PI

Prof. Yong-Xin Liu. He gained PhD from the University of Chinese Academy of Sciences in Bioinformatics in 2014, and then worked as a senior engineer in the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. In October 2022, he joined the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences. His research interests are metagenomic methods, food microbiome, and science communication. Participated in the QIIME 2 project, and led the development of pipeline such as EasyAmplicon, EasyMetagenome, Culturome; microbiome data analysis and visualization webserver (EVenn, ImageGP) and R packages (amplicon, ggClusterNet), with the goal of building methodological infrastructure for metagenomics and promoting microbiome development. He has published more than 40 papers in bioinformatics & microbiome field, which have been cited 10,000+ times, include 20 papers in Nature Biotechnology, Nature Microbiology, iMeta, etc. as the (co) first or corresponding author, and > 20 papers in Science, Cell Host & Microbe, Microbiome, etc. Established a public account of Meta-genome, followed by 140,000+ peers, shared more than 3,000 blogs with over 30 million readings, which is the most influential science communication platform in Chinese. One of the founders of iMeta journal, attract thousands of experts all over the world to join, which aim to be top interdisciplinary journal in metagenomics and bioinformatics.

Research Experience

2022/10 - now      Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences      Professor / Principal Investigator

2021/1 - 2022/9     Institute of Genetics and Developmental Biology, Chinese Academy of Sciences  Senior Engineer

2016/8 - 2020/12     Institute of Genetics and Developmental Biology, Chinese Academy of Sciences  Engineer

2014/7 - 2016/7     Institute of Genetics and Developmental Biology, Chinese Academy of Sciences  Postdoctoral Fellow

Education

2011/9 – 2014/6         University of Chinese Academy of Sciences         Ph.D. of Bioinformatics, Supervised by Prof. Xiu-Jie Wang

2008/9 – 2011/6         Northeast Agricultural University         Master of Crop Genetics and Breeding, Supervised by Prof. Wenbin Li

2004/9 – 2018/6         Northeast Agricultural University            Bachelor of Biotechnology & Microbiology

Research Interest

At present, our lab focuses on metagenomics methods and food microbiome. Metagenomics methods is the fundamental infrastructure for this field (Figure 1). We now working on the method optimization in sequencing library preparation, synthetic community, and sterile culture system, to provide an effective research system for revealing the function of the microbiome.

Figure 1. Metagenomics Methods. Multi-omics builds a bridge for the host to microbiome research, and reveal the interaction mechanism between the microbiome and the host.

The scientific question is about interactions among the human genome, gut microbiota, and food nutrition (Figure 2). The gut bacterial culture collection will be established, and the functional verification work will be performed in animal models and organoids to investigate the mechanism of key species and genes of the microbes in food nutrition metabolism and human health (Figure 2).

Figure 2. Interactions among human genome, gut microbiota and food nutrition. We focus on the functions and mechanisms of gut microbiota involved in food nutrition metabolism and to investigate their impacts on human health.

Selected Publication

“#” represents the co-first author, “*” represents the corresponding author, IF is the abbreviation of impact factor of Journal Citation Reports.

1. 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, https://doi.org/10.1007/s13238-020-00724-8 (IF = 15.328, Highly Cited)

2. Yong-Xin Liu, Yuan Qin & Yang Bai*. (2019). Reductionist synthetic community approaches in root microbiome research.  Current Opinion in Microbiology  49, 97-102, https://doi.org/10.1016/j.mib.2019.10.010 (IF = 7.584)

3. Wenjun Li#, Likun Wang#, Xiaofang Li*, Xin Zheng, Michael F. Cohen, Yong-Xin Liu*. 2022. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes.  Genomics Proteomics Bioinformatics https://doi.org/10.1016/j.gpb.2022.08.006 (IF = 6.409)

4. 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, https://doi.org/10.1038/s41587-019-0104-4 (IF = 68.164, Highly Cited, Hot Paper, Cover Story)

5. Sunde Xu#, Yong-Xin Liu#, Tomislav Cernava#, Hongkai Wang, Shugeng Cao, Yaqi Zhou, Gabriele Berg, Tie Xia, 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). Bacteria within the fungal fruiting-body microbiome reduce fungal infections in cereal by disrupting lipid rafts.  Nature Microbiology  7, 831-843, https://doi.org/10.1038/s41564-022-01131-x (IF = 30.964)

