Me, Myself, and a Hundred Trillion

Dining With Your Gut Microbiome

Do you really want to eat that second slice of cake?

Oh, no — you look great! I only ask because it may not actually be you who wants it.

Let me explain. What if I told you that there were a few trillion extra cells inside your body scarfing down the food you eat, controlling your immune system, and even influencing your cravings for sugar and fat? Scientists have recently suggested that our gut microbiome — the enormous collection of microbial cells that coexists peacefully alongside our human cells in our digestive tract — may have the capacity to influence our diet to meet their own nutritional needs.

It turns out that we are totally dependent on cells that are not even our own for daily functioning. Though invisible to the naked eye, the gut microbiome fends off harmful germs, hones our immune responses, and even helps us get the most out of our food. And sure, these processes benefit the microbes, but they improve the wellbeing of actual human cells as well. After all, we provide the microbes a habitat, so keeping us healthy is to everyone’s advantage.

In particular, digestion just wouldn’t be the same without the bacteria in our gut: not only do they help us digest the complex molecules in our food, but, in doing so, also produce compounds essential for our health. Every time you eat, you’re eating for trillions of non-human cells — and life wouldn’t be the same without them.

The Power Within: Our Gut Microbiome

Microbes are found all over the body. Each of our bodies is home to about two to five pounds of living microbes; compare that to the human brain, which clocks in at about three pounds. The dozens of trillions of microbial cells in and on each human body actually outnumber our own — in this way, you could say we’re more bacterial than human.

Picture yourself as a giant donut, with the hole in the middle starting from your mouth and ending at your bum — all this can be considered the “outside” of your body. And every last bit of the outside of your body is teeming with microbes, the grains of sugar every powdered donut is incomplete without. The biggest and most diverse population, however, is found in your colon. After all, it’s the easiest way for our microbes to access the food they like best: molecules that have already been liberated by the digestive enzymes in our intestinal tract and far from the harsh acidic conditions of the stomach. From here, though, these microbes power reactions that resonate throughout the rest of the body, producing molecules that help our immune system distinguish friend from foe, affect how full or hungry we feel, and even influence brain activity. All this is made possible because, in our guts, bacteria can access the partially digested food passing through our intestines and turn it into a few essential substances we cannot produce on our own.

Chew on This: Our Second Stomach

We eat to survive — that much is obvious. But nutrition is not simply about calories. To be healthy, we also need to extract nutrients, vitamins, and minerals from our food. This means getting the right balance of carbohydrates, fats, and proteins, as well as accessing the important chemicals our body needs to function but cannot manufacture itself.

The human body is quite good at extracting fats and proteins from food. But the story gets a little more complicated when we consider carbohydrates. The machinery of the human body can easily digest simple carbohydrates, like those found in milk, fruits, processed foods, and foods containing refined sugar. Simple carbohydrates are “simple” because they are mono- or disaccharides — that is, molecules containing only one or two sugar rings in their chemical structure. Monosaccharides can be directly utilized by the body with molecular machines called enzymes.

On the other hand, complex carbohydrates, those found in “starchy” foods like potatoes, corn, and beans, require some work by more sophisticated human enzymes. In particular, a human enzyme called amylase plays a large role here. Think of when you’ve held bread or rice in your mouth for a while before swallowing — it starts to taste sweet because amylase has already begun the process of breaking the starches down into simple sugars.

However, amylase and its partners are useless when it comes to dietary fiber, the poop-friendly component of most plant-based foods that our doctors are always pushing on us. Fiber is most abundant in fruits, vegetables, beans, and whole grains, and is made up of sugars bonded together with some links that human enzymes cannot break.

However, with the help of our gut microbes, we can get as much as 10% of our daily caloric intake out of otherwise indigestible dietary fiber. In fact, scientists have found that mice that have been raised without gut microbes — so-called “germ-free” mice — eat more and weigh less. But the importance of fiber goes far beyond a boost in calories liberated by our microbiome.

Say you’ve just taken a bite of a bean burrito. Some of the bean starches will break down by the time they reach your small intestine, but the beans’ fiber will travel unscathed through the gastrointestinal tract until it reaches the colon. Here, bacteria will break down and enthusiastically ferment the fiber into short-chain fatty acids.

