Summary

Gary Schoolnik, Chair
George Weinstock, Jo Handelsman, Co-chairs

The metagenomic study of microbial communities, specifically the examination of microbial organisms that live in and on the human body (the human microbiome), has garnered much attention in the biological research community recently. The National Institutes of Health (NIH) took the opportunity to hold a workshop on April 22 and 23, 2007, to examine the possibility of supporting a project to understand the human microbiome, potentially through the NIH Roadmap program. The workshop brought together fifty experts in the fields of microbiology, medicine, metagenomics, microbial ecology, computational science, genomics and bioethics, along with international representatives from other metagenomics efforts and NIH staff.

After presentations of current views of and activities relating to metagenomics (in human and other systems), the participants discussed possible scientific strategies and addressed potential challenges relevant to a Human Microbiome Project (HMP). The group covered such topics as: technology development, informatics needs, data analysis requirements and the ethical, legal and social implications (ELSI). Overall, the participants endorsed the concept of an NIH-supported HMP because of its potential for providing significant insights into the relationship between the microbial communities that inhabit the human body and affect human health.

The recommendations from the workshop are summarized as follows:

1. Reference Microbial Genomes. Initial efforts should be aimed at sequencing and annotating individual microbial genomes, those that can be cultivated with current techniques, including bacteria, archaea, viruses and microbial eukaryotes. This collection will be a reference data set that will be needed in the analysis of sequences from metagenomic samples that will be generated in the latter part of the program. Part of the effort in assembling the reference data set will be to examine multiple isolates of the same organism in order to evaluate the extent of sequence variation within those microbial species. The participants estimated that perhaps 1000 full genomes of microbes obtained from all body sites will be needed, although that number is considered a rough estimate. As technologies for isolating uncultivable organisms mature, sequencing of those genomes as part of the reference set should be pursued.
    
2. Microbiome Complexity. Decisions about strategies for analyzing the microbial communities at individual body sites need to start with assessment of the organismal complexity of each community. Such estimation should be done by an initial 16S rRNA "light coverage"; sequence survey of the microbial floras from a large number of body sites (30-100) in a significant number of individuals (about 100) in order to identify the microbial species present at each body site. This should be followed by deeper 16S rRNA sequencing of a smaller number of sites in fewer individuals to get a more accurate assessment of community complexity. The participants endorsed the concept of using this sequence-based approach to begin to answer the question of whether there is a core microbiome at each site. Gene expression data would serve as a complementary data set to the 16S rRNA sequence data.
    
3. Microbiome and Human Health. As the reference data set is being compiled and microbial community complexity is being examined, metagenomic studies to examine the correlations between the human microbiome and human health can commence. The central question to be answered is whether changes in the microbiome can be correlated with disease state, and whether such changes are the cause of the disease or are caused by the disease. Individual, investigator-initiated approaches to answering this question were endorsed as an effective way to go forward. Additionally, the use of animal models was endorsed as an effective means for conducting follow-up functional studies based on the observations made in humans.
    
4. Technology Development. Short-term technology challenges lie in developing robust sampling and cultivation techniques that are needed immediately for success of the HMP. Long-term needs include:
   • Very rapid, inexpensive sequencing methods. New sequencing technologies are becoming available and are already being implemented at large sequencing centers to deliver faster and cheaper sequencing from single DNA molecules.
   • Single-cell profiling technologies. Site-specific detection and dynamic measurement of DNA, RNA, protein and metabolite levels from single cells. A number of such techniques are showing promise that they may be quickly refined and adopted to meet the needs of the HMP.
   • Cost-effective technologies for imaging of single cells outside of their natural environments, as well as in situ.
      
5. Bioinformatics Needs. While the bioinformatics challenges are substantial, the participants believed that they can be managed. The participants encouraged development of metadata standards and establishment of a policy of immediate data release without restrictions on data use. Support for investigator-initiated bioinformatics tool development should be given to target advancement in the identification of individual organisms from sequence data, open reading frame detection, gene calling, functional determination and phylogenetic analyses.
    
6. Human Microbiome Resources. An HMP will need to build sequence data resource infrastructures for the use and dissemination of the HMP data. A sample repository is essential to assure the availability of sample materials (DNA, for example).
    
7. ELSI Issues. Short-term questions that should be addressed include "ownership"; of one's own microbiome and whether a microbiome profile will reveal personal information. Long-term ELSI issues that may be unique to the HMP and should be studied include:
   • Clinical and health applications such as: probiotic use, "microbiome transplants"; and effects of the microbiome on behavior.
   • Potential forensic uses of microbiome profiles.
   • Uses of new technology driven by the human microbiome study.
      
8. An International Consortium for the Human Microbiome Project. Finally, any NIH-funded HMP should encourage formation of an international human microbiome consortium to coordinate efforts. This coordination will reduce redundancy through sharing of information about challenges and solutions regarding strategy, sequencing targets, resources, technology and bioinformatics. Importantly and as in previous international genomics projects, agreement to an immediate data release policy should be a requirement for membership in such an international organization.