Publications

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*co-first author, #co-corresponding author, LD Lab members

Selected highlights

• Exploring functional insights into the human gut microbiome via the structural proteome. Hongbin Liu*, Juntao Shen*, Zhiwei Zhang* , Jiuming Wang*, Chengxin Zhang*, Linggang Zheng, Haoran Ni, Liang Hong, Jieqiong Zhang, Dongfang Xue, Jiayang Chen, Qinze Yu, Zepeng Qu, Yingfei Ma, Tong Si, Liangzhen Zheng, Sheng Wang, Changtao Jiang, Yu Li^#, Kai Wang^#, Lei Dai^#. Cell Host & Microbe (2026)
• Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models.Qinze Yu*, Hongbin Liu*, Haimei Shi*, Yerzhan Abdrakhmanov, Junbo Shen, Chunhe Zhang, Zhihang Dong, Licheng Zong, Longlong Si, Lei Dai^#, Yu Li^#. Nature Biomedical Engineering (2026)
• Data-driven prediction of colonization outcomes for complex microbial communities. Lu Wu* , Xu-Wen Wang* , Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu^# , Lei Dai^#. Nature Communications (2024)
• Spatial profiling of microbial communities by sequential FISH with error-robust encoding Zhaohui Cao*, Wenlong Zuo*, Lanxiang Wang, Junyu Chen, Zepeng Qu, Fan Jin, Lei Dai. Nature Communications (2023)
• Large-scale phage cultivation for commensal human gut bacteria. Juntao Shen, Jieqiong Zhang, Luofei Mo, Yanchen Li, Yake Li, Cun Li, Xiaoxian Kuang, Zining Tao, Zepeng Qu, Lu Wu, Junyu Chen, Shiying Liu, Linfang Zeng, Zexi He, Zuohong Chen, Yu Deng, Tong Zhang, Bing Li, Lei Dai#, Yingfei Ma#. Cell Host & Microbe (2023)

LD Lab publications (full list)

Preprint

• Discovery of potent inhibitors of rumen methane metabolism via an AI-assisted workflow. Xiong Xia*, Liangzhen Zheng*, Jinjie Zhou*, Haoran Ni, Guoliang Zhu, Hongbin Liu, Ruiyue Chen, Haimei Shi, Huizeng Sun, Meng Li^#, Sheng Wang^#, Lei Dai^#. LangTaoSha Preprint Server
• Deciphering the Functional Landscape of Microbiome-Mediated Invasion Resistance to Plant Pathogens. Wenlong Zuo* , Lanxiang Wang* , Yang Bai, Jonathan Friedman, Yang-Yu Liu^# , Lei Dai^#. LangTaoSha Preprint Server
• Targeted genomic editing of human gut Bacteroides species based on CRISPR-associated transposases. Yucan Hu*, Qingmei Li*, Yingying Li, Yu Zeng, Linggang Zheng, Juntao Shen, Xiang Gao, Guo-Ping Zhao, Wei Zhao^#, Lei Dai^#. LangTaoSha Preprint Server

2026

• Spatial mapping of microbial communities by an integrated automation platform of sequential FISH. Zhaohui Cao, Wenlong Zuo, Lanxiang Wang, Lei Dai. Cell Reports Methods (2026)
• Systematic profiling of human gut bacteria with cyclic di-AMP secretion to enhance anti-tumor immunity. Linggang Zheng*, Jumin Huang*, Haoran Ni, Xiaoxian Kuang, Jin Liao, Zepeng Qu, Hongbin Liu, Chen Huang, Lili Yu, Lei Dai^#, Elaine Lai-Han Leung^# . Journal of Advanced Research (2026)
• Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models. Qinze Yu*, Hongbin Liu*, Haimei Shi*, Yerzhan Abdrakhmanov, Junbo Shen, Chunhe Zhang, Zhihang Dong, Licheng Zong, Longlong Si, Lei Dai^#, Yu Li^#. Nature Biomedical Engineering (2026)
• Exploring functional insights into the human gut microbiome via the structural proteome. Hongbin Liu* , Juntao Shen*, Zhiwei Zhang* , Jiuming Wang*, Chengxin Zhang*, Linggang Zheng, Haoran Ni, Liang Hong, Jieqiong Zhang, Dongfang Xue, Jiayang Chen, Qinze Yu, Zepeng Qu, Yingfei Ma, Tong Si, Liangzhen Zheng, Sheng Wang, Changtao Jiang, Yu Li^#, Kai Wang^#, Lei Dai^#. Cell Host & Microbe (2025) featured on the Cover
  • Preview: Illuminating the functional dark matter of the gut microbiome
  • Human Gut Microbial Protein Structure Database (GMPS): https://gmpsdb.cn/

