You are what you feed

The problem of identity – and its flip-side, change – has been vexing philosophers ever since the discipline got started in ancient Greece. As early as 500 years BC, Heraclitus was musing about the ever-changing nature of a flowing river, recorded by his contemporary Plato with the enduring line, “You cannot step in the same river twice.”

This issue comes up everywhere. In an astronomy course I took at university, the professor gave us a mind-boggling assignment: calculate the number of atoms in your body that were once part of a living dinosaur. The answer was a lot, and though I don’t recall the exact number, the question could have just as easily been about sharing atoms with Heraclitus, or Plato, for that matter. The point is that most of the molecules in our bodies are being replaced and recycled, all of the time¹. Like a flowing river, you are literally not the same bag of stuff that you were last year, or even last week; although a more accurate way to put it might be that you are a bag of somewhat different stuff than you contained before.

This raises a tough question. If a different collection of matter can be the same person, how much has to change before you aren’t yourself anymore? The implications are nearer than you might think. Organ transplants, bionic limbs and electronic implants – including devices implanted in the brain – are all within the range of current medicine. How much of a person’s body can we replace and still consider them to be the same person?

I don’t have the answer, and I’m not sure anyone ever will, although some would argue that it is a mistake to assume that there is anything like a constant “you” in the first place. For example, the philosopher Daniel Dennett contends that the idea of a continuous self is really just an illusion produced by the brain².

Biology has a thing or two to say about the matter. It turns out that part of what makes you you is other species. Specifically, the ones living inside you: the veritable ecosystem of bacteria and other microscopic organisms inside your gut. Evidence is mounting that the microcosm within is an important part of who we are: it provides a unique signature of individuality. It can also determine future health. It might even be part of what defines us as human, since a new study shows that as we evolved from ape ancestors, so did our inner ecosystems³.

First, a little background. We all start out sterile – in the womb, our intestinal tracts are germ-free. This is open real estate; at birth, we are rapidly colonized by a huge variety of critters⁴. Historically, it was difficult for science to study the micro-organisms living within because many could not survive outside of their natural environment⁴. Advances in DNA sequencing, and in the computational power required to analyze reams of sequence data, have led to a revolution in our understanding of human micro-flora⁵. We have more cells of other things, inside and all over our bodies, than we do of our own – ten times as many to be exact⁶. Even places like our lungs that we long thought were sterile are teeming with life⁵. What’s more, we cannot live without these critters^5,7. Many of the microbes in our intestines perform essential metabolic functions, digesting things that we cannot break down ourselves. For this reason, medical researchers have characterized the 2-5 pounds of gut flora we all carry around as our “forgotten organ”⁴.

Massive efforts to sequence DNA from gut flora have yielded surprising diversity, with thousands of species coexisting, many previously unknown to science^6,8. These bugs can make a real difference in the way we experience life, including serious impacts on health. People with digestive disorders often have different intestinal flora compared to healthy individuals. Our inner ecosystem might also influence whether or not we develop certain allergies, respiratory disorders and even obesity^9-12. As Carl Zimmer recently described in the New York Times, a new kind of transplant is being used to treat some lethal intestinal infections, and it’s not for the faint of heart. In bacteriotherapy, the ailing patient’s gut is seeded with bacteria from a healthy person’s feces⁵.

In addition to determining the course of our lives, the kinds of bacteria we harbour might also indicate something about us as individuals. Men and women, for example, have different skin flora¹³. The community of skin bacteria even varies between our two hands, with a different set of species living on the dominant hand used for writing¹³. We might be able to harness the power of skin bacteria as a forensic identification tool. Micro-ecologist Noah Fierer found that he could identify the last person to touch a computer mouse or keyboard, just by sequencing DNA from bacteria on the surface of the object – even after it had gone untouched for two weeks¹⁴.

But what about identity in an evolutionary sense? Scientists have long known that organisms living on or in another species – whether helpers or parasites – tend to track the evolution of their hosts. This can lead to cospeciation: when organisms live in close contact, they often diverge into new species in concert with one another. Entomologists studying parasites around the turn of the last century were first to appreciate this, when they noticed that the evolutionary history of lice often maps neatly onto that of their host animals¹⁵.

A similar process has gone on for mammals and their gut bacteria. Recently, enterprising microbiologist Ruth Ley and her colleagues used high-throughput DNA sequencing on fecal bacteria from 60 different mammal species – including humans – to demonstrate that gut bacteria coevolve with their hosts¹⁶. Ley found that herbivores contain more microbial diversity than carnivores. At the same time, closely-related mammals have more similarities in gut flora than distant relatives¹⁶. Overall, the pattern of divergence among the stowaways mirrors the evolutionary tree of the mammals in which they are found, consistent with the idea of host-bacteria cospeciation¹⁶.

The latest word on this subject comes from Howard Ochman at Yale University, and a far-flung group of collaborators from the US, France, Taiwan and the Congo. In Ruth Ley’s earlier study, only 100-200 bacterial sequences were sampled per host mammal, and most of these animals were housed in zoos¹⁶. Ochman and his colleagues focused in on our closest relatives, the great apes, examining wild gorillas, chimpanzees and bonobos from sites across their native ranges in Africa³. Ochman’s team also used a different method of high-coverage gene sequencing, providing a more detailed picture of the abundance of different microbes in the gut flora of each ape. To analyse their data, the authors borrowed from the comparative method in biology. They treated the gut community like a morphological trait, where the abundance of each microbe represents a different dimension – similar to the way paleontologists compare many dimensions of skeletal size and shape.

Ochman and his colleagues found that evolution left its mark on the microcosm. As in Ruth Ley’s earlier study, the changes in gut flora map nicely on to the primate evolutionary tree. However, the new results are the first to demonstrate that this pattern occurs at the level of gut ecology. In other words, host evolution does not just influence microbe speciation – it also shapes the types and abundances of microbes harboured within.

Because the primates used in Ochman’s study came from the wild, with some individuals overlapping in diet and others overlapping in geographic range, the authors could also test which of these factors is most important in determining the composition of gut flora. In this case, evolutionary history trumps diet and location. The journal PLoS Biology reported on this finding, summing it up as, “You Aren’t Always What You Eat“¹⁷. Two primate species that eat similar things can have very different gut bacteria.

I think it’s better characterized as, “You are what you feed”. There is ample evidence from the medical field that what we eat affects the organisms we support; the new results show that this flexibility only occurs within the bounds of evolutionary legacy. In other words, the kinds of critters we are able to feed are part of what makes us human.

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