Fibrous and Fermented Fixes for Foundational Health

Keep your trillions of gut bugs happy and healthy

At Rootstock, everyone pitches in. We all share jobs — farm pick-ups, printing packing labels labels, packing bags, and making deliveries. One of those shared jobs is responding to customer emails.

Recently, while helping a customer renew her membership for fall, I noticed her email signature:

Dept. of Microbiology and Immunology,
Stanford University School of Medicine.

I thought, oooohhh, that’s interesting.

That’s how we met Dr. Erica Sonnenburg, who — along with her husband Justin — runs a lab at Stanford dedicated to studying the gut microbiome. She kindly agreed to chat with us about her research into how what we eat — including the fresh produce in your Rootstock bag — shapes the ecosystem inside our digestive tract.

Meet the Gut Microbiome

“The microbiome is the collection of microbes that inhabit our gut,” Dr. Sonnenburg explained. “It’s a community of bacteria, viruses, and fungi that live in the digestive tract, primarily in the large intestine.”

Dr Sonnenburg and her husband have been working in the gut microbiome for about 25 years. When they started, very few people were paying attention to the bacteria in our gut. 

“We were just young scientists trying to find a field that had interesting questions and we're like, oh, these bacteria in the gut, we don't know that much about 'em.”

That started to change during their training at Washington University, in the lab of Jeff Gordon, where they witnessed a groundbreaking experiment. When microbes from an obese person were transferred into germ-free mice, those mice began gaining weight even without any change in diet. By contrast, mice given microbes from a lean individual did not gain weight. This finding was the initial spark behind today’s more widespread interest in gut health. Scientists are still learning about what goes on in there, but we now know gut bacteria don’t just help us digest food — they influence metabolism, immunity, and health throughout the body.

Since that original study came out, there's been a steady stream of studies linking the gut microbiome to basically everything. 

“Autism, mood disorders, the immune system, autoimmune diseases, and of course inflammatory bowel disease, colorectal cancer… I mean, you name it and there's a paper out there connecting it to the microbiome.” Sonnenburg says.

What’s Happening to Our Guts?

Modern life stresses our gut microbiome in many ways. 

Antibiotic Carpet Bombs

Antibiotics, while powerful, lifesaving, and necessary are “carpet bombing” our guts, says Sonnenburg. These miracle drugs are wiping out both harmful and helpful bacteria. Researchers are now working on new kinds of antibiotics that can target the bad while sparing the good, but those medicines don’t yet exist. 

Picked Too Early, Shipped Too Far

Industrial food systems add another potential challenge. Because produce is often picked before it ripens and stored for long periods during transport, many of the natural compounds that develop in fresh food are lost—compounds our microbiome evolved to expect over hundreds of thousands of years.

“A lot of molecules are produced in plants as they ripen.” Sonnenburg explained. “When you pick early for shipping, you interrupt that process. We don’t yet know how all of those compounds affect the microbiome — but our best guess is that fresher food more closely matches what our bodies evolved to expect.”

The Gut Feeds On Fiber

Our diets are dangerously low in fiber, which means nutrients don’t make it all the way down to the lower part of our digestive tract. Most of what we eat—sugars and fats—gets absorbed quickly in the upper digestive tract. What reaches the colon, and therefore the microbes that live there, is mostly dietary fiber. Fruits, vegetables, legumes, whole grains and nuts are the foods that keep our gut bacteria well-fed and working on our behalf. In our modern diets, fiber is missing.

The average American eats only about 15 grams of fiber per day, far below the recommended 25 to 30 grams. By comparison, hunter-gatherer populations like the ones Sonnenburg has studied in Tanzania consume close to 100 grams of fiber daily, which supports a much richer gut ecosystem—trillions of bacteria, 6 or 7 hundred species—as compared to the average american with maybe 70 or 100 species. Many of our gut bacteria are actually extinct.

“High fiber foods like legumes, whole grains, fruits, vegetables—that's what makes it to the colon. If nothing gets down there, we're not delivering any nutrients to that end of the gut.”

Fermented Foods Fell out of Fashion

Fermented foods such as yogurt, kefir, sauerkraut, and kombucha are all produced by microbes breaking down raw ingredients outside the body—fermenting milk, cabbage, or tea. In the process, those microbes generate a host of compounds, much like the bacteria in our own intestines do when they ferment fiber. When we eat fermented foods, we’re not just consuming beneficial microbes; we’re also taking in the molecules they’ve already produced, which can influence our health in powerful ways. 

In many cultures, fermented foods are quite common—kimchi in Korea, miso in Japan, kefir and sauerkraut in Europe— but in in the US these days it’s much less common. Fermented foods can be tangy, sour, or funky — flavors that many people aren’t accustomed to, especially in Western diets. And again, the industrialized food system favors shelf-stable, pasteurized and processed foods.

What can we do?

In case it’s not obvious, the most powerful step you can take to keep your gut healthy is to eat more fiber — fruits, vegetables, legumes, nuts, and whole grains — and to increase your intake of fermented foods like yogurt, kefir, sauerkraut, kimchi, miso, or kombucha.

It’s also wise to limit unnecessary antibiotics (always follow your doctor’s advice), since they can wipe out good bacteria along with the bad. And beyond diet, simple lifestyle factors — getting enough sleep, exercising regularly, and cutting back on highly processed foods — all help create a healthier environment for your gut ecosystem.

At Rootstock, we’re glad to play our part. Our fall harvest selection has you covered on the fiber front, and we’ve recently added Wise Goat Supergreen Sauerkraut for your fermentation fix. 

Dr. Sonnenburg and her family value farmers’ markets, backyard gardens, and yes — Rootstock — as a steady source of food that’s rich in fiber, fresh, seasonal, and nutritionally dense.

Want to Learn More?

Dr. Sonnenburg and her husband wrote The Good Gut, a groundbreaking book when they wrote it 10 years ago, but its core lessons remain just as relevant today. The book makes the science approachable and is packed with actionable tips, recipes and menu plans.

The Sonnenburgs also appear in the Netflix documentary Hack Your Health: The Secrets of Your Gut released in 2024. The film makes microbiome science easy to understand, blending expert insights with personal stories. The film shows how everyday choices—like what we eat—can shape the bacteria that influence our health.

Next time you bite into a crisp Rootstock apple, picture the trillions of gut bugs waiting at the end of your digestive tract — and how happy they’ll be when that apple makes its way all the way down there.