About the Human Microbiome

The Human Microbiome is the collection of all the microorganisms living in association with the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses. Bacteria in an average human body number ten times more than human cells, for a total of about 1000 more genes than are present in the human genome. Because of their small size, however, microorganisms make up only about 1 to 3 percent of our body mass (that's 2 to 6 pounds of bacteria in a 200-pound adult). These microbes are generally not harmful to us, in fact they are essential for maintaining health. For example, they produce some vitamins that we do not have the genes to make, break down our food to extract nutrients we need to survive, teach our immune systems how to recognize dangerous invaders and even produce helpful anti-inflammatory compounds that fight off other disease-causing microbes. An ever-growing number of studies have demonstrated that changes in the composition of our microbiomes correlate with numerous disease states, raising the possibility that manipulation of these communities could be used to treat disease.

The Human Microbiome Project

The NIH Common Fund Human Microbiome Project (HMP) was established in 2008, with the mission of generating resources that would enable the comprehensive characterization of the human microbiome and analysis of its role in human health and disease.

Traditional microbiology has focused on the study of individual species as isolated units. However the vast majority of microbial species have never been successfully isolated as viable specimens for analysis, presumably because their growth is dependent upon a specific microenvironment that has not been, or cannot be, reproduced experimentally. Advances in DNA sequencing technologies have created a new field of research, called metagenomics, allowing comprehensive examination of microbial communities, without the need for cultivation. Instead of examining the genome of an individual bacterial strain that has been grown in a laboratory, the metagenomic approach examines the collection of genomes derived from microbial communities sampled from natural environments. In the HMP, this method will complement genetic analyses of known isolated strains, providing unprecedented information about the complexity of human microbial communities.

The HMP has characterized the microbial communities found at several different sites on the human body: nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract. The project has examined the role of these microbes in human health and disease. The 5 stated aims of the project included:

The HMP is an interdisciplinary effort funded by the NIH Common Fund. HMP1 included four sequencing centers — the Broad Institute, the Baylor College of Medicine, Washington University School of Medicine, and the J. Craig Venter Institute, the Data and Analysis and Coordination Center (DACC), and several investigators.


  • Over 2,200 reference strains isolated from the human body have been sequenced
  • 300 healthy adults between the ages of 18 and 40 were sampled at five major body sites: oral cavity, nasal cavity, skin, gastrointestinal tract and urogenital tract; with a total of 15 or 18 specific body sites. Subjects were sampled at one to three visits, for a total of over 11,000 samples. See Data Model for more details.
  • Raw and processed sequencing data for both reference and metagenomic strains are available through the legacy HMP1 Data Browser. Metagenomic data is also availabkle through the HMP Portal.
  • The iHMP Consortium published two landmark papers in the June 14, 2012 issue of Nature and a series of companion papers in several PLoS journals. These papers establish a foundation to catalyze and aid a myriad of studies ranging from basic to translational to clinical.

Nature Papers

Public Library of Science (PLOS) Papers

Member Organizations