Human Microbiome ProjectEdit

1. Aims and ObjectivesEdit


This illustration shows the body sites that will be sampled from volunteers for the Human Microbiome Project, part of the National Institutes of Health's Roadmap for Medical Research. (Credit: NIH Medical Arts and Printing)

The mission of the Human Microbiome Project (HMP) is to generate resources enabling comprehensive characterization of the human microbiota and to analyze its role in human health and disease.

More specifically, the HMP aims to

  • Determine whether individuals share a core human microbiome
  • Understand whether changes in the human microbiome can be correlated with changes in human health
  • Develop the new technological and bioinformatic tools needed to support these goals
  • Address the ethical, legal and social implications raised by human microbiome research.

In order to achieve these goals, the following roadmap is currently being implemented:

  • Sequencing of ~600 genomes from cultured and uncultured bacteria to achieve eventual reference set of approx 1000 genomes
  • Sampling of microbiomes from several locations of the human body and sequencing of 16S rRNA to characterize community membership
  • Establishment of a data analysis and coordinating center to deal with the accumulating data

The ultimate objective of the HMP is to demonstrate that there are opportunities to improve human health through monitoring or manipulation of the human microbiome

2. ImpactEdit

  • The characterization of multiple microbiomes from healthy patients will be a useful reference set to compare to microbiomes taken in the clinic, which will become increasingly relevant in practice with the cost of large-scale sequencing continuing to drop.
  • Techniques and technologies developed by the HMP will be applicable to the study of microbes in a wide range of biological processes.

3. Project organizationEdit

The project started in Dec 2007 and is a 5 year effort. It is funded as part of the NIH Common Fund's Roadmap for Medical Research. Many groups from the USA are involved and are distributed to different areas of expertise:

  • Experimental validation: 15 groups
  • Sequencing: 4 groups
  • Legal, ethical and social issues: 6 groups
  • Data analysis and coordination: 1 groups
  • Development of new tools: 28 groups

For a complete list of the groups involved refer to:

4. Access to dataEdit

Main project websiteEdit

Data produced by this project can be found at the human microbiome project webpage ( Data includes sequencing information of the reference genomes and analysis of the microbiome. This data includes access to the raw data, protocols used to extract it and the analysis performed by the members of the project.

Microbiome analyses include:

  • Phylogenetic Analysis of 16S rRNA sequence using RDB classifier

  • Taxonomic binning of metagenomic wgs sequence

  • Read-based community comparisons of metagenomic wgs sequence

  • Functional annotation of the human microbiome, and identification of gene classes of particular interest

  • Identification of metabolic pathways

  • Comparisons of microbiomes from different body sites/subjects on multiple levels: organisms, genes, pathways

Physical storageEdit

BEI Resources establishes and administers the resource repository. It stores materials and reagents generated under the Human Microbiome Project including:

  • Cultured organisms

  • Amplified DNA from uncultured organisms

  • Metagenomic DNA samples

Genome sequence storageEdit

While the genome sequencing data may be found in the main project website, it is also stored at the National Library of Medicine's National Center for Biotechnology Information, part of NIH. (

5. Published resultsEdit

General publications:Edit

Specific publications:Edit

The human oral microbiome database:

Sequencing of 178 reference genomes of the gastrointestingal track:

For a complete list of publications related to this project, please, refer to:

6. Related projectsEdit

1. International human microbiome project

The goal of the IMHC is to work under a common set of principles and policies to study and understand the role of the human microbiome in the maintenance of health and causation of disease and to use that knowledge to improve the ability to prevent and treat disease. The Consortium’s efforts are focused on generating a shared comprehensive data resource that will enable investigators to characterize the relationship between the composition of the human microbiome (or of parts of the human microbiome) and human health and disease.

2.- International Human Microbiome Standards project

This project seeks to coordinate development of standard operating procedures and protocols that will optimize data comparisons in the human microbiome field and thus improve the synergy between all the projects.

It focuses on three key aspects of data generation:

1) Human sample collection, processing and identification;

2) DNA sequence quality obtained;

3) Analysis of DNA sequence

Importantly, it organises public access to the standard operating procedures and protocols and enables exchanges between the users and providers of the standards.

7. Useful linksEdit

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