Welcome to the Microbiome

microbe.jpgMuch swell stuff out of this weekend’s SciFoo conference. But probably the coolest thing that I saw was Jonathan Eisen’s presentation on the Microbiome. As the genome is to genes, the microbiome is to microbes - the comprehensive catalog of all the microbes in an ecosystem - in Eisen’s talk, the human body.

As Eisen describes it on his blog:

In essence the human microbiome is the sum collection of all the microbes found in or on people. The human microbiome has become an important research field because the microbes that live in and among us play critical roles in human disease and health. An important aspect of this is the idea that microbes can be and are beneficial. For example, in the gut the normal microbes help with digestion and nutrient absorption as well as protect from infection. In addition, a variety of diseases (e.g., IBD, Chrohns) seem likely to be caused by disruption in the normal microbial flora. In general, it seems likely that other ailments, like autoimmune diseases, allergies, etc will be found to have a connection to disruptions in the beneficial microbes that live among us.

The cool thing here is it makes perfect sense and is at once both comprehesible and profound to most people. Everybody knows we’ve got stuff in our gut helping us digest stuff (the booming probiotics trend testifies to this). But the idea that these organisms are essential, not simply beneficial, and that they may be instrumental in our understanding of disease, immunology, and so forth - well, that’s simply stunning.

As Eisen explains, the NIH just created the Human Microbiome Project - an effort to genetically sequence and catalog all of these microbes and start to suss out what they do (the analogy to the Human Genome Project and the ensuing efforts to understand the function of human genes is deliberate and inescapable). The NIH has designated the project part of its NIH Roadmap for Medical Research, a fast track for developing new technologies.

The trick, of course, is actually finding out what’s in and on us. There are, Eisen estimates, 100 times as many microbic cells affixed to a body as there are in that body - meaning there are likely thousands of microbes in a given person, and there is a tremendous variety from person to person.

It was a great talk especially because of the quality of the questions - and of the questioners. At one point Freeman Dyson was offering a quip and Drew Endy was urging Eisen on and George Church was sitting in the back, comparing notes with various folks.

Published by: tgoetz on August 6th, 2007 | Filed under Disease, Genetics

5 Responses to “Welcome to the Microbiome”

  1. Attila Csordas Says:

    Hello Thomas, actually the estimation concerning microbe numbers is based on this reference: Sears CL. 2005. A dynamic partnership: Celebrating our gut flora. Anaerobe, Volume 11, Issue 5, October 2005, Pages 247-251.
    normal flora.
    It is estimated that 500 to 1000 different species of bacteria live in the human body (Sears, 2005). Bacterial cells are much smaller than human cells, and there are about ten times as many bacteria as human cells in the body (1000 trillion (1015) versus 100 trillion (1014); Sears, 2005).

  2. Jonathan Eisen Says:

    If I only knew where to begin with this …

    First, don’t trust Wikipedia.

    Second, the estimates from Sears paper are not done in the paper. If you follow the citation trail you find out that all of this is based upon very old and possibly inaccurate estimates.

    Third, while it is true that most of the bacteria in humans are probably in the gut, there are many in other places.

    Fourth, in addition, as far as I can tell, these numbers are based on culturing, not cell counts and thus will greatly underestimate the total number of bacterial cells.

    Finally, these numbers are only for bacteria and not archaea and eukaryotes – and I said “microbial.” I stand by my estimate of 100 fold as many microbial cells than human cells and am working on publishing a formal estimate.

  3. Attila Csordas Says:

    What we need is a good microbial density map of the human body, and the ratios of microbial/human cells concerning particular tissues and organs. But for that we need the accurate human cell numbers (or at least the order of magnitude) depending on tissues, organs and cell types, and that was exactly the topic of my session on SciFoo and a current project I’ve just started. Maybe we should cooperate as the projects are complementary ones.

    “Fourth, in addition, as far as I can tell, these numbers are based on culturing, not cell counts and thus will greatly underestimate the total number of bacterial cells.”

    Let me explain this a bit more to the non-biologist: microbe numbers based on culturing are the numbers of colonies growed out of the original sample, not the cells, and if the limiting dilution was chosen improperly, it lead us to an over- or underestimation.The main source of underestimation is that there could be microbes too in large numbers that were not cultured successfully, so left out of the estimation.

  4. VentureBeat » A human microbiome project? Says:

    […] the “microbiome” in earnest. I stumbled across this notion on Epidemix, where Tom Goetz notes a recent talk by UC Davis evolutionary biologist Jonathan Eisen about a new effort to sequence the […]

  5. Jonathan Eisen Says:

    Love to cooperate on the numbers of cells thing. I missed your session. Can you explanin more?

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