Short-chain fatty acids are a compound that the human body cannot produce itself, but supply an enormous amount of energy to the cells that line our gut. From there, they can also be utilized to nourish the rest of the body. In recent years, scientists have come to truly appreciate the importance of these compounds, and have tied them to colonic health in several ways. For instance, short-chain fatty acids tend to be less abundant in patients with severe inflammatory bowel disease. What’s more, preliminary studies have shown that short-chain fatty acids may actually serve as a powerful therapeutic to treat everything from diarrhea to Crohn’s disease. In a way, short-chain fatty acids are the crux of many of the health-conferring benefits of having a gut microbiome in the first place. Not only do they nourish and sustain us, but they also keep the cells of the gut in good working order.

Short-chain fatty acids are made available courtesy of our gut bacteria which harbor genes that encode carbohydrate-digesting enzymes distinct from ours — enzymes that can break the bonds in dietary fiber and convert the sugars within into key nutrients. The downside is the most notable byproduct of this process — gas, including carbon dioxide, hydrogen, and methane.

This process applies not only to dietary fiber, but also an array of other non-digestibles. If you suffer from lactose intolerance, you can blame your gut microbiome for your symptoms. During infancy, all humans produce lactase, an enzyme that breaks down lactose, the main sugar present in milk, allowing our bodies to derive precious energy from our mother’s milk. But after humans are weaned off milk, many people stop producing lactase, meaning lactose does not get broken down in our intestines.. Undigested lactose passing through the colon is fermented into fatty acids and gases, causing flatulence and bloating. A similar process occurs when humans ingest sugar alcohols, which are often used as low-calorie sweeteners in sugar-free products (like these infamous gummy bears) and many other processed foods. Our bodies do a poor job of breaking down sugar alcohols, leaving many of them, including xylitol and sorbitol, free to be fermented by the gut microbiome.

And that’s not all. Our gut microbes also play a big role in manufacturing vitamin K and several B vitamins, and aid in the absorption of essential minerals. In fact, the American Academy of Pediatrics recommends a shot of vitamin K at birth to ensure proper blood clotting, in part because infants’ microbiome are not yet developed enough to produce sufficient vitamin K.

You Are What You Eat

Image: Olgierd Rudak

After the first few months of life, the microbes in our gut mature, and the composition of the population stays mostly the same throughout our adult life. However, microbiomes vary from person to person — and these populations are subject to change. There’s good evidence that what we eat influences the makeup of our gut microbiome.

Scientists agree that a diverse microbiome is a healthy microbiome. Eating a diet rich in sugar, meat, and processed foods appears to diminish the diversity of your gut microbes, and this has been shown to contribute to inflammation and obesity. But just like there is not one healthy way to live, there is clearly not one healthy or ideal microbiome — no one size fits all. And it’s never too late to start cultivating a more robust, healthy microbiome with more fruit, vegetables, whole grains, and beans — whole, unprocessed, plant-based foods rich in fiber.

The diet-microbiome relationship also appears to be a two-way street. Certain members of the gut microbiome influence human cravings for nutrients so bacteria can access the sugars and fats they need. Scientists are not entirely sure how this works, but this much is clear: microbes living in our gut produce functional chemicals that can send signals to the brain. Replacing the microbiome of an anxious mouse with that of an adventurous mouse can make the formerly nervous mouse more outgoing (and vice versa). If it’s a similar story for us, it’s very possible that the microbe-derived molecules in our gut may be affecting both our mood and food cravings.

So before you sheepishly scrap your Friday night burrito plans, sit back and appreciate the bustling community hard at work in your gut at this very moment. Every mouthful that passes through your midsection represents another delivery of nutrients flooding your body, another essential molecule being synthesized, another signal reverberating to the neurons in your head — and infinitely more. Sit back and enjoy the ride — just, maybe warn the guy sitting next to you first.

Katherine Wu is a PhD candidate at Harvard University, where she studies bacterial stress responses. She is Co-Director of Science in the News, a graduate student organization that trains scientists to better communicate with the general public.


I Contain Multitudes is a multi-part video series dedicated to exploring the wonderful, hidden world of the microbiome. The series is hosted by science writer Ed Yong and produced by HHMI Tangled Bank Studios in association with Room 608.