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Human Microbiome Project awards funds for technology development, data analysis and ethical research

The National Institutes of Health (NIH) today announced the first awards for its Human Microbiome Project, which will lay a foundation for efforts to explore how complex communities of microbes interact with the human body to influence health and disease. The funding, estimated to be up to approximately $21.2 million, will support the development of innovative technologies and computational tools, coordination of data analysis and an examination of some of the ethical, legal and social implications of human microbiome research.

The human microbiome consists of all of the DNA, or genomes, of all the microorganisms present in or on the human body. Launched in 2007 as part of the NIH's Roadmap for Medical Research, the Human Microbiome Project is a five-year effort that will produce a resource for researchers who are seeking to use information about the microbiome to improve human health.

"Today marks the beginning of efforts by researchers to put in place the framework for understanding how microorganisms interact with our bodies to affect health and disease," said NIH Director Elias A. Zerhouni, M.D. "Developing new and more cost-effective technologies will be essential to applying knowledge about the human microbiome to the prevention, diagnosis and treatment of a wide array of conditions."

Initially, researchers plan to sequence 600 microbial genomes, completing a collection that will total some 1,000 microbial genomes. The remaining microbial genomes are being contributed to the collection by individual NIH institutes and internationally funded projects. Those data will then be used to characterize the microbial communities present in samples taken from healthy human volunteers. The samples will be collected from five areas of the body: the digestive tract, the mouth, the skin, the nose and the vagina.

After researchers generate profiles of microbial communities in healthy people, they will conduct demonstration projects to sample the microbiomes of volunteers with specific diseases. This will allow researchers to see if there are changes in the microbiome at particular body sites that correlate to specific diseases.

Traditionally, microbiology has focused on the study of individual species of microorganisms as isolated units, making it difficult to inventory all of the microbes in and on the human body. Because microbial growth is dependent upon a specific natural environment, it often is difficult to recreate microbe-host interactions in the laboratory.

Recent advances in DNA sequencing technologies have accelerated a process called metagenomic sequencing. Instead of focusing on the genomes of individual microbes, metagenomic sequencing analyzes all of the DNA of all of the microbes found within a sample.

Much of the work being funded in the first round of the Human Microbiome Project is aimed at improving and refining the identification of microbes that constitute the microbiome. Computational tools will also be developed to optimize the assembly of sequencing data to infer the location and function of genes, as well to classify microbial species.

"The development of new tools and technologies is central to our ability to meet the goals of the Human Microbiome Project," said Alan Krensky, M.D., director of the Office of Portfolio Analysis and Strategic Initiatives, which oversees the NIH Roadmap for Medical Research. "An exceptional amount of information will be generated by this project and we need robust technologies and analytical tools that are equal to the task."

The principal investigators who will develop new technologies and computational tools, their approximate funding levels and their areas of research are:

Technology Development

Eugene B. Chang, M.D., The University of Chicago Medical Center; $410,000 (2 years); Technologies for the Discovery of Novel Human Colonic Mucosal-Associated Microbes.

Andre Marziali, Ph.D., Boreal Genomics, Inc., North Vancouver, British Columbia; $770,000 (2 years); DNA Extraction to Normalize Species Representation.

David Relman, M.D., Stanford University, Palo Alto, Calif.; $1.6 million (3 years); Optimization of a Microfluidic Device for Single Bacterial Cell Genomics.

Thomas Schmidt, Ph.D., Michigan State University, East Lansing and Vincent Young, M.D., Ph.D., University of Michigan, Ann Arbor; $1.3 million (3 years); Cultivation and Characterization of the Microaerobes from the Mucosa of the Gastrointestinal Tract.

Kun Zhang, Ph.D. and Yu-Hwa Lo, Ph.D., University of California, San Diego; $1.8 million (3 years); An Integrated Lab-On-Chip System for Genome Sequencing of Single Microbial Cells

Computational Tools

Daniel Haft, Ph.D., J. Craig Venter Institute, Rockville, Md.; $1.6 million (3 years); Algorithmically Tuned Protein Families, Rule Base and Characterized Proteins

Robin Knight, Ph.D., University of Colorado at Boulder; $1.1 million (3 years); New Tools for Understanding the Composition and Dynamics of Microbial Communities

Mihai Pop, Ph.D., University of Maryland, College Park; $780,000 (3 years); Assembly and Analysis Software for Exploring the Human Microbiome

Yuzhen Ye, Ph.D., Indiana University, Bloomington; $770,000 (3 years); Fragment Assembly and Metabolic Species Diversity Analysis for the Human Microbiome The NIH also awarded a cooperative agreement of approximately $9.9 million over five years to establish the Human Microbiome Project Data Analysis and Coordination Center, which will be led by Owen White, Ph.D., University of Maryland School of Medicine, Baltimore. As a community resource project, all data generated by the Human Microbiome Project will be deposited in the Data Analysis and Coordination Center as well as other public databases, including those supported by the National Center for Biotechnology Information (, part of the National Library of Medicine. In addition, the Human Microbiome Project awarded approximately $1.2 million over three years to Richard Sharp, Ph.D. and Ruth Farrell, M.D., of the Cleveland Clinic to examine some of the ethical, legal and social implications of human microbiome research. Specifically, Dr. Sharp and his team will study patient perceptions about probiotic (beneficial bacteria) therapies and other potential clinical applications of human microbiome research.


Contact: Geoff Spencer
NIH/National Human Genome Research Institute

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