 1915-1928.
29. Wei Wang#, Jing Yang#, Jian Zhang, Yong-Xin Liu, Caiping Tian, Baoyuan Qu, Chulei Gao, Peiyong Xin, Shujing Cheng, Wenjing Zhang, Pei Miao, Lei Li, Xiaojuan Zhang, Jinfang Chu, Jianru Zuo, Jiayang Li, Yang Bai, Xiaoguang Lei*, Jian-Min Zhou*. (2020). An Arabidopsis secondary metabolite directly targets expression of the bacterial type III secretion system to inhibit bacterial virulence. Cell Host & Microbe, 27: 601-613.
30. Ancheng C. Huang#, Ting Jiang#, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai*, Anne Osbourn*. (2019). A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science, 364: eaau6389.
31. Jingying Zhang#, Yong-Xin Liu#, Na Zhang#, Bin Hu#, Tao Jin#, Haoran Xu, Yuan Qin, Pengxu Yan, Xiaoning Zhang, Xiaoxuan Guo, Jing Hui, Shouyun Cao, Xin Wang, Chao Wang, Hui Wang, Baoyuan Qu, Guangyi Fan, Lixing Yuan, Ruben Garrido-Oter, Chengcai Chu*, Yang Bai*. (2019). NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature Biotechnology, 37: 676-684.
32. Evan Bolyen#, Jai Ram Rideout#, Matthew R. Dillon#, Nicholas A. Bokulich#, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K. Cope, Ricardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G. I. Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey V. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J. J. van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H. D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J. Gregory Caporaso*. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37: 852-857.
33. Mathias J. E. E. E. Voges, Yang Bai, Paul Schulze-Lefert, Elizabeth S. Sattely*. (2019). Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. PNAS. 116: 12558-12565.
34. Qingwen Chen#, Ting Jiang#, Yong-Xin Liu, Haili Liu, Tao Zhao, Zhixi Liu, Xiaochao Gan, Asis Hallab, Xuemei Wang, Juan He, Yihua Ma, Fengxia Zhang, Tao Jin, M.Eric Schranz, Yong Wang, Yang Bai*, Guodong Wang*. (2019). Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota. Science China Life Sciences, 62: 947-958.
35. Yong-Xin Liu, Yuan Qin, Yang Bai*. (2019). Reductionist synthetic community approaches in root microbiome research. Current Opinion in Microbiology, 49: 97-102.
36. Chunlei Zhang, Youming Zhang, Zhaojun Ding*, Yang Bai*. (2019). Contribution of microbial inter-kingdom balance to plant health. Molecular Plant, 12: 148-149.
37. Kabin Xie*, Liang Guo, Yang Bai, Wende Liu, Jianbing Yan, Marcel Bucher*. (2019). Microbiomics and plant health: an interdisciplinary and international workshop on the plant microbiome. Molecular Plant, 12: 1-3.
38. Jingying Zhang#, Na Zhang#, Yong-Xin Liu#, Xiaoning Zhang, Bin Hu, Yuan Qin, Haoran Xu, Hui Wang, Xiaoxuan Guo, Jingmei Qian, Wei Wang, Pengfan Zhang, Tao Jin*, Chengcai Chu*, Yang Bai*. (2018). Root microbiota shift in rice correlates with resident time in the field and developmental stage. Science China Life Sciences, 61: 613-621.
39. Jun Yuan, Jun Zhao, Tao Wen, Mengli Zhao, Rong Li, Pim Goossens, Qiwei Huang, Yang Bai, Jorge M. Vivanco, George A. Kowalchuk, Roeland L. Berendsen, Qirong Shen*. (2018). Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome, 6: 156.
40. Hirokazu Toju*, Kabir G. Peay, Masato Yamamichi, Kazuhiko Narisawa, Kei Hiruma, Ken Naito, Shinji Fukuda, Masayuki Ushio, Shinji Nakaoka, Yusuke Onoda, Kentaro Yoshida, Klaus Schlaeppi, Yang Bai, Ryo Sugiura, Yasunori Ichihashi, Kiwamu Minamisawa, E. Toby Kiers. (2018). Core microbiomes for sustainable agroecosystems. Nature Plants, 4: 247-257.