6. 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, https://doi.org/10.1038/s41596-020-00444-7 (IF = 17.021, Highly Cited,)

7. Yong-Xin Liu, Meng Wang & Xiu-Jie Wang*. (2014). Endogenous small RNA clusters in plants.  Genomics Proteomics Bioinformatics  12, 64-71, https://doi.org/10.1016/j.gpb.2014.04.003 (IF = 6.409)

8. Xu-Bo Qian#, Tong Chen#, Yi-Ping Xu, Lei Chen, Fu-Xiang Sun, Mei-Ping Lu* & Yong-Xin Liu. (2020). A guide to human microbiome research: study design, sample collection, and bioinformatics analysis.  Chinese Medical Journal , https://doi.org/10.1097/cm9.0000000000000871 (IF = 6.151)

9. 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, https://doi.org/10.1007/s11427-018-9284-4 (IF = 10.42, Cover Story)

10. Tong Chen, Haiyan Zhang, Yu Liu, Yong-Xin Liu*, Luqi Huang* (2021). EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online.  Journal of Genetics and Genomics , https://doi.org/10.1016/j.jgg.2021.07.007 (IF = 5.733)

11. Tao Wen#, Penghao Xie#, Shengdie Yang, Guoqing Niu, Xiaoyu Liu, Zhexu Ding, Chao Xue, Yong-Xin Liu*, Qirong Shen, Jun Yuan*. (2022). ggClusterNet: An R package for microbiome network analysis and modularity-based multiple network layouts.  iMeta  1: e32. https://doi.org/10.1002/imt2.32

12. Tong Chen, Yong-Xin Liu*, Luqi Huang*. (2022). ImageGP: An easy-to-use data visualization web server for scientific researchers.  iMeta  1: e5. https://doi.org/10.1002/imt2.5

13. Yong-Xin Liu*, Tong Chen*, Danyi Li, Jingyuan Fu*, Shuang-Jiang Liu*. (2022). iMeta: Integrated meta-omics for biology and environments.  iMeta  1: e15. https://doi.org/10.1002/imt2.15

14. Xubo Qian#, Yong-Xin Liu#, Xiaohong Ye, Wenjie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wenqin Wang, Weihan Wang, Xianning Zhang & Meiping Lu*. (2020). Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction.  BMC Genomics  21, 286, https://doi.org/10.1186/s12864-020-6703-0 (IF = 4.560)

15. Yong-Xin Liu#, Wei Chang#, Ying-peng Han, Quan Zou, Mao-zu Guo & Wen-bin Li*. (2011). In silico detection of novel microRNAs genes in soybean genome.  Agricultural Sciences in China  10, 1336-1345, https://doi.org/10.1016/S1671-2927(11)60126-0 (IF = 4.384)

16. Yong-Xin Liu, Ying-peng Han, Wei Chang, Quan Zou, Mao-zu Guo & Wen-bin Li*. (2010). Genomic analysis of microRNA promoters and their cis-acting elements in soybean.  Agricultural Sciences in China  9, 1561-1570, https://doi.org/10.1016/S1671-2927(09)60252-2 (IF = 4.384)

17. Jing Li#, Yong-Xin Liu#, Ying-peng Han, Yong-guang Li, Mao-zu Guo, Wen-bin Li*. (2013). MicroRNA primary transcripts and promoter elements analysis in soybean (Glycine max L. Merril.). J ournal of Integrative Agriculture  12, 1522-1529, https://doi.org/10.1016/S2095-3119(13)60500-6 (IF = 4.384)

18. 刘永鑫, 秦媛, 郭晓璇 & 白洋*. (2019). 微生物组数据分析方法与应用.  遗传  41, 845-826, https://doi.org/10.16288/j.yczz.19-222

19. 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, https://doi.org/10.1126/science.aau6389 (IF =" 63.798, Highly Cited)

20. 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, https://doi.org/10.1038/s41587-019-0209-9 (IF = 68.164)

21. 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.e607, https://doi.org/10.1016/j.chom.2020.03.004 (IF = 31.316)

