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Program Snapshot


The Common Fund's Human Microbiome Project (HMP) is developing research resources to enable the study of the microbial communities that live in and on our bodies and the roles they play in human health and disease.


Program Highlights

The Gut Microbiome Influences Circadian Rhythms

A study by HMP awardee Dr. Eugene B. Chang and colleagues explores the relationships between diet, the gut microbiome, and the host circadian clock. Read more.



A Novel Approach to Gene Sequencing Reveals Hidden Depths in Microbial Diversity

Advances in DNA sequencing technologies have been a boon for modern human microbiome studies. However, until very recently, these technologies have also had an important limitation. Read more.


For more information, contact Lita M Proctor, PhD | Coordinator, Human Microbiome Project | Lita.proctor@nih.gov | (301) 496-4550

For more information about microbiome related funding opportunities see a table of key points of contact at each NIH institute funding microbiome research.

The integrative Human Microbiome Project (iHMP): HMP Phase 2

More information about the iHMP program can be found here or by visiting the iHMP website.

The three current iHMP projects are:

Pregnancy and Preterm BirthPregnancy and Preterm Birth




Onset of Inflammatory Bowel DiseaseIBD Logo




Onset of Type 2 DiabetesT2D Logo


Research Enabled by HMP Generated Data

The data generated by the HMP project have allowed researchers to answer numerous questions about the way the microbiome interacts with our bodies and our health.   A few examples of this are listed below.

  • One study by Dr. Fischbach and colleagues showed that some bacteria can actually synthesize a certain neurotransmitter. Though uncommon in many other environments, using HMP data this study estimated that about 10% of humans appear to have at least one bacterium in their gut which can produce this neurotransmitter.
  • Iron scavenging from blood has been shown to be an adaptive strategy for pathogenic bacteria but little is known about the iron acquisition mechanisms of other members of the microbiome. Another study by Dr. Highlander and colleagues used the HMP datasets to demonstrate that iron acquisition strategies are common across all bacterial types and not limited to pathogenic bacteria.
  • Prebiotics are dietary compounds which promote growth of beneficial microbes. A study by Dr. Chen and colleagues used the HMP data to help show that one such prebiotic (found in foods such as bananas, onions, garlic and asparagus) promotes the growth of about half of the bacteria in the gut microbiome including some pathogenic bacteria, thereby suggesting that not all prebiotics support only beneficial microbes.
  • The HMP datasets were also used to estimate the contribution of the human microbiome to the diversity of bacterial species that exist on our planet.  Dr. Simmons and colleagues found that humans support a surprisingly high diversity (approx. 3%) of all animal-associated microbes and livestock support 14-20% of all animal-associated microbes despite the lower abundance of these large animals compared to smaller animals such as insects.
  • The gut microbiome provides many protective functions including a particular bacterium protecting against kidney stone formation.  A study by Dr. Blaser and colleagues used the HMP data to show that about 31% of the healthy adults in this study carried this bacterium at relatively high levels and that this carriage was stable over time.

More examples can be found here.

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