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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

Dramatic Fluctuations of the Gut Microbiome in Individuals with Inflammatory Bowel Disease

IBD logoA study by iHMP researcher Dr. Janet K. Jansson and colleagues has shown that the make-up of gut microbiome changes much more rapidly in patients with Inflammatory Bowel Disease compared to healthy patients. More information about this study. More information about this study.

Watch a video describing this study.

The genome sequence of Christensenella minuta now published: the most highly heritable bacterium of the gut microbiota which may also play a role in host weight

Researchers from the HMP at WashU have published the genome sequence of Christensenella minuta, a resident of the gut microbiome which is thought to be the most heritable member of the gut microbiota that may also play a role in regulating the weight of the person it inhabits. Read more about C. minuta.

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

The second phase of HMP (integrative HMP or “iHMP”) is profiling the microbiome and host characteristics in three microbiome-related health conditions. More information about the iHMP program can be found here or by visiting the iHMP website.

The three current iHMP projects are focused on:

Pregnancy Program WebsiteIBD Program WebsiteDiabetes Logo with Test

Dr. Michael Fischbach, UCSF, on the Impact of the HMP on His Research

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.

  • 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.

Join HMP investigators for a Microbiome Analysis in the Cloud training workshop on June 15-16, 2017 at the University of Maryland Medical Center. The workshop will provide hands-on training the in the use of HMP generated, cloud-based data and tools. Applications are due May 15th. For more information and to apply please visit the UMMC website.

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