41. Kunkun Fan, Pamela Weisenhorn, Jack A Gilbert, Yu Shi, Yang Bai, Haiyan Chu*. (2018). Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields. Soil Biology and Biochemistry, 121: 185-192.
42. Wei Wang#, Bin Hu#, Dingyang Yuan, Yongqiang Liu, Ronghui Che, Yingchun Hu, Shujun Ou, Zhihua Zhang, Hongru Wang, Hua Li, Zhimin Jiang, Zhengli Zhang, Xiaokai Gao, Yahong Qiu, Xiangbing Meng, Yong-Xin Liu, Yang Bai, Yan Liang, Yi-Qin Wang, Lianhe Zhang, Legong Li, Sodmergen Sodmergen, Hai-Chun Jing, Jiayang Li, Chengcai Chu*. (2018). Expression of the nitrate transporter gene OsNRT1.1A/OsNPF6.3 confers high yield and early maturation in rice. The Plant Cell, 30: 638-651.
43. Alexander Sczyrba#*, Peter Hofmann#, Peter Belmann#, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvočiūtė, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael D. Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy*. (2017). Critical assessment of metagenome interpretation—a benchmark of metagenomics software. Nature Methods, 14: 1063.
44. Tao Jin#, Yayu Wang#, Yueying Huang#, Jin Xu#, Pengfan Zhang, Nian Wang, Xin Liu, Haiyan Chu, Guang Liu, Honggang Jiang, Yuzhen Li, Jing Xu, Karsten Kristiansen, Liang Xiao, Yunzeng Zhang, Gengyun Zhang, Guohua Du, Houbao Zhang, Hongfeng Zou, Haifeng Zhang, Zhuye Jie, Suisha Liang, Huijue Jia, Jingwang Wan, Dechun Lin, Jinying Li, Guangyi Fan, Huanming Yang, Jian Wang, Yang Bai*, Xun Xu*. (2017). Taxonomic structure and functional association of foxtail millet root microbiome. GigaScience, 6: 1-12.
45. Shujuan Tian#, Jingjing Wu#, Fen Li, Jianwei Zou, Yuwen Liu, Bing Zhou, Yang Bai, Meng-Xiang Sun*. (2016). NtKRP, a kinesin-12 protein, regulates embryo/seed size and seed germination via involving in cell cycle progression at the G2/M transition. Scientific Reports, 6: 35641.
46. Daniel B. Müller, Christine Vogel, Yang Bai, Julia A. Vorholt*. (2016). The plant microbiota: systems-level insights and perspectives. Annual Review of Genetics, 50: 211-234.
47. Yang Bai#, Daniel Müller#, Girish Srinivas#, Ruben Garrido-Oter#, Eva Potthoff, Matthias Rott, Nina Dombrowski, Philipp Münch, Stijn Spaepen, Mitja Remus-Emsermann, Bruno Hüttel, Alice McHardy, Julia Vorholt*, Paul Schulze-Lefert*. (2015). Functional overlap of the Arabidopsis leaf and root microbiota. Nature, 528: 364-369.
48. Christos Zamioudis, Jolanda Korteland, Johan A. Van Pelt, Muriël van Hamersveld, Nina Dombrowski, Yang Bai, Johannes Hanson, Marcel C. Van Verk, Hong-Qing Ling, Paul Schulze-Lefert & Corné M. J. Pieterse. (2015). Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses. The Plant Journal, 84: 309-322.
49. Yang Bai, Prasad Vaddepalli, Lynette Fulton, Hemal Bhasin, Martin Hülskamp & Kay Schneitz. (2013). ANGUSTIFOLIA is a central component of tissue morphogenesis mediated by the atypical receptor-like kinase STRUBBELIG. BMC Plant Biology, 13: 16.
50. Yang Bai, Stefanie Falk, Arp Schnittger, Marc J. Jakoby & Martin Hülskamp. (2010). Tissue layer specific regulation of leaf length and width in Arabidopsis as revealed by the cell autonomous action of ANGUSTIFOLIA. The Plant Journal 61: 191-199.
