More on the Human Microbiome Program Workshop – Day1

As a follow up to my previous blog I am posting some additional information here about the NIH Roadmap Human Microbiome Project Workshop, which was held in Bethesda, MD.

The general outline of the meeting was as follows:

  • Sunday Night
    • Introduction
      • Welcome by Francis Collins (NHGRI), Hugh Auchincloss (NIAID) and Griffin Rodgers (NIDDK)
      • Comments by Gary Schoolnik
      • Overview of the NAS report on metagenomics by Jim Tiedje
      • Overview of the NIH Roadmap program by Francis Collins
    • Introductory talks on human microbiome
      • Jeff Gordon
      • David Relman
      • Gary Huffnagle
      • Jo Handelsman
  • Monday AM
    • Technological issues
      • Elaine Mardis
      • Jill Banfield
      • Deirdre Meldrum
    • Bioinformatics issues
      • Lior Pachter
      • Rolf Apweiler
      • Peer Bork
    • ELSI Issues Pilar Ossorio
  • Lunch
  • Monday PM – Breakout sessions and discussion
    • Group 1 – Reference microbiome (Claire Fraser and Martin Blaser)
    • Group 2 – Changes in microbiome and human health (Rita Colwell and Martin Rosenberg)
    • Group 3 – Enabling technologies (Bruce Birren and Mary Lidstrom)
    • Group 4 – Bioinformatics tools (Ewan Birney and Owen White)
    • Group 5 – Ethical legal and social issues (Midred Cho)
  • Wrap up

Overall, I found the Sunday night talks very useful to set the stage. The introductory talks by the representatives from NHGRI, NIAID, and NIDDK clearly indicated that NIH as well as others consider the human microbiome an incredibly important research area. Then Jim Tiedje gave a nice overview of the recent NAS report on metagenomics (which was about metagenomics in general, not specifically for the human microbiome). The main points of the report are basically: microbes rule the world, metagenomics is a very powerful tool in studying them, and there is a need for a more coordinated effort among funding agencies to push metagenomics as a tool and a field. (My only complaint about Tiedje’s presentation was he kept using the term “higher organisms” for those multicellular species with nuclei. But otherwise, he did a good job of concicely summarizing the report and the benefits as well as challenges of metagenomics).

Francis Collins then gave an overview of the NIH Roadmap Program. The Roadmap was started in ~2003 as an initaitive to identify projects that would need coordination across multiple NIH agencies. These projects should meet certain characteristics: truly transforming, require all NIH, must need incubator scape, and the outcome should produce material into the public domain. Collins then discussed how, from among hundreds of suggestions, the Human Microbiome was picked as one of five topic areas for in depth consideration for the new round of Roadmap competition. Thus the point of this workshop was to discuss this in more detail and help provide material and ideas for the full consideration of an HMP program.

I should note, I found one thing disappointing in the introduction which was a response to my question concerning whether this project would be limited only to studies of humans or would allow for studies of model systems that inform human work. The answer was basically that this would likely be limited to humans. I think this is a big mistake. The human genome project came to the realization that comparative studies with other species were critical to understanding and interpreting studies of the human genome. The same will be true of the human microbiome program.

Jeff Gordon then gave an overview of human microbiome studies, and focused on what are the key questions that need to be answered. Among the key questions: Do we share a core set of microbes? How should we view differences in microbes between people and over time? How do we relate communities of microbes to health and disease? How should we sample microbial communities to characterize them? What determines robustness of microbial communities in people?

To start to answer these and other questions, he suggested that we have three tiers of data collection: (1) deep draft assemblies of microbial communities and reference genomes, (2) reference microbiome work (deep characterization of individuals including information about the familiy history and genetics) (3) 16s surveys of communities (a global human microbial diversity survey). I basically liked all of his ideas. He did talk about work in model organisms too. His work has shown just how important this is … and I think as I said above it needs to be emphasized more in the HMP.

David Relman, from Stanford, then talked about patterns in human microbial diversity. He talked about some of the challenges in such studies as well as results of his and others work. He discussed many interesting aspects of the diversity of samples, and the shapes of diversity. Some of the patterns he emphasized were that history plays a role in the diversity, that archaea generally seem to have limited presence, that diversity is uneven and complex.

Then Gary Huffnagle discussed in more detail the interaction of microbes with the host immune system. And Jo Handelsman discussed what she calls functional metagenomics, which involves focusing on the functions of genes found in the environment on top of examining the phylogenetic diversity of communities. Unfortauntely, I did not take extensive notes for these two talks so do not have much to base my comments on here. In addition, I confess, the fact that the room in which the meeting was held was incredibly crowded and boiling hot, and the fact that I had flown in from California earlier in the day, made taking notes challenging at this point. However, that did not stop me from going out afterwards for a beer with Julian Parkhill, Ewan Birney, Owen White, and Jacques Ravel. The worst part of going out for the beer – I grew up in Bethesda but I made multiple wrong turns in the two blocks to the brew pub. I am sure from now on Julian and Ewan will never trust my directions. Fortunately, the fact that the pub had the RedSox pummeling the Yankees on TV made up for my direction problems.

I will post more about the second day soon.

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

6 thoughts on “More on the Human Microbiome Program Workshop – Day1”

  1. Did Collins discuss how the human microbiome might reveal God to us? Can you say “lack of credibility”?Anon (by necessity)


  2. Regarding the comment above by anonymous, sure I was a little worried about some of Collins’ latest book tour playing a role in the discussion. But in all fairness to him he does a pretty good job of not letting his personal beliefs affect his work in any obvious way. And, regardless, he is a big supporter of comparative and evolutionary biology, which is not the rule in all parts of NIH.


  3. All very cool however why do 16S studies when there is potentially tremendous micro-diversity. Why not use the ITS which provides potentially much greater resolution?To add my two cents to the God comments: Collins is a very credible scientist and he uses evidence to make informed choices. He has a great track record and its hard to complain with his ideas. On the other hand God is a topic for which evidence is ambiguous at best so certainly he is entitled to an opinion.Anon (for the hell of it)


  4. I agree. When Collins book came out, I read it. I have some complaints about it – especially the part where he makes arguments about altruism that do not reflect the current literature on the topic. So I started looking at his work and must say he does more than just give lip service to evolution. He uses it as a key part of his work and it is well supported within NHGRI. No complaints there.


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