Welcome to the Xu lab. Our research focuses on microbiome and host interaction. We apply bioinformatics, microbiology, and animal model to understand how microbiome can be precisely engineered to modulate host phenotypes. Specifically, we are working on the following areas:

microbiome bioinformatics: Microbiome data have some idiosyncratic properties (eg sparse and compositional) and require careful treatment. We have been developing scalable and robust bioinformatic tools to mine multi-omic data and discover patterns and knowledge. We are part of the QIIME2 development team and involved in developing multiple tools including scikit-bio, deblur, and calour. These are successfully applied to microbiome studies.

genomics: We have developed algorithms to identify novel regulatory ncRNAs and predict their secondary structures. With the ever-increasing microbial genomes available from whole-genomic and metagenomic shotgun sequencing data, there is a bottleneck to understand the function potential (ncRNA, coding gene, CRPISPR, prophage, etc.) of these genomes. We are using deep learning techniques to develop high-quality, consistent annotations for comparative genomics.

zebrafish model: We are using zebrafish as a model to study microbiome & host interaction because of the advantages of zebrafish model, including low cost, scalability, genetic tractability, transparency for imaging, and system for complex social behavior analysis.

We are looking for prospective students and faculty to join us on this exciting research field.

Meet the Team

We are always seeking students and postdocs to join the lab! If you work on related research and want to collaborate, please feel free to contact me too!

Lab Member


We Want You

prospective lab members


Zhenjiang Zech Xu


microbiome, synthetic biology, food & nutrition, algorithm, statistics & machine learning


Hui Lu


brain-gut axis, food and nutrition, Chinese herbal medicine


Yichen Hu

Ph.D. student

human microbiome, machine learning, oral microbiota dynamics


Ping Li

Ph.D. student

human microbiome, nutrition, zebrafish in biomedical research


Charles Hantsing Wang

Ph.D. student

Gut Microbiome, Zebrafish Disease Models, Synthetic Biology, Neurogenesis


Ming Li

M.S. student

human gut microbiome, food nutrition


Tao Wu

M.S. student

gut microbiome, metabonomics, nutrition


Yan Li

M.S. student

human microbiome, food, biological engineering


Huan Zhang

M.S. student

microbiome, computer programing, food science


Qiwen Zhang

M.S. student

gut microbes, food engineering, nutrition

Recent Publications

Quickly discover relevant content by filtering publications.

Chlorogenic acid attenuates cadmium-induced intestinal injury in Sprague–Dawley rats

Chronic exposure to cadmium (Cd) causes remarkable damage to the liver and gastrointestinal tract. Previous studies have revealed that …

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

Abstract Microbes can be used effectively as trace evidence, at least in research settings. However, it is unknown whether skin …

Recent Posts

news, thoughts, guides, tutorials

Guide for beginners to bioinformatics

以下为开启生物信息学习的简易入门教程及小贴士,仅供参考。 LINUX 推荐书籍 阅读原则:第一遍阅读快速浏览,熟悉命令行。大概记住常用命令的使用,实际使用

Calour is out in mSystems.

file naming and organizing conventions

There are only two hard things in Computer Science: cache invalidation and naming things — Phil Karlton Naming things is important. …


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