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3 Ways to Love Your Gut

A microbiologist gives the scoop on feeding the microbes that make us healthy

By Denise Logeland

A microbiologist gives the scoop on feeding the microbes that make us healthy

Everything from immune strength to weight to emotional health appears to depend on how well we take care of our guts.

More specifically, when we do take care of our “gut microbiota” —  the two or so pounds of bacteria and other organisms that live in our intestines — our gut repays us with better health.

Intestinal organisms “influence everything in our body in some direct or indirect way,” says Justin Sonnenburg, an assistant professor of microbiology and immunology at the Stanford University School of Medicine, whose lab is one of the country’s research hubs on gut microbes.

You may know that these microbes help digest our food. What’s less known is that they regulate our metabolism and our susceptibility to disease. And “there are hints that they may be doing a lot to influence our central nervous system, things like moods and behavior,” Sonnenburg says.

These discoveries are “redefining what it means to be human,” he adds. “We are actually not just a collection of human cells. We’re a collection of human cells and microbial cells.”

Sonnenburg’s lab and others are looking at how our human and microbial sides affect each other and how we can support a healthier microbiota. But to understand his advice — and why he’s concerned about what his research is showing — it helps to know a few basics about how our microbiota works with the rest of our bodies.

Healthy Immune Systems

Just as we feed our gut microbes with the food we eat, they feed us with what they excrete. Gross, right? But our microbiota is essential for breaking down foods we otherwise couldn’t digest — complex plant fibers, for instance — and the microbial “feces” that result are also essential to us.

We take these short-chain fatty acids and other metabolites into our bloodstream and they regulate organs and systems throughout our bodies.

A second major way gut microbes influence our health is through our immune system.

“There’s a lot of our immune system that resides within our gut — within our digestive tract — for the express purpose of interacting with the microbiota,” Sonnenburg says. They constantly monitor and send feedback to each other to maintain balance and protect themselves from each other. But there’s also evidence in mouse studies that having or lacking particular microbes “can dictate your success in fighting an ensuing infection.”

Which particular microbes do we need? Even with much more time and research, that’s something we probably won’t be able to make blanket statements about, Sonnenburg says. The complex relationship between microbes and their environment — the mix of other organisms around them, the unique genetic makeup of our bodies as hosts, changes in our immune systems as we age — make simple labels like “good” and “bad” microbes difficult to place.

What is known, he says, is that we evolved with and still need a densely populated and diverse microbiota for good health. Yet in western cultures, we’ve been degrading the culture that lives in our guts, with potentially devastating consequences.

Think of Your Gut as Your Pet

We wipe out gut organisms when we use antibiotics or when we don’t include enough fiber in our diets. When this happens, Sonnenburg’s research shows that “indeed there are species that go extinct” in our individual digestive systems.

Plant fiber is especially important because the microbiota thrives on it. If the microbiota is starved of the fuel it likes best, it begins eating another form of carbohydrate that certain species of microbes can get by on: the mucus lining of the intestinal tract.


Sonnenburg says that as these mucus-eating organisms become a more predominant part of the mix, we create what is, in historical context, a “foreign entity” in our guts.

“To have a microbiota selected on the basis of mucus eating, we don’t really know the long-term implications of that,” he says. “But it’s possible that having a bunch of mucus-eating microbes in your gut could lead to more inflammation.”

His advice? Think of your microbiota as a “forgotten organ” or as a pet that needs care and feeding. Then give it what it needs to thrive.

3 Ways to Build Gut Health

Here are three ways you can build your gut health:

1. Avoid antibiotics. “Just a five-day treatment of Cipro,” for example, “can cause the microbiota to crash, both in terms of density and diversity,” Sonnenburg says. It takes weeks to months for the microbiota to recover, if it ever does completely.

2. Eat more plant fiber. Fiber from whole grains, fruits and vegetables is the main fuel that gut microbes need. Ancient humans ate an estimated 100 grams or more of fiber each day. The current recommended level is 30 grams daily, Sonnenburg says, but “most Americans get around 10 or 15 grams.”

3. Eat fermented foods. Ancient people “were constantly eating microbes from food stored in soil, fermented foods that had been rotting or were starting to go bad," Sonnenburg says. It’s not clear yet exactly what mechanism gives fermentation a positive effect, he says, but there’s growing consensus among researchers that eating yogurt, kefir, and other fermented foods “is probably a good thing.”

Denise Logeland is a longtime business writer and editor whose beats have included the health care industry and financing for medical technology start-ups.

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Denise Logeland is a writer and editor in Minneapolis who has covered business, health and health care. She is the author of Next Avenue's ebook, 10 Things Every Family Should Know: Aging With Dignity and Independence. Read More
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