Publications

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

Selected recent highlights

• 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)
• 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)
• 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)
• 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)

LD Lab publications (full list)

To be published

• 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^#. bioRxiv
• Relative enrichment of oral bacteria in feces indicates loss of intestinal commensals with implications for host health. Chen Liao*, Thierry Rolling*, Ana Djukovic, Hongbin Liu, Lei Dai, Bing Zhai, Jonathan U. Peled, Marcel R.M. van den Brink, Tobias M. Hohl, Joao B. Xavier. bioRxiv
• 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. bioRxiv

2023

• Applications of CRISPR-Cas Technologies in Microbiome Engineering (Invited 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, Jia Ke, Tao Ding, Wenjing Zhao, Wai Ming Cheng, Zhanhao Luo, Qilang He, Wanyi Zeng, Jing Yu, Na Jiao, Yanmin Liu, Bin Zheng, 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
  (Invited 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 by Lei

Molecular evolution

• 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 microbial ecology

• 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)