The University of Texas at Austin. Illustration by Jenna Luecke.
The University of Texas at Austin. Illustration by Jenna Luecke.

Our Gut Microbiome Evolved Alongside Us, Study Finds

The University of Texas at Austin. Illustration by Jenna Luecke.
The University of Texas at Austin. Illustration by Jenna Luecke.

A new study in the journal Science examining the genetics of the bacteria living in the guts of African great apes and people from Connecticut supports the idea that our microbiome has been evolving with us, despite bacteria-affecting changes in environment, diet, geography, and for humans, medicine usage.

Using fecal samples, an international team of scientists led by researchers from the University of Texas at Austin created evolutionary trees for three different groups of bacteria that make up one-fifth of the human gut microbiome, tracing bacterial species back millions of years. They found that our gut microbiome can be traced all the way back to before the human species existed, to the common ancestor that both humans and great apes evolved from millions of years ago. Gut microbes have evolved in parallel with the different species, they say, with genetic splits in bacteria occurring at the same time as gorillas diverged from other hominids about 15.6 million years ago (which is much earlier than some previous estimates) and humans split from chimps and bonobos roughly 5.3 million years ago.

This means that though our environment does affect our microbiome (eating less fiber, for instance, has been shown to alter the bacterial makeup, as has using deodorant), genetics play a major role in the types of species we play host to.

There’s potential that some of our bacterial lineage may be shared with species even farther back in the evolutionary tree, the researchers say. “Maybe we can trace our gut microbes back to our common ancestors with all mammals, all reptiles, all amphibians, maybe even all vertebrates,” study author Andrew Moeller postulates. This research doesn’t dive quite so deep, but future studies might explore those issues.

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Essential Science
What Is a Scientific Theory?
Dean Mouhtaropoulos/Getty Images
Dean Mouhtaropoulos/Getty Images

In casual conversation, people often use the word theory to mean "hunch" or "guess": If you see the same man riding the northbound bus every morning, you might theorize that he has a job in the north end of the city; if you forget to put the bread in the breadbox and discover chunks have been taken out of it the next morning, you might theorize that you have mice in your kitchen.

In science, a theory is a stronger assertion. Typically, it's a claim about the relationship between various facts; a way of providing a concise explanation for what's been observed. The American Museum of Natural History puts it this way: "A theory is a well-substantiated explanation of an aspect of the natural world that can incorporate laws, hypotheses and facts."

For example, Newton's theory of gravity—also known as his law of universal gravitation—says that every object, anywhere in the universe, responds to the force of gravity in the same way. Observational data from the Moon's motion around the Earth, the motion of Jupiter's moons around Jupiter, and the downward fall of a dropped hammer are all consistent with Newton's theory. So Newton's theory provides a concise way of summarizing what we know about the motion of these objects—indeed, of any object responding to the force of gravity.

A scientific theory "organizes experience," James Robert Brown, a philosopher of science at the University of Toronto, tells Mental Floss. "It puts it into some kind of systematic form."


A theory's ability to account for already known facts lays a solid foundation for its acceptance. Let's take a closer look at Newton's theory of gravity as an example.

In the late 17th century, the planets were known to move in elliptical orbits around the Sun, but no one had a clear idea of why the orbits had to be shaped like ellipses. Similarly, the movement of falling objects had been well understood since the work of Galileo a half-century earlier; the Italian scientist had worked out a mathematical formula that describes how the speed of a falling object increases over time. Newton's great breakthrough was to tie all of this together. According to legend, his moment of insight came as he gazed upon a falling apple in his native Lincolnshire.

In Newton's theory, every object is attracted to every other object with a force that’s proportional to the masses of the objects, but inversely proportional to the square of the distance between them. This is known as an “inverse square” law. For example, if the distance between the Sun and the Earth were doubled, the gravitational attraction between the Earth and the Sun would be cut to one-quarter of its current strength. Newton, using his theories and a bit of calculus, was able to show that the gravitational force between the Sun and the planets as they move through space meant that orbits had to be elliptical.

Newton's theory is powerful because it explains so much: the falling apple, the motion of the Moon around the Earth, and the motion of all of the planets—and even comets—around the Sun. All of it now made sense.


A theory gains even more support if it predicts new, observable phenomena. The English astronomer Edmond Halley used Newton's theory of gravity to calculate the orbit of the comet that now bears his name. Taking into account the gravitational pull of the Sun, Jupiter, and Saturn, in 1705, he predicted that the comet, which had last been seen in 1682, would return in 1758. Sure enough, it did, reappearing in December of that year. (Unfortunately, Halley didn't live to see it; he died in 1742.) The predicted return of Halley's Comet, Brown says, was "a spectacular triumph" of Newton's theory.

