Reconstructing the ancestral microbiome: the American Gut approach

hadza-615I came across the human food project website today. This site is run by the American Gut project folks. You may have heard of their work before: you send them $99 and they send you a home sampling kit. You swab yourself, and they give you a list of the microbes living in your gut. Neat, right? And besides yielding fun information for you, it provides a rich data source for them to analyze (with the goal being to learn more about what Americans are carrying around in their intestines).

I’m waiting for my results to come back from uBiome, a similar service.

Anyway, on the website, I noticed a section entitled Ancestral Microbiome. Exciting! I’ve actually been thinking about how one could go about reconstructing the ancestral microbiome a lot myself lately. Recently, I published a paper entitled Genomics, the origins of agriculture, and our changing microbe-scape in the Yearbook of Physical Anthropology with George Armelagos. One thing we looked at is attempts to learn more about the pre-agricultural microbiome. This is a really tough problem, for several reasons.

One approach would be to use aDNA to characterize microbiomes from ancient remains. The aDNA approach has worked out for some ancient post-agricultural remains (check out Insights from characterizing extinct human gut microbiomes by Tito et al.), but so far nobody has gotten it to work on remains dating prior to the advent of agriculture. Bummer.

Another approach is to study contemporary hunter gatherer groups. This is pretty problematic too, though. First, the very few hunter gatherer groups that are still around have been able to protect their way of life primarily by fending off agriculturalist intruders. This means that they are probably not amenable to being studied by swab-bearing scientists. Second, learning about the hunter gatherer groups around today isn’t necessarily going to tell you all that much about the typical hunter gatherer group living tens of thousands of years ago. The very fact that a hunter gatherer society is still around in a very agriculturalist world suggests that it may be unique in some way. Third, even though some hunter gatherer groups have been able to maintain their traditional subsistence strategies, more or less, it’s possible that they have still been exposed to agriculturalist microbes, which might have altered their microflora.

So how are the Human Food project researchers going about reconstructing the ancestral microbiome? They are studying the Hadza of Tanzania. About 1,000 Hadza live around Lake Eyasi in the northern part of the country, and roughly one-quarter of them live as hunter-gatherers (no crops, no livestock). Not surprisingly, the Hadza are not completely cut off from the world outside their homeland. Contact with agriculturalists stretches back for at least a century. Most Hadza now speak Swahili fluently. Alcohol has become a problem for some, and microbes like TB have been introduced. In the mid 1990s, anthropologist Frank Marlowe found that about 10% of calories that came into Hadza camps was from non-foraged food delivered by missionaries or obtained through trade with agriculturalist neighbors. It’s possible that an increasing stream of money from tourism may result in more calories being obtained from purchased crops nowadays.

It will definitely be interesting to see how the microbiomes of the Hadza differ from those found in other groups in the area. I think this is a project worth doing. But my guess is that there has been a lot of “microbe-creep” between the Hadza and these neighboring groups (and perhaps even foreign tourists). This, along with the other problems I pointed out, would compromise our ability to draw conclusions about the “ancestral” genome. I’m eager to see how this will play out–and curious to hear what other people think.

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