John Hawks highlights a new article in today’s Science, Metagenomic Analysis of the Human Distal Gut Microbiome. This goes nicely with the posts here recently on the topic of how our microbes affect our health and weight (part I; part II). A bit of discussion of the new article below…

First, I want to briefly mention what “metagenomics” means. There’s a nice overview of it here on wikipedia. Basically, instead of sequencing and assembling a genome one at a time, you take a raw sample (such as dental plaque, sea water, soil, or fecal material, in this case), isolate the DNA, sequence it all, and then piece it together. The advantage is that you don’t need a pure culture of an organism in order to study it, making it ideal for organisms that we currently can’t culture using traditional means. In the new paper, the authors used this strategy to examine the gut “microbiome” of 2 study participants.

But as John points out, comparisons of 2 people is just the tip o’ the iceberg. It’s an interesting start (and, not too surprisingly, they already found some significant differences between the two), but it’ll take a lot more work until we get to the point where we have the power to detect reproducible associations between a particular “poo print” and disease status. The paper mentions this, but is optimistic:

Future studies are needed to provide deeper coverage of the microbiome and to assess the effects of age, diet, and pathologic states (e.g., inflammatory bowel diseases, obesity, and cancer) on the distal gut microbiome of humans living in different environments. Periodic sampling of the distal gut microbiome (and of our other microbial communities) may provide insights into the effects of environmental change on our “microevolution.” The results should provide a broader view of human biology, including new biomarkers for defining our health; new ways for optimizing our personal nutrition; new ways for predicting the bioavailability of orally administered drugs; and new ways to forecast our individual and societal predispositions to disorders such as infections with pathogens, obesity, and misdirected or maladapted host immune responses of the gut.

It’s exciting that we’ll soon know a whole lot more about the life forms that we’re most intimately in contact with.


Gill et al. 2006. Metagenomic Analysis of the Human Distal Gut Microbiome. Science. 312:1355-1359.


  1. #1 EMC
    June 2, 2006

    This expands on a paper published in Science last year that surveryed the microbial populations of 3 adults and found that each had a unique gut flora population.

    It’s an immense amount of working sequencing every ribosomal RNA from a person’s poo. You’d think they could develop some sort of chip that would provide a more rapid survey of microbial diversity.

    But it’s kind of cool to think of your gut as a microbial universe unto itself.

  2. #2 impatientpatient
    June 3, 2006

    Macleans magazine in canada just had an article about allergies. In it was a discussion of the “poo prints” of people and how our varieties or lack of varieties of bugs in our gut might have something to do with our rising “epidemic” of allergies. I put epidemic in quotations because I am wondering if that is the right word to use.

    Anyway- can bugs in the gut contribute to the formation of allergies, and if so, what do we do? Do antibiotics predispose babies to allergies because they mess up the gut flora and wipe out certain needed bugs in the effort to combat ear infections and colds.

    Back to my breastfeeding questions on your breastfeeding post- how does this help?

    How – If this is all provable- do scientists educate doctors so they can educate parents about how all of these things can be inter-related?

    How effective would it be to follow a cohort of kids by their poo prints to see if what was happening in their body was seen in their poo?
    Start at birth coollecting fecal samples and then intervals after that with info on antibiotic use, diet and allegern exposure up to age two or three? Then follow them til they were teenagers and adults to see if there was any differences or similarities in their disease rates, kinds of diseases, etc…

    Allergies are horrific– I know a few kids who could die after a *tch* of peanut exposure and the like.

    These things bother me, as I am constantly vigilant while they are in my care and do not like the possibility that they could die or end up in hospital if I was not extremely careful.

  3. #3 Tara C. Smith
    June 5, 2006

    Re: gut bugs and allergies–that’s part of the “hygiene hypothesis,”, that suggests that having a too-clean environment as a young child may predispose to allergies and asthma. It’s still somewhat controversial, but there is a good deal of evidence for it. And indeed, some studies have been carried out looking at antibiotic use and allergies. Some have found a connection, some not, but it’s a bit difficult to tease out cause from effect in the ones done thus far (at least, the ones that I’ve seen): do the babies have increased antibiotic usage because of some pre-existing condition or genetic makeup (that may also lead to allergies, etc.), or are the allergies/etc. due to the antibiotic use? A study like the one you suggest is needed (for not only allergies but other diseases that are linked to exposure to pathogens in childhood or even in utero but only show up later in life), but they’re very expensive and because they can take 20-30 years to have good results, you can imagine how often they’re funded.

  4. #4 g bruno
    June 6, 2006

    As I get older I must eat less food to maintain the same weight. (especially post 55 years, I am now 57)

    1) My gut bugs have learned (or populations have changed )to convert more indigestables
    2) Older people fidget less.