22. Leli Wang, Qihang Liu, Yuwei Chen, Xinlei Zheng, Chuni Wang, Yining Qi, Yachao Dong, Yue Xiao, Cang Chen, Taohong Chen, Qiuyun Huang, Zongzhao Zhai, Cimin Long, Huansheng Yang, Jianzhong Li, Lei Wang, Gaihua Zhang, Peng Liao, Yong-Xin Liu, Peng Huang, Jialu Huang, Qiye Wang, Huanhuan Chu, Jia Yin & Yulong Yin. (2022). Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets.  Microbiome  10: 83, https://doi.org/s40168-022-01278-z (IF = 16.837)

23. 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, https://doi.org/10.1105/tpc.17.00809 (IF = 12.085, Highly Cited)

24. Maosheng Zheng, Nan Zhou, Shufeng Liu, Chenyuan Dang, Yong-Xin Liu, Shishi He, Yijun Zhao, Wen Liu & Xiangke Wang*. (2019). N2O and NO emission from a biological aerated filter treating coking wastewater: Main source and microbial community.  Journal of Cleaner Production  213, 365-374, https://doi.org/10.1016/j.jclepro.2018.12.182 (IF = 11.072)

25. 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, https://doi.org/10.1007/s11427-019-9521-2 (IF =" 10.42)

26. Handong Su#, Yalin Liu#, Yong‐Xin Liu, Zhenling Lv, Hongyao Li, Shaojun Xie, Zhi Gao, Junling Pang, Xiu‐Jie Wang, Jinsheng Lai & Fangpu Han*. (2016). Dynamic chromatin changes associated with de novo centromere formation in maize euchromatin.  Plant Journal  1, 1-17, https://doi.org/10.1111/tpj.13305 (IF = 7.091)

27. Jiao Xi#, Beilei Lei#, Yong-Xin Liu, Zanbo Ding, Jiaxi Liu, Tengqi Xu, Lijun Hou, Siqi Han, Xun Qian, Yongqing Ma, Quanhong Xue, Jinming Gao, Jie Gu*, James M. Tiedje*, Yanbing Lin*. (2022). Microbial community roles and chemical mechanisms in the parasitic development of  Orobanche cumana .  iMeta  1: e31. https://doi.org/10.1002/imt2.31

28. Xin Zheng#, Likun Wang#, Linhao You, Yong-Xin Liu, Michael Cohen, Siyu Tian, Wenjun Li, Xiaofang Li. (2022). Dietary licorice enhances in vivo cadmium detoxification and modulates gut microbial metabolism in mice.  iMeta  1: e7. https://doi.org/10.1002/imt2.7

29. Rong-Min Zhang, Jian Sun, Ruan-Yang Sun, Min-Ge Wang, Chao-Yue Cui, Liang-Xing Fang, Mei-Na Liao, Xiao-Qing Lu, Yong-Xin Liu, Xiao-Ping Liao, Ya-Hong Liu & Wei-Hua Chen. (2021). Source Tracking and Global Distribution of the Tigecycline Non-Susceptible tet(X).  Microbiology Spectrum  9: e01164-01121. https://doi.org/10.1128/Spectrum.01164-21 (IF = 9.043)

30. Maosheng Zheng, Shishi He, Yueqi Feng, Mingyuan Wang, Yong-Xin Liu, Chenyuan Dang, Jiawen Wang*. (2021). Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems.  Journal of Environmental Sciences  102 273-282 https://doi.org/10.1016/j.jes.2020.09.039 (IF = 6.796)

31. Zhiyao Lv, Rui Dai, Haoran Xu, Yong‐Xin 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 , https://doi.org/10.1016/j.jgg.2021.06.005  (IF = 5.733)

32. Jun Xu#, Jie-Ni Zhang#, Bo-Hui Sun, Qing Liu, Juan Ma, Qian Zhang, Yong-Xin Liu, Ning Chen* & Feng Chen*. (2021). The role of genotype and diet in shaping gut microbiome in a genetic Vitamin A deficient mouse model.  Journal of Genetics and Genomics , https://doi.org/10.1016/j.jgg.2021.08.015 (IF = 5.733)