Welcome to Bailab

Bailab is dedicated to studying the mechanisms of beneficial interactions between the microbiome and plant hosts, with a focus on non-model microorganisms. These non-model microorganisms make up the vast majority of the microbiome and form mutually beneficial relationships with the host, which are crucial for the host's growth and health. However, our understanding of them is still very limited.

Research Focus

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.

Research Direction 2: Based on microbial genomics and metagenomics resources, this research aims to efficiently uncover undiscovered "dark matter" within microorganisms, explore novel biological processes, and investigate their potential in practical applications.

Research Direction 3: By combining microbial molecular genetics, bioinformatics, and other methods, this research aims to develop key technologies that will drive the advancement of the microbiome field.

Members

Publications

Jingying Zhang, Weidong Liu, Binglei Wang, Qianhang Zhai, Yang Bai*.

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*.

Yaqi Zhou, Hongkai Wang, Jiaxin Sun, Wisnu Adi Wicaksono, Chao Liu, Yinghao He, Yuxuan Qin, Gabriele Berg, Lei Li, Houwen Lin, Yunrong Chai, Yang Bai, Zhonghua Ma, Tomislav Cernava, Yun Chen*.

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*.

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*.

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*.

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*.

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*.

Limeng Liu#*, Xusheng Hao#, Yang Bai*, Ye Tian*.

Jingying Zhang, Haoran Xu, Yang Bai*.

Weidong Liu, Haoran Xu, Jinghang Zhou, Yuhang He, Di Zou, Yang Bai*, Jingying Zhang*.

Xiaochen Wang, Jingying Zhang, Xinjun Lu, Yang Bai*, Guodong Wang*.

Zengwei Feng, Qiuhong Liang, Qing Yao*, Yang Bai*, Honghui Zhu*.

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*

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.

Jingying Zhang, Weidong Liu, Jingshu Bu, Yanbing Lin, Yang Bai*.

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*.

Xuhui Deng, Na Zhang, Yuchan Li, Chengzhi Zhu, Baoyuan Qu, Hongjun Liu, Rong Li*, Yang Bai, Qirong Shen, Joana Falcao Salles.

Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang*, Yang Bai*.

Kunkun Fan, Hannah Holland-Moritz, Corinne Walsh, Xisheng Guo, Daozhong Wang, Yang Bai, Yong-guan Zhu, Noah Fierer, Haiyan Chu.

Jingying Zhang#, Yong-Xin Liu#, Xiaoxuan Guo, Yuan Qin, Ruben Garrido-Oter*, Paul Schulze-Lefert* & Yang Bai*.

Jing-Mei Qian & Yang Bai*.

Zhiyao Lv#, Rui Dai#, Haoran Xu#, Yongxin Liu, Bo Bai, Ying Meng, Haiyan Li, Xiaofeng Cao*, Yang Bai*, Xianwei Song*, Jingying Zhang*.

YongXin Liu#*, Yuan Qin#, Tong Chen#, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai*.

Pengfan Zhang, Stjin Spaepen, Yang Bai, Stephane Hacquard, Ruben Garrido-Oter.

Baoyuan Qu, Yuan Qin, Yang Bai*.

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*.

Qin Han, Qun Ma, Yong Chen, Bing Tian, Lanxi Xu, Yang Bai*, Wenfeng Chen*, Xia Li*.

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*.

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*.

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*.

Mathias J. E. E. E. Voges, Yang Bai, Paul Schulze-Lefert, Elizabeth S. Sattely*.

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*.

YongXin Liu, Yuan Qin, Yang Bai*.

Chunlei Zhang, Youming Zhang, Zhaojun Ding*, Yang Bai*.

Kabin Xie*, Liang Guo, Yang Bai, Wende Liu, Jianbing Yan, Marcel Bucher*.

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*.

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*.

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.

Kunkun Fan, Pamela Weisenhorn, Jack A Gilbert, Yu Shi, Yang Bai, Haiyan Chu*.

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*.

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*.

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*.

Shujuan Tian#, Jingjing Wu#, Fen Li, Jianwei Zou, Yuwen Liu, Bing Zhou, Yang Bai, Meng-Xiang Sun*.

Daniel B. Müller, Christine Vogel, Yang Bai, Julia A. Vorholt*.

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*.

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.

Yang Bai, Prasad Vaddepalli, Lynette Fulton, Hemal Bhasin, Martin Hülskamp & Kay Schneitz.

Yang Bai, Stefanie Falk, Arp Schnittger, Marc J. Jakoby & Martin Hülskamp.

Resource

Crop Microbiome

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

Crop Microbiome Website

CRVC

9,736 Genomes
7,653 Species
3,097 Genus

Pipelines

Culturome analysis

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

Culturome analysis pipeline

Workflow of bioinformatic analysis to identify cultivated bacteria

CRBC and CRVC Workflow

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

CRBC and CRVC

Design and overview of the CRBC and CRVC

Lab News

Select a news item to view details.

地图加载中...

No.5, Yiheyuan Road, Haidian District, Beijing

rootmicrobiome@pku.edu.cn

010-62758611

Let's Talk