The NIH Roadmapand the Human

Microbiome Project

Francis S. Collins, M.D., Ph.D.National Human Genome Research Institute

April 22, 2007

The NIH Roadmap Program• Roadmap projects were initiated in 2003, and

are funded from a central NIH source (the “common fund”)

• Characteristics:– Must be truly transforming– Must require participation of NIH as a whole, and

address a gap that no single IC or entity outside NIH is likely to fill

– Ideally must provide a benefit by placing the outcome of the project in the public domain

– Must be in need of development in “incubator space” in order to jump start the field

Three Themes for Three Themes for Roadmap 1.0Roadmap 1.0

New Pathwaysto Discovery

Re-engineering theClinical Research Enterprise

Research Teamsof the Future

Re-engineering the Clinical Research

Enterprise

Public-PrivatePartnerships

High-riskResearch

Interdisciplinary Research Nanomedicine

Bioinformatics and Computational Biology

StructuralBiology

Building Blocks, Biological Pathways

and Networks

Molecular Libraries

and Imaging

ImplementationGroups

New Pathways to Discovery

Research Teams of the Future

ClinicalEnterprise

Initiatives within Roadmap 1.0

The NIH Roadmap Program• Roadmap projects were initiated in 2003, and are

funded from a central NIH source (the “common fund”)• Characteristics:

– Must be truly transforming– Must require participation of NIH as a whole, and address a

gap that no single IC or entity outside NIH is likely to fill– Ideally must provide a benefit by placing the outcome of the

project in the public domain– Must be in need of development in “incubator space” in order

to jump start the field

• A new competition for projects (“Roadmap 1.5”) is currently underway, with funding anticipated to start in FY08

Roadmap 1.5: What areas might be included in an HMP Proposal?

• Sequencing of a set of reference genomes from specified body sites (possibly, oral, intestinal, nasal/pharyngeal, urogenital, skin)

• Deep metagenomic sequencing of those sites to explore microbial complexity and the question of whether there is a core microbiome

Roadmap 1.5: What areas might be included in an HMP Proposal?

• Demonstration projects to test whether changes in the human microbiome can be related to human health– Multiple tissue sites, environmental factors, and

disease states

• Technology development -- for example, efficient technology to purify genomic DNA from single microbial cells

• Development of bioinformatics tools for analysis and data handling

Roadmap 1.5: What areas might be included in an HMP Proposal?

• Data analysis and coordination effort for the entire project, to enhance the utility of the data for the biomedical research community, and to coordinate international efforts

• Data repository • Resource repository to store samples, starting

material, DNA, etc.• ELSI projects, if needed, to explore challenges

unique to the HMP endeavor

Trans-NIH

Working Group formed

Trans NIH Working Group begins planning HMP Workshop and ASM HMP

Symposium

HMP Roadmap idea chosen as 1

of 5 for further consideration

HMP Workshop

Roadmap initiative

submission due

Roadmap initiatives discussed

by IC Directors

2004Sep Nov Mar Apr May Jun Jul Aug Sep Nov Feb Apr Jun

NHGRI centers

approved to sequence 100 gut

microbial genomes

NIDCR funds Oral Microbiome

Project

NIDCR renews gut microbiome

program

NIAID initiates vaginal

metagenomics project

NHGRI centers funded to

sequence 200 genomes (gut and vaginal microbes)

2005

HMP Roadmap

idea submitted

NIH - sponsored ASM HMP

Symposium

NIH Brainstorming

Session

2006

Metagenomics Meeting, Paris

2007

NIH call for Roadmap proposals

NIDDK and NIDCR fund ongoing programs in microbiomics of oral

cavity and gut

MayFeb

Expected decision on Roadmap

funding

Human Microbiome Project: Context and Timeline

Potential for coordination of the HMP on several levels

• International coordination — potential EC, Japanese and Chinese projects

• Coordination of analysis in different projects• Interagency coordination to develop

technologies and data standards that can be used in all metagenomics projects

• Interagency cooperation on storage of cultured organisms and metagenomic samples