The human gut microbiome

One of the really exciting developments within evolutionary and human biology over the past decade has been the gradual expansion in understanding of what an individual represents. Not much more than a decade ago, a lot of people might have said that at its root, an individual was a set of genes in a given environment. The development of genomics has made that more complex as we have become aware of complicated intra- and extra-genetic interactions that go beyond the genes themselves to the structure of the larger genome. And even more recently we have become aware that the basic operation of the human body is dependent on millions and millions of closely associated microbes, all with their own genetic material.

Thinking about this development, Ken Weiss, writing at The Mermaid’s Tale, says this:

Again, as with sex, we may have been misled by Noah’s ark, Linnaeus, and Darwin into life science based on organism, when that is only one aspect of how things are organized. The idea that Nature is composed of a series of distinct species, a legacy of classical thinking up to the present, is actually a large subject with much that is interesting and perhaps truly profound to think about. We’ll discuss it in a subsequent post.

What prompts this discussion is the publication today in Nature of work by a host of people, led by Tanya Yatsunenko, of variation in the human “microbiome” across age in three human population samples; Americans, Amazonian basin Venezuelans and Malawians. The paper has an extraordinary amount of information packed into it, and I will refer you to Ed Yong, writing for Discover, for an excellent recap of the major findings.

First, the similarities. Yatsunenko found that in all three countries, newborn babies have the greatest variety of gut bacteria, both in the species and the genes they carry. As they grow up, especially in their first three years, their microbiomes diversify, while the differences between individuals shrink. This means that adults end up with more diverse gut communities compared to babies, but more similar ones compared to each other. No one really knows why this happens, although studies are afoot to find out. But for now, it tells us that the microbiome matures along a “consistent developmental program”, according to Knight.

Now, the differences. The genetic variation within human populations is greater than the variation between them. The same is true of our microbiomes. That being said, Yatsunenko did find distinct differences between the microbes of all three countries, and especially between the Americans and the other two.

These differences seemed to be largely driven by different diets. For example, Malawian and Venezuelan babies had more gut genes for making vitamin B2 compared to American ones. The vitamin is found in breast milk, meat and dairy products, and it may be that American babies (whose mothers eat more dairy and meat) get more vitamin B2 than those from the other countries.

Given the diversity of environments occupied by humans, the huge range of diets and lifestyles that people and populations lead, and the incredibly rapid transition in those factors within and between populations over the past 30,000 years, the evolution of the human microbiome is an infinitely fascinating topic for studies of human evolutionary history. From a conceptual standpoint it seems an obvious area to look for rapid adaptive evolution given the likely relative ease of changes to the particulate composition of a microbiome as opposed to the complex structure of a human genome.

This paper is just the beginning of this process and an early part of the Human Microbiome Project outlined in 2007 by Peter Turnbaugh and colleagues (including Rob Knight and Jeffrey Gordon, both authors on today’s paper – the image above is drawn from their work). As with my initial thoughts yesterday on the rise of personal genomics and the essential role Anthropology should play, the study of the microbiome is another area that Anthropologists across the sub-fields should have an immense amount of knowledge to contribute.


1. Yatsunenko, T., F. E. Rey, et al. (2012). “Human gut microbiome viewed across age and geography.” doi:10.1038/nature11053.

2. Turnbaugh, P. J., R. E. Ley, et al. (2007). “The Human Microbiome Project.” Nature 449(7164): 804-810. doi:10.1038/nature06244.

About Adam Van Arsdale

I am biological anthropologist with a specialization in paleoanthropology. My research focuses on the pattern of evolutionary change in humans over the past two million years, with an emphasis on the early evolution and dispersal of our genus, Homo. My work spans a number of areas including comparative anatomy, genetics and demography.
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