Research Direction 1: Using microbiome data analysis, high-throughput microbial cultivation, and molecular genetics techniques, this research aims to explore the role of the rhizosphere microbiome in the growth and health of plants such as rice and Arabidopsis, as well as the potential molecular mechanisms involved.
Principal Investigator, School of Life Sciences, Peking University
Dr. Yang Bai obtained his Bachelor's and Master's degrees from Wuhan University. He then pursued his Ph.D. in plant developmental biology at the University of Cologne, Germany. In 2011, he joined the laboratory of Prof. Paul Schulze-Lefert at the Max Planck Institute for Plant Breeding Research as a postdoctoral researcher, where he focused on plant microbiome studies. His research was the first to reveal the functional redundancy between the leaf and root microbiota of Arabidopsis thaliana. In 2016, Dr. Bai joined the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, as a Principal Investigator. In 2024, he joined the School of Life Sciences of Peking University as a principal investigator.
Associate Research Fellow, School of Life Sciences, Peking University
Dr. Zhang obtained her Ph.D. from the Institute of Ecology and Environmental Sciences, Chinese Academy of Sciences. In 2016, she began her postdoctoral research at the Institute of Genetics and Developmental Biology, CAS, and was promoted to Assistant Researcher in 2019 and Associate Research Fellow in 2021. In 2025, she joined the School of Life Sciences at Peking University as Associate Research Fellow and Boya Young Scholar. She has received funding from the National Natural Science Foundation of China's Excellent Young Scientists Fund and the Young Scientist Award for Outstanding Paper from the Chinese Society of Plant Physiology and Molecular Biology, among other honors.
Juan Lin
Lab Manager
Jin-Wei Wei
Postdoc
Binglei Wang
Postdoc
Weidong Liu
Graduate Student
Quan Liu
Graduate Student
Xiaoran Yang
Graduate Student
Lin joined Bailab in February 2024, responsible for managing laboratory funding, daily reimbursements, and other administrative tasks.
Odio soluta enim quos sit asperiores rerum rerum repudiandae cum. Vel voluptatem alias qui assumenda iure et expedita voluptatem. Ratione officiis quae.
Wang joined Bailab in December 2024 to begin his postdoctoral research. His research interests lie in bioinformatics and microbial genomics, with a focus on decoding the underlying mechanisms of plant-microbiome interactions through computational analysis.
I joined the Bai Lab in 2025, focusing primarily on interactions between crops and their root microbiota under abiotic stress conditions.
Odio soluta enim quos sit asperiores rerum rerum repudiandae cum. Vel voluptatem alias qui assumenda iure et expedita voluptatem. Ratione officiis quae.
I am an incoming PhD student of the School of Life Sciences in Peking University. In 2025, I joined Bailab and participated research in bioinformatics.
Cell April 2025
Jingying Zhang#, Bing Wang#, Haoran Xu#, Weidong Liu#, Jingwei Yu#, Qiuxia Wang#, Hong Yu#, Jin-wei Wei#, Rui Dai, Jinghang Zhou, uhang He, Di Zou, Jinhua Yang, Xinwei Ban, Qingliang Hu, Xiangbing Meng, Yong-Xin Liu, Binglei Wang, 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*.
Cell March 2025
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 Schlaeppi1, Yang Bai*.
Frontiers of Agricultural Science and Engineering February 2025
Haoran Xu, Weidong Liu, Yuhang He, Di Zou, Jinghang Zhou, Jingying Zhang*, Yang Bai*.
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*.
Microbiome October 2024
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*.
Aging Cell November 2024
Limeng Liu#*, Xusheng Hao#, Yang Bai*, Ye Tian*.
Current Biology February 2024
Jingying Zhang, Haoran Xu, Yang Bai*.
Fundamental Research April 2024
Weidong Liu, Haoran Xu, Jinghang Zhou, Yuhang He, Di Zou, Yang Bai*, Jingying Zhang*.
Journal of Genetics and Genomics May 2024
Xiaochen Wang, Jingying Zhang, Xinjun Lu, Yang Bai*, Guodong Wang*.
Environmental Microbiome November 2024
Zengwei Feng, Qiuhong Liang, Qing Yao*, Yang Bai*, Honghui Zhu*.
PLoS biology November 2024
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*
Current Biology June 2023
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.
Current Opinion in Microbiology April 2023
Jingying Zhang, Weidong Liu, Jingshu Bu, Yanbing Lin, Yang Bai*.
Nature Microbiology May 2022
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*.
New Phytologist May 2022
Xuhui Deng, Na Zhang, Yuchan Li, Chengzhi Zhu, Baoyuan Qu, Hongjun Liu, Rong Li*, Yang Bai, Qirong Shen, Joana Falcao Salles.
Journal of Integrative Plant Biology January 2022
Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang*, Yang Bai*.
Soil Biology and Biochemistry March 2022
Kunkun Fan, Hannah Holland-Moritz, Corinne Walsh, Xisheng Guo, Daozhong Wang, Yang Bai, Yong-guan Zhu, Noah Fierer, Haiyan Chu.
Nature Protocols January 2021
Jingying Zhang#, Yong-Xin Liu#, Xiaoxuan Guo, Yuan Qin, Ruben Garrido-Oter*, Paul Schulze-Lefert* & Yang Bai*.
Cell Host & Microbe October 2021
Jing-Mei Qian & Yang Bai*.
Journal of Genetics and Genomics September 2021
Zhiyao Lv#, Rui Dai#, Haoran Xu#, Yongxin Liu, Bo Bai, Ying Meng, Haiyan Li, Xiaofeng Cao*, Yang Bai*, Xianwei Song*, Jingying Zhang*.
Protein Cell May 2021
YongXin Liu#*, Yuan Qin#, Tong Chen#, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai*.
ISME Communications December 2021
Pengfan Zhang, Stjin Spaepen, Yang Bai, Stephane Hacquard, Ruben Garrido-Oter.
Science China Life Sciences September 2020
Baoyuan Qu, Yuan Qin, Yang Bai*.
Plant Communications January 2020
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*.
The ISME Journal April 2020
Qin Han, Qun Ma, Yong Chen, Bing Tian, Lanxi Xu, Yang Bai*, Wenfeng Chen*, Xia Li*.
Cell Host & Microbe April 2020
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*.
Ancheng C. Huang#, Ting Jiang#, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai*, Anne Osbourn*.
Nature Biotechnology April 2019
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*.
Nature Biotechnology July 2019
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*.
PNAS May 2019
Mathias J. E. E. E. Voges, Yang Bai, Paul Schulze-Lefert, Elizabeth S. Sattely*.
Science China Life Sciences May 2019
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*.
Current Opinion in Microbiology June 2019
YongXin Liu, Yuan Qin, Yang Bai*.
Molecular Plant February 2019
Chunlei Zhang, Youming Zhang, Zhaojun Ding*, Yang Bai*.
Molecular Plant January 2019
Kabin Xie*, Liang Guo, Yang Bai, Wende Liu, Jianbing Yan, Marcel Bucher*.
Science China Life Sciences March 2018
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*.
Microbiome September 2018
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*.
Nature Plants April 2018
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.
Soil Biology and Biochemistry June 2018
Kunkun Fan, Pamela Weisenhorn, Jack A Gilbert, Yu Shi, Yang Bai, Haiyan Chu*.
The Plant Cell March 2018
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*.
Nature Methods October 2017
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*.
GigaScience October 2017
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*.
Scientific Reports October 2016
Shujuan Tian#, Jingjing Wu#, Fen Li, Jianwei Zou, Yuwen Liu, Bing Zhou, Yang Bai, Meng-Xiang Sun*.
Annual Review of Genetics September 2016
Daniel B. Müller, Christine Vogel, Yang Bai, Julia A. Vorholt*.
Nature December 2015
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*.
The Plant Journal August 2015
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.
BMC Plant Biology January 2013
Yang Bai, Prasad Vaddepalli, Lynette Fulton, Hemal Bhasin, Martin Hülskamp & Kay Schneitz.
The Plant Journal January 2010
Yang Bai, Stefanie Falk, Arp Schnittger, Marc J. Jakoby & Martin Hülskamp.
Root microbial reference genomes are crucial for metagenomic analysis and in-depth studies of crop root microbiomes. By integrating high-throughput bacterial cultivation with metagenomic sequencing, we systematically developed a comprehensive Crop Root Bacterial Genome Collection (CRBC) and Crop Root Viral Genome Collection (CRVC) from wheat, rice, maize, and Medicago.
Rui Dai, Jingying Zhang, Fang Liu, et al,. Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns. Cell. 2025
We've developed a high-throughput protocol for isolating native bacteria from plant roots, which is crucial for studying root microbiota functions related to plant growth and health. The method uses limiting dilution to ensure single bacterial strain isolation, followed by strain characterization with a two-sided barcode PCR system for pure and mixed cultures. This approach overcomes traditional isolation challenges, such as varying growth rates, and significantly increases throughput. Additionally, we created a user-friendly bioinformatics pipeline, 'Culturome', to streamline data processing.
Jingying Zhang, Yong-Xin Liu, et al,. High-throughput cultivation and identification of bacteria from the plant root microbiota. Nature Protocols. 2021
Workflow of bioinformatic analysis to identify cultivated bacteria
We integrated high-throughput bacterial cultivation with shotgun metagenomic sequencing to establish two comprehensive databases: the Crop Root Bacterial Genome Collection (CRBC) and the Crop Root Viral Genome Collection (CRVC). These collections include bacterial and viral genomes from the roots of multiple crop species. Through bioinformatic analysis of metagenomic and culture-based sequencing data, we identified 6,699 bacterial genomes and 9,736 viral genomes. Taxonomic and functional diversity analyses revealed conserved genetic characteristics of root microbiomes.
Rui Dai, Jingying Zhang, Fang Liu, et al,. Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns. Cell. 2025
Design and overview of the CRBC and CRVC
The mountain does not see me, yet I will go to meet the mountain
Jin Guang Building, Peking University
