The Microbiome Is Science’s Hot New Kid

As Americans, we love the concept of self-improvement.

Self-help books line bookstore shelves, psychologists have taken over network TV, and smartphone apps track our every step and calorie. Many months ago, a lot of us made New Year’s resolutions to be happier, stronger, and healthier. We’re constant improvement projects—fixer-uppers if you will—with positive affirmations and sticky note reminders to get to the gym TODAY.

But change is hard. It takes work, and sometimes no matter what we do we’re still cranky, dysfunctional sofa sloths.

Self-help culture implies that our dysfunction is simple laziness. If only we worked harder, ate less, exercised more—then and only then will we be the person we are meant to be! We blame ourselves for not being happy or losing weight. Even more satisfying: We blame our parents for the subpar genetics we inherited that made us this way.

But what if we had something else to explain our behaviors, our weight, or our risk for disease? What if it had to do with the trillions of organisms living inside us—especially those in the gut? The trillions of organisms making up our microbiome are the subject of an exploding field of research now touching almost every field of medicine. It turns out that our poop has just become very interesting. New research tools in genomic sequencing and molecular biology have allowed us to discover that our microbiome really matters—a lot.

So what is the microbiome exactly? Our microbiota is the ecosystem of organisms that live in and on our body. It includes all the bacteria, viruses, and fungi that we carry with us on our skin, in our mouths, and throughout our gut. There are so many of them, in fact, that we are really more them than us: Bacterial cells outnumber our own human cells 10 to 1. That means that we are more non-self than self (meditate on that one, people!)

We’ve known for a long time about how individual organisms make us sick, and we’ve been hell-bent on slaughtering them with antibiotics. We also know that drug-resistant bacteria are taking over hospitals and clinics. It’s becoming increasingly clear that we are no longer winning the battle against bacteria and viruses—they are so much smarter than us. In the midst of rushing to develop stronger antibiotics (which only briefly overcome microbial resistance strategies), a new paradigm for thinking about how to treat infections has emerged and it has to do with manipulating our microbiome.

We have, in fact, been manipulating our microbiome with diet since the first humanoid decided that fermented leftovers were mighty tasty. And we continue the tradition today with yogurt, kimchee, kombucha, sauerkraut, and all the other stuff that smells kinda weird but our gut just loves. What we didn’t know then but have started to appreciate now is that foods full of microflora influence our health because they influence our microbiome.

We’re told (thanks Jamie Lee Curtis!) to ingest yogurt laden with the probiotic bacteria Lactobacillus and Bifidobacterium because it makes us “regular.” What these good bacteria also do is to prevent pathogens from taking over and causing infection. The probiotic “healthy bugs,” known as commensal organisms, digest dietary fiber from the fruits and vegetables that our own bodies can’t digest, producing products like short chain fatty acids (SCFAs) that help to improve our immune function.

In addition to preventing infection and enhancing immune function, researchers have started using probiotics to actually treat infection. Let’s repeat that: They’re using bacteria to treat bacterial infections instead of using antibiotics. This has revolutionized how we think about treating infectious disease. Instead of wiping out an entire ecosystem of organisms with antibiotics, we can make our microbiome healthier and more capable of outcompeting pathogens.

It’s akin to learning that clear-cutting a forest and growing a single crop isn’t healthy for the planet, and that maybe supporting a more diverse ecosystem is the way to go—except the ecosystem we need to support is made up of organisms in our gut. And clear-cutting our own diverse community of bacteria with antibiotics is without a doubt making us sicker. And crankier. And more likely to gain weight and develop type II diabetes.

New studies support that our microbiome influences more than what goes on in our gut. If food is the way to the heart, it may also be the way to the mind.

Germ-free mice that have no bacteria, viruses, or fungi (and therefore no microbiota) exhibited greater anxiety behaviors. When these mice are given certain strains of bacteria like Bifidobacterium infantis (one of the bacteria found in yogurt—Ms. Curtis would be so proud!), they exhibited hormone levels consistent with decreased stress levels. If germ-free mice are given the microbiota of another mouse, they developed behaviors similar to that of the donor mouse: Timid mice became more daring when they received the gut microbiota of a more adventurous chap, and vice versa.

Those critters in your gut also influence weight and are, in turn, influenced by diet and the use of antibiotics. Mice exposed to penicillin were found to have a substantially increased level of body fat compared to those who had not been given any antibiotics. Furthermore, the microbiota of the penicillin-exposed mice were then given to germ-free mice who also developed increased body fat. The combination of penicillin and a high-fat diet led to substantially greater fasting insulin levels than either condition (antibiotics or diet) alone. And higher fasting insulin levels leads to the development of diabetes.

But not to worry, right? Avoid antibiotics and chase your salad with a diet soda, you might say. But it turns out that although overweight mice who were given aspartame—the artificial sweetener in most diet drinks—gained less weight and consumed fewer calories, they developed higher levels of insulin-resistance, consistent with a higher risk of diabetes. And as expected, microbiota were to blame: Aspartame encouraged the growth of certain types of bacteria in the gut, which are known to exert a negative influence on insulin tolerance.

So how can we win? Not surprisingly, we can be nice to our microbiota and eat more fruits and vegetables, fermented foods, and avoid antibiotics and diet drinks. We might actually be leaner, healthier, and happier—perhaps even less cranky and dysfunctional.