Feed Your Gut Microbiota for Health

Your gut microbiome is responsible for your health, from your tummy to your brain, so learn how to feed your gut microbiota well for good health.

Your gut is teeming with microscopic organisms that play a huge role in your health. “By cell number, we are more microbial than we are human,” says Justin L. Sonnenburg, PhD, a leading gut microbiota expert and associate professor at the Stanford University School of Medicine. Sonnenburg explains that we have 100 times more genes in our microbial genome (our complete collection of genetic material) than in our human genome, saying, “We are a fancy culturing flask.” In the gut microbiome, the community of microorganisms (or microbiota) living in your intestinal tract, the microbiota living there are not only essential to the breakdown and absorption of nutrients from food, they are closely linked to our overall health.

Feed Your Gut Microbiota for Health

Key to Gut Microbial Terms



Gut microbiota Microorganisms living in your gut
Gut microbiome The community of microorganisms living in your intestinal tract
Microbial genome The complete collection of genetic material in the body’s microbiome
Dietary fiber The indigestible portion of food derived from plants
Short chain fatty acids Produced by bacteria in the gut during fermentation of fiber
Gut microbiota diversity Range of different types of microorganisms in the gut microbiota
Probiotics A microorganism introduced into the body for beneficial qualities, such as yogurt or supplements
Prebiotics A nondigestible food ingredient that promotes the growth of gut microorganisms
Feed your gut bacteria with fiber, such as this fiber-rich recipe for Oats and Spicy Nut Butter with Apples.

Microbial Control Center. Your intestinal community of microorganisms is what Sonnenburg calls a “control center” for human biology. It’s responsible for more than just digestion. The gut microbiota control all of human biology, including the immune system and metabolism, influencing diseases like obesity and metabolic syndrome—a cluster of risk factors that raise the risk for cardiovascular and metabolic diseases.

A seminal study (Nature, 2006) found that the microbiota actually can promote disease. The microbiota of obese humans and mice both show an increased ratio of Firmicutes Bacteroidetes (two major types of bacteria in the gut) compared to that of lean individuals. In the study, the microbiota of obese mice were transferred into lean mice by fecal transplant. The lean mice became obese. “The microbiota was causing them to be obese,” Sonnenburg says about this first batch of data to show this result. Just six years later, a human study found that the transfer of the intestinal microbiota from lean donors increased insulin sensitivity in people with metabolic syndrome (Gastroenterology, 2012).

This recipe for Vegetarian Baked Beans provides an excellent source of fiber.

Feeding Your Friendly Bacteria with Fiber. When you eat food, the digestible nutrients are absorbed in the small intestines, leaving the indigestible dietary fiber from plant foods behind. The fiber moves to the large intestine where the microbiota live, becoming their only food source—in return the microbiota make short chain fatty acids, the end products of fermentation which are beneficial for metabolism. If fiber isn’t available, the microbiota start eating away at the carbohydrate-rich mucus layer of the gut, inciting inflammation.

“Our microbiota has no option but to start eating away at the gut’s mucus layer if there’s no dietary fiber. The resulting inflammation is weakening our immune systems and leading to disease,” says Sonnenburg. With the rise of Western diseases, such as heart disease and type 2 diabetes and with inflammation at the root of all of these diseases, diet plays a huge role.

“Time has changed the way we eat in this country. We used to eat a lot of fiber, but today we eat a lot of processed foods,” says Sonnenburg.

Lower calorie, nutrient-rich, high-fiber foods, such as this Moroccan Chickpea Sorghum Bowl, are important for boosting gut bacteria diversity.

Diminishing Diversity. Lack of dietary fiber also leads to a decline in gut microbiota diversity, which is linked to poor health. A 2013 study in Nature showed low diversity microbiota is linked to many negative health effects, like increased fat storage and accumulation, increased cholesterol and triglyceride levels, and higher rates of insulin resistance. The study also found that dietary intervention—lower calories, increased fiber, low-glycemic foods—leads to higher microbiota diversity and better health, with lower body fat, decreased inflammatory and triglyceride levels, and improved insulin sensitivity.

Include more fermented foods, such as this recipe for Creamy Peach Yogurt Parfait.

Focus on Probiotics and Fermented Foods. “Fermented foods and probiotics often have many health benefits and can help increase microbiota diversity,” says Sonnenburg. Probiotics, live microorganisms that benefit health, are found in cultured dairy products, like yogurt or kefir; fermented foods like sauerkraut, miso and tempeh; and supplements. Increasing total fiber from plant food sources, such as whole grains, pulses, fruits, vegetables, nuts, and seeds, is important for a healthy microbiome. Consuming prebiotics—indigestible plant fibers that feed the probiotics—is also key (see “Prebiotic Stars”).

The good news is that a healthy change in your gut microbiota happens quickly—as soon as one week! The body is very sensitive to dietary change. It takes only a few days for the activity and composition of gut bacteria to alter and affect our health.

Herbed Grilled Artichokes

Prebiotic Stars

The following foods contain indigestible, fermentable carbohydrates, which can help nourish your gut microbiota.

  • Artichokes
  • Asparagus
  • Burdock
  • Chicory
  • Dandelion greens
  • Garlic
  • Leafy greens
  • Jerusalem artichoke
  • Jicama
  • Leeks
  • Lettuce
  • Onions
  • Onions, green
  • Salsify
  • Shallots
  • Yacon
  • Bananas

For other blogs on promoting a healthy gut microbiota, check out these:

Learning All About Probiotics
Good Gut Bacteria Boost Immune Health

Written by Sharon Palmer, MSFS, RDN

Image: Beets at the Pasadena Farmers Market, Sharon Palmer, MSFS, RDN

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