The Common Fund's Human Microbiome Project (HMP) developed 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.
The first phase of HMP was focused on the development of DNA sequence datasets and computational tools for characterizing the microbiome in healthy adults and in people with specific microbiome-associated diseases. An Ethical, Legal and Societal Implications (ELSI) component of the program evaluated issues which arise from human microbiome research. The second phase of HMP, known as the integrative HMP or iHMP, was focused on creating integrated datasets of multiple biological properties from both the microbiome and the host over time in people with specific microbiome-associated diseases. The long-term objective of iHMP was to develop datasets and tools that the community can use to evaluate which biological properties of the microbiome and host yield important new insights in understanding human health and disease.
Highlights of the HMP’s major accomplishments include:
- Sequencing of ~3000 reference bacterial genomes isolated from the human body
- Comprehensive profile of the microbiome from over 300 healthy humans
- World’s largest metagenome sequence dataset from one human cohort
- World’s only complete dataset of bacterial, fungal, viral and protist community composition from one human cohort
- Integrated datasets of metagenomic, transcript, protein and metabolite profiles from both microbiome and host in multiple human cohorts
- Software and online resources to aid in the study of the microbiome
More information about the HMP including the datasets, tools, and methods developed can be found by visiting the HMP Data Analysis and Coordinationng Center website.
By the end of 2017, HMP investigators published over 650 scientific papers that had been cited over 70,000 times. For a list of all papers generated from HMP funding visit our publications page.
Major Consortium Papers*:
- Structure, function and diversity of the healthy human microbiome (2012)
- Strains, functions and dynamics in the expanded Human Microbiome Project (2017)
- The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease (2014)
Featured Technology Development Papers:
- QIIME allows analysis of high-throughput community sequencing data (2010)
- Metagenomic microbial community profiling using unique clade-specific marker genes (2012)
- Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences (2013)
Profiling beyond bacteria:
- Metagenomic analysis of double-stranded DNA viruses in healthy adults (2014)
- The gut mycobiome of the Human Microbiome Project healthy cohort (2017)
*The key findings of the second phase of the HMP (iHMP) are due to be published in 2019.
This page last reviewed on March 6, 2019