NIH’s Human Microbiome Projects Publishes Results of the Biggest Human Microbial Diversity Study

The Human Microbiome Consortium Profiles Microbial Diversity in Healthy HumansNIH’s Human Human Microbiome Project (HMP) has published a numbers of papers in Nature and  PLoS journals.  The Human Microbiome Project studied the microbiomes of over  240 healthy individuals using high-throughput and deep sequencing technologies. The ambitious project is our first attempt to get a comprehensive view of the human living partners and used genome sequencing to create the first reference data for microbes living with healthy humans.

The Human Microbiome Project consortium consists of over 200 researchers from over 80 research institutes and tool little over five years (started in 2007) to study and publish the findings. The outcome of such a humongous endeavor is 5Tb of genomic data and a catalogue of over 5 million microbial genes.

Here is the abstract of two Nature papers and the link to 14 more papers published in PLoS journals by the Human Microbiome Consortium (

  1. Structure, function and diversity of the healthy human microbiome, The Human Microbiome Consortium, Nature 486, 207–214 (14 June 2012)
  2. Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

  3. A framework for human microbiome research, The Human Microbiome Project Consortium, Nature 486, 215–221 (14 June 2012)

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.