2025

• Profiling the heterogeneity of microbial populations and communities at the single-cell level (Review). Lu Wu* , Wenlong Zuo*, Zhaohui Cao, Zepeng Qu, Lei Dai. mLife (2025)
• Development of a miniaturized CRISPR/Cas gene editing tool for human gut Bacteroides (in Chinese). 肠道拟杆菌小型CRISPR/Cas基因编辑工具的开发 Yiwen Zhan*, Linggang Zheng*, Juntao Shen, Yucan Hu, Xuegang Luo^# , Lei Dai^#. Chinese Journal of Biotechnology 生物工程学报 (2025)
• Longitudinal profiling of the human gut microbiome reveals temporal and personalized responses to inulin. Lu Wu* , Hong-Bin Liu* , Xu-Wen Wang, Zi-Ning Tao, Ze-Peng Qu, Chao-Bi Lei, Yang-Yu Liu^# , Lei Dai^# . iMetaOmics (2025)
• Skin microbiome engineering: challenges and opportunities in skin diseases treatment (Review). Yi-Ang Lyu* , Juntao Shen*, You Che, Lei Dai. iMetaOmics (2025)
• Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species. Zepeng Qu*, Hongbin Liu*, Ji Yang*, Linggang Zheng, Jumin Huang, Ziming Wang, Chun Xie, Wenlong Zuo, Xiong Xia, Lin Sun, Yifa Zhou, Ying Xie, Jingguang Lu, Yizhun Zhu, Lili Yu, Lihua Liu, Hua Zhou^#, Lei Dai^# , Elaine Lai-Han Leung^# . Nature Communications (2025)
• Applications of bacteriophages in precision engineering of the human gut microbiome (Review). Xiaoxian Kuang*, Juntao Shen*, Linggang Zheng, Yi Duan, Yingfei Ma, Elaine Lai-Han Leung, Lei Dai. Engineering Microbiology (2025)

2024

• Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid. 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^#. PLOS Biology (2024)
• Assembly of functional microbial ecosystems: from molecular circuits to communities (Review). Shengbo Wu, Yongsheng Zhou, Lei Dai^#, Aidong Yang^#, Jianjun Qiao^#. FEMS Microbiology Reviews (2024)
• Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria. Junbo Tang*, Wenlong Zuo*, Lizhen Guo, Zhihao Han, Chengfeng Yang, Benfeng Han, Lei Dai^#, Xue Zhang^#, Xin Zhou^#. Nature Communications (2024)
• Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes. Chen Liao*, Thierry Rolling*, …, Hongbin Liu, …, Lei Dai, … Tobias M. Hohl, Joao B. Xavier. Nature Microbiology (2024)
• Data-driven prediction of colonization outcomes for complex microbial communities. Lu Wu* , Xu-Wen Wang* , Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu^# , Lei Dai^#. Nature Communications (2024)
• Bile acids modified by the intestinal microbiota promote colorectal cancer growth by suppressing CD8+ T cell effector functions. Jingjing Cong, Pianpian Liu, Zili Han, … Juntao Shen, …, Lei Dai, Linfeng Sun, Wen Pan, Shu Zhu. Immunity (2024)
• Genome engineering of the human gut microbiome (Review). Linggang Zheng*, Juntao Shen*, Ruiyue Chen, Yucan Hu, Wei Zhao, Elaine Lai-Han Leung^#, Lei Dai^# . Journal of Genetics & Genomics (2024)

