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


Zhenjiang Zech Xu


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


Zhenjiang Zech Xu


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

Recent Publications

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Meta-Analysis Reveals Helicobacter Pylori Mutual Exclusivity and Reproducible Gastric Microbiome Alterations during Gastric Carcinoma Progression

Accumulating evidence shows that the gastric bacterial community may contribute to the development of gastric cancer (GC). However, the …

Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/– Bacteria

The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing …

Systematic Evaluation of Antimicrobial Food Preservatives on Glucose Metabolism and Gut Microbiota in Healthy Mice

Certain antimicrobial preservatives (APs) have been shown to perturb gut microbiota. So far, it is not yet fully known that whether …

Diurnal and Eating-Associated Microbial Patterns Revealed via High-Frequency Saliva Sampling

The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, …

Recent Posts

news, thoughts, guides, tutorials

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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