In the early 20th century, Newton's theory of gravity would itself be superseded—as physicists put it—by Einstein's, known as general relativity. (Where Newton envisioned gravity as a force acting between objects, Einstein described gravity as the result of a curving or warping of space itself.) General relativity was able to explain certain phenomena that Newton's theory couldn't account for, such as an anomaly in the orbit of Mercury, which slowly rotates—the technical term for this is "precession"—so that while each loop the planet takes around the Sun is an ellipse, over the years Mercury traces out a spiral path similar to one you may have made as a kid on a Spirograph.

Significantly, Einstein’s theory also made predictions that differed from Newton's. One was the idea that gravity can bend starlight, which was spectacularly confirmed during a solar eclipse in 1919 (and made Einstein an overnight celebrity). Nearly 100 years later, in 2016, the discovery of gravitational waves confirmed yet another prediction. In the century between, at least eight predictions of Einstein's theory have been confirmed.


And yet physicists believe that Einstein's theory will one day give way to a new, more complete theory. It already seems to conflict with quantum mechanics, the theory that provides our best description of the subatomic world. The way the two theories describe the world is very different. General relativity describes the universe as containing particles with definite positions and speeds, moving about in response to gravitational fields that permeate all of space. Quantum mechanics, in contrast, yields only the probability that each particle will be found in some particular location at some particular time.

What would a "unified theory of physics"—one that combines quantum mechanics and Einstein's theory of gravity—look like? Presumably it would combine the explanatory power of both theories, allowing scientists to make sense of both the very large and the very small in the universe.


Let's shift from physics to biology for a moment. It is precisely because of its vast explanatory power that biologists hold Darwin's theory of evolution—which allows scientists to make sense of data from genetics, physiology, biochemistry, paleontology, biogeography, and many other fields—in such high esteem. As the biologist Theodosius Dobzhansky put it in an influential essay in 1973, "Nothing in biology makes sense except in the light of evolution."

Interestingly, the word evolution can be used to refer to both a theory and a fact—something Darwin himself realized. "Darwin, when he was talking about evolution, distinguished between the fact of evolution and the theory of evolution," Brown says. "The fact of evolution was that species had, in fact, evolved [i.e. changed over time]—and he had all sorts of evidence for this. The theory of evolution is an attempt to explain this evolutionary process." The explanation that Darwin eventually came up with was the idea of natural selection—roughly, the idea that an organism's offspring will vary, and that those offspring with more favorable traits will be more likely to survive, thus passing those traits on to the next generation.


Many theories are rock-solid: Scientists have just as much confidence in the theories of relativity, quantum mechanics, evolution, plate tectonics, and thermodynamics as they do in the statement that the Earth revolves around the Sun.

Other theories, closer to the cutting-edge of current research, are more tentative, like string theory (the idea that everything in the universe is made up of tiny, vibrating strings or loops of pure energy) or the various multiverse theories (the idea that our entire universe is just one of many). String theory and multiverse theories remain controversial because of the lack of direct experimental evidence for them, and some critics claim that multiverse theories aren't even testable in principle. They argue that there's no conceivable experiment that one could perform that would reveal the existence of these other universes.

Sometimes more than one theory is put forward to explain observations of natural phenomena; these theories might be said to "compete," with scientists judging which one provides the best explanation for the observations.

"That's how it should ideally work," Brown says. "You put forward your theory, I put forward my theory; we accumulate a lot of evidence. Eventually, one of our theories might prove to obviously be better than the other, over some period of time. At that point, the losing theory sort of falls away. And the winning theory will probably fight battles in the future."

iStock/Chloe Effron
Why Does My Skin Wrinkle in Water?
iStock/Chloe Effron
iStock/Chloe Effron

WHY? is our attempt to answer all the questions every little kid asks. Do you have a question? Send it to

Have you ever noticed that your fingers and toes get wrinkled when you’ve been soaking in water for a while? We often call this “prune hands,” because it makes your fingers look shriveled like a prune. (A prune is a dried plum.) The shriveling happens when blood vessels under your skin get narrower. This is caused by your autonomic (Aw-toe-NAW-mick) nervous system. This system keeps your lungs breathing and your heart beating without you having to think about it. 

The wrinkles seem to help us grip and not slip! Look at the bottom of your shoe. Does it have grooves? Those are called treads. The tires on cars and buses have treads too. The water that goes into those narrow grooves gets pushed away. It works the same way with your skin. Water drains from your hands through these grooves. We think this helps us to hold onto objects better. Scientists tested this theory with an experiment. They asked people with wet, wrinkled hands to pick up wet marbles and dry marbles. People picked up the wet marbles faster with wet, wrinkled hands.

Some scientists now think that humans evolved (Ee-VAWLVD)—changed over time—to have this reaction. Being able to hold onto wet things might have helped our ancient ancestors survive. Think about it: if your food lives in a wet place, like a river, ocean, or rainforest, you have a better chance of grabbing it if your fingers “stick” to it. If you are climbing a wet tree, wrinkled fingers might help keep you from falling. Wrinkled toes can help, too. If you’re barefoot, your toes need a good grip in wet or muddy places. 

Want to hear more about the marble experiment? Watch this video from SciShow.


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