2023

• Oral magnesium prevents acetaminophen-induced acute liver injury by modulating microbial metabolism. Dongping Li, Yu Chen, Meijuan Wan, Fengyi Mei, Fangzhao Wang , …, Hongbin Liu, Lei Dai, …, Yong Jiang, Qiang Ma, Peng Chen. Cell Host & Microbe (2023)
• Identifying keystone species in microbial communities using deep learning. Xu-Wen Wang, Zheng Sun, Huijue Jia, Sebastian Michel-Mata, Marco Tulio Angulo, Lei Dai, Xuesong He, Scott T. Weiss, Yang-Yu Liu. Nature Ecology & Evolution (2023)
• Applications of CRISPR-Cas Technologies in Microbiome Engineering (Review, in Chinese). CRISPR⁃Cas基因编辑技术在微生物组工程中的应用. Yucan Hu, Zhaohui Cao, Linggang Zheng, Juntao Shen, Wei Zhao, Lei Dai. Chem. J. Chinese Universities (2023)
• Large-scale phage cultivation for commensal human gut bacteria. Juntao Shen, Jieqiong Zhang, Luofei Mo, Yanchen Li, Yake Li, Cun Li, Xiaoxian Kuang, Zining Tao, Zepeng Qu, Lu Wu, Junyu Chen, Shiying Liu, Linfang Zeng, Zexi He, Zuohong Chen, Yu Deng, Tong Zhang, Bing Li, Lei Dai^# , Yingfei Ma^#. Cell Host & Microbe (2023)
• Amelioration of colitis by a gut bacterial consortium producing anti-inflammatory secondary bile acids Chunhua Zhou, Ying Wang, Cun Li, Zhiyong Xie^#, Lei Dai^#. Microbiology Spectrum (2023)
• Spatial profiling of microbial communities by sequential FISH with error-robust encoding Zhaohui Cao*, Wenlong Zuo*, Lanxiang Wang, Junyu Chen, Zepeng Qu, Fan Jin, Lei Dai. Nature Communications (2023)
• Ecological dynamics imposes fundamental challenges in community-based microbial source tracking Xu-Wen Wang, Lu Wu, Lei Dai, Xiaole Yin, Tong Zhang, Scott T. Weiss, Yang-Yu Liu. iMeta (2023)
• Microbiome-mediated signal transduction within the plant holobiont (Review) Jian-HongLi, Mehtab Muhammad Aslam, Yang-Yang Gao, Lei Dai, Ge-FeiHao, ZhongWei, Mo-XianChen, Francisco Dini-Andreote. Trends in Microbiology (2023)

2022

• Multifaceted roles of flavonoids mediating plant-microbe interactions (Review) Lanxiang Wang*, Moxian Chen*, Pui-Ying Lam, Francisco Dini-Andreote, Lei Dai^# , Zhong Wei^#. Microbiome (2022)
• StrainPanDA: linked reconstruction of strain composition and gene contents from metagenomic data Han Hu*, Yuxiang Tan*, Chenhao Li*, Junyu Chen, Yan Kou, Zhenjiang Zech Xu, Yang-Yu Liu, Yan Tan^# , Lei Dai^# . iMeta (2022)
• Profiling of d-alanine production by the microbial isolates of rat gut microbiota Cindy J. Lee*, Tian A. Qi*, Zhilai Hong*, Zhenkun Zhang, Yuhao Min, ,Linzixuan Zhang, Lei Dai, Huimin Zhao, Tong Si^# , Jonathan V. Sweedler^#. FASEB Journal (2022)
• Ecological dynamics of the gut microbiome in response to dietary fiber
  Hongbin Liu*, Chen Liao*, Lu Wu, Jinhui Tang, Junyu Chen, Chaobi Lei, Linggang Zheng, Chenhong Zhang, Yang-Yu Liu, Joao Xavier, Lei Dai. The ISME Journal (2022)
• Biosynthesis of Gut-Microbiota-Derived Lantibiotics Reveals a Subgroup of S8 Family Proteases for Class III Leader Removal
  Yingying Zhang*, Zhilai Hong*, Liang Zhou*, Zhenkun Zhang, Ting Tang, Erpeng Guo, Jie Zheng, Ciji Wang, Lei Dai, Tong Si^#, Huan Wang^#. Angewandte Chemie (2022)
• CRISPR/Cas-based genome editing for human gut commensal Bacteroides species
  Linggang Zheng*, Yang Tan*, Yucan Hu, Juntao Shen, Zepeng Qu, Xianbo Chen, Chun Loong Ho, Elaine Lai-Han Leung, Wei Zhao, Lei Dai. ACS Synthetic Biology (2022)

2021

• Establishment and resilience of transplanted gut microbiota in aged mice Ying Wang*, Jinhui Tang*, Qingqing Lv, Yuxiang Tan, Xiaoxiao Dong, Hongbin Liu, Nannan Zhao, Zhen He, Yan Kou, Yan Tan, Xin-an Liu, Liping Wang, Yang-Yu Liu, Lei Dai. iScience (2021)
• Microbiota in mesenteric adipose tissue from Crohn’s disease promote colitis in mice
  Zhen He, Jinjie Wu, Junli Gong, …, Lei Dai, Min Zhi, Xiaojian Wu, Christian Jobin, Ping Lan. Microbiome (2021)
• Living fabrication of functional semi-interpenetrating polymeric materials
  Zhuojun Dai, Xiaoyu Yang, Feilun Wu, Lihua Wang, Kun Xiang, Pengcheng Li, Qingqing Lv, Jinhui Tang, Anders Dohlman, Lei Dai, Xiling Shen, Lingchong You. Nature Communications (2021)
• Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants
  Yu Deng, Yue Huang, You Che, Yu Yang, Xiaole Yin, Aixin Yan, Lei Dai, Yang-Yu Liu, Martin Polz, Tong Zhang. The ISME Journal (2021)
• Evaluation of the Anti-Inflammatory and Anti-Oxidative Effects of Therapeutic Human Lactoferrin Fragments
  Yu Pan, Zhao Liu, Yijie Wang, Linshen Zhang, Niying Chua, Lei Dai, Jun Chen, Chun Loong Ho. Frontiers in Bioengineering and Biotechnology (2021)
• Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath
  Tie‐Yuan Liu, Nenghui Ye, Xinyu Wang, Debatosh Das, Yuxiang Tan, Xiangkai You, Mingxiu Long, Tianming Hu, Lei Dai, Jianhua Zhang, Mo‐Xian Chen. Journal of Integrative Plant Biology (2021)
• Accelerating strain engineering in biofuel research via build and test automation of synthetic biology (Review) Jianzhi Zhang, Yongcan Chen, Lihao Fu, Erpeng Guo, Bo Wang, Lei Dai, Tong Si. Current Opinion in Biotechnology (2021)

2020

• Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data Yan Kou, Xiaomin Xu, Zhengnong Zhu, Lei Dai^# , Yan Tan^#. Scientific Reports (2020)
• Engineered Live Biotherapeutics: Progress and Challenges (Review) Yang Tan, Juntao Shen, Tong Si, Chun Loong Ho, Yinqing Li, Lei Dai. Biotechnology Journal (2020)
• Advances in Bacterial Biofilm Management for Maintaining Microbiome Homeostasis (Review) Zhao Liu, Can‐Jian Hong, Yongshuai Yang, Lei Dai, Chun Loong Ho. Biotechnology Journal (2020)
• Research progress and applications of strain analysis based on metagenomic data
  (Review, in Chinese) 基于宏基因组数据的菌株分析方法及其应用 Yuxiang Tan*, Han Hu*, Chenhao Li, Xiaozhou Luo, Yan Tan, Lei Dai. Chinese Journal of Biotechnology 生物工程学报(2020)
• Research advances in synthetic microbial communities (Invited Review, in Chinese) 合成微生物群落研究进展 Zepeng Qu, Moxian Chen, Zhaohui Cao, Wenlong Zuo, Ye Chen, Lei Dai. Synthetic Biology Journal 合成生物学 (2020)
• Design and application of synthetic microbial communities (Invited Review, in Chinese) 合成微生物群落的构建与应用 Moxian Chen, Zhong Wei, Liang Tian, Yang Tan, Jiandong Huang, Lei Dai. Chinese Science Bulletin 科学通报 (2020)

Selected previous works

Protein evolution (Postdoc)

• Quantifying the evolutionary constraints and potential of Hepatitis C Virus NS5A protein
  Dai, L.*, Du, Y.*, … Lloyd-Smith, J.O., Sun, R. mSystems (2021)
• Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease
  Zhang, T.*,Dai, L.*# , Barton JP , … Lloyd-Smith, J.O., Sun, R#. PLoS Genetics (2020)
• Evolving generalists in switching rugged landscapes
  Wang, S., Dai, L. PLoS Computational Biology (2019) 
• Adaptation in protein fitness landscapes is facilitated by indirect paths
  Wu, N.C.*, Dai, L.*, Olson, C.A., Lloyd-Smith, J.O., Sun, R.  eLife (2016)

Quantitative biology (Ph.D.)

• Relation between stability and resilience determines the performance of early warning signals under different environmental drivers 
  Dai, L.#, Korolev, K.S., Gore, J. PNAS (2015)
• Dynamics of a producer-freeloader ecosystem on the brink of collapse
  Chen, A., Sanchez, A., Dai, L., Gore, J. Nature Communications (2014)
• Slower recovery in space before collapse of connected populations
  Dai, L.#, Korolev, K.S., Gore, J#. Nature (2013)
• Generic indicators for loss of resilience before a tipping point leading to population collapse
  Dai, L.*, Vorselen, D.*, Korolev, K.S., Gore, J. Science (2012)