The Human Microbiome

Over the last seven years, the Broad Institute of MIT and Harvard has helped systematically uncover, catalog, and analyze the microbial inhabitants of the human microbiome. Research is now focused on using “multi-omics” techniques, including whole genome sequencing, as well as proteomic, metabolomic, and transcriptomic analyses, to better understand how the microbiota is acting on and interacting with its human hosts in health, and during disease progression.

Broad was part of the Human Microbiome Project (HMP) Consortium, an NIH-funded collaboration between several genome sequencing centers dedicated to understanding the properties of the microbial communities living in the human body, and to analyzing their roles in human health and disease. Broad researchers are now involved in phase two of HMP, the Integrative Human Microbiome Project (iHMP), where they lead a multi-institutional effort to understand how the human gut microbiome changes over time in adults and children with IBD.

In addition to research on IBD, Broad scientists are building tools and methods to accelerate research on the microbiome, and are actively investigating the role of microbiota in the development of various diseases and conditions such as type I diabetes, cancer and inflammatory bowel disease. Microbiome research at Broad interacts synergistically with the Center for Microbiome Informatics and Therapeutics at MIT, whose mission is to streamline discovery of diagnostics and treatments for microbiome-associated disease.


  • Integrative Human Microbiome Project (iHMP)
    • Inflammatory Bowel Disease
  • Human Functional Genomics Project
  • Immunodeficiency disorders, GVHD
  • Autoimmune disease (DIABIMMUNE, TEDDY, IgG4 disease, RA)
  • Gastrointestinal Cancers
    • Cancer Immunotherapy and microbiome
    • Identify microbiome determinants that lead to loss of treatment response
    • Urinary tract infections
    • Cardiometabolic disease (Framingham cohort) and obesity