Metagenomics

The human environment

    “I don't know why the Human Microbiome Project bubbled to the top now instead of previously,” says Jane Peterson from the National Institutes of Health (NIH). “Certainly there have been metagenomic studies done with the old technologies.” But Peterson thinks recent reports exploring the human gut microbial community, along with new, advanced sequencing technologies, might have been enough to pique the interest of the reviewers who decided to fund the Human Microbiome Project (HMP).

    The project is a 5-year, US$115-million effort to study the microbial communities inhabiting several regions of the human body, including the gastrointestinal and female urogenital tracts, oral cavity, nasal and pharyngeal tract, and skin, and how those communities influence human health and disease. The effort is viewed by many researchers in the metagenomics community as particularly timely as most agree improvements in sample collection standards and analysis tools are much needed. Karen Nelson from the J. Craig Venter Institute, who is also a participating investigator in the HMP, says these issues can finally be addressed with a project of this scope as all samples will collected and treated in the same way, and standards will be put in placefor annotation of the metagenomic data.

    The project will fund research in several areas, although the construction of a data resource for sequencing DNA samples from as many as 250 individuals, and projects aimed at demonstrating how changes in the human microbiome are related to health and disease are centrepieces of the programme. Other project initiatives include the development of new metagenomics technology to isolate bacteria that are currently cannot be cultured, development of new bioinformatic programs and tools for analysis of large genomic data sets, data analysis and coordination centres, and analysing and understanding the ethical, legal and social issues of the project.

    The HMP's initial sequencing efforts began this year. Peterson says that towards the end of the last fiscal year, the NIH Roadmap office had funds available for the HMP. Through existing relationships with large sequencing groups, the HMP was able to start quickly and generate preliminary sequencing data, which are being used for the other demonstration projects. This initial effort will result in the sequencing of 200 new bacterial organisms, recruitment of patients for metagenomic studies, and some 16S ribosomal RNA metagenomic sequencing to assess microbial diversity at the various sites.

    Peterson says that the protocols for sampling and recruitment have provided some early challenges. The HMP hopes to sample the same sites on all 250 individuals, but with so many sites, standardizing sampling can be tricky. “The protocol for the different sites has to be well worked out,” she says, “the oral community has to be happy with the requirements that the skin community brings to the table.”

    Although it is just at the beginning, the HMP is scheduled to award its first rounds of grants to researchers this autumn. Peterson says that in the future the project's standardization efforts might not be restricted to the United States. “We are also forming an international consortium to coordinate international projects.”

    N.B.

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    The human environment. Nature 453, 689 (2008) doi:10.1038/453689a

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