NIAID Microbiome Program

Visualization and localization of commensal bacteria by Fluorescence in situ Hybridization (FISH) in the small intestine of Toxoplasma gondii-infected mice.

Credit: NIAID

The NIAID Microbiome Program is a collaborative effort to explore the metaorganism using existing and new facilities and personnel. The program has developed a microbiome sequencing facility with bioinformatics support and a gnotobiotic mouse facility, and is currently expanding microbiology resources. The program has supported over 35 groups across the National Institutes of Health (NIH) in their research related to the exploration of the metaorganism.  

Main Areas of Focus

  • To promote the exploration of the metaorganism in order to address questions of relevance to NIAID’s mission in both experimental and clinical settings
  • To address research topics such as:
    • The role of microbiota in the development and function of the immune system
    • How changes to the microbiota promote the emergence or speed of multidrug-resistant pathogens
    • How dysregulation of host-microbiota interactions leads to chronic inflammatory diseases
    • How pathogens, their expressed genes, and their metabolites directly affect their own proliferation and/or immune signaling networks to exacerbate disease


How To Get Started

  • Before beginning a project, a project proposal must be submitted to an oversight committee to be reviewed for scientific rationale and feasibility.
  • Please contact Xing He for Sequencing and Microbiology projects, and Nicolas Bouladoux for Gnotobiotic projects.


Steering Committee


Read scholarly publications about research related to the NIAID Microbiome Program.

Selected publications

Contact Information

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