Eating for Your Microbiome

By: Christy Harrison, M.P.H., R.D.

It seems like everywhere you turn these days, there’s another story about the wonders of intestinal bacteria. Recent research has linked organisms in the gut to conditions including bowel diseases, obesity and even changes in mood and behavior. A few studies have also indicated that what we eat significantly affects the makeup of our gut bugs. So what does this mean for nutrition? Should healthy eating now include eating for gut health—and what would that entail?

First, a little background. The trillions of microorganisms, or “microbiota,” in our guts form a kind of ecosystem known as the microbiome. (You may have also heard the microbiome referred to as intestinal flora or microflora, but those terms have fallen out of favor because they imply that our intestines are colonized by tiny plants.) These organisms outnumber human intestinal cells by about 10 to 1 and play an important role in our immune system.

Research began focusing seriously on the microbiome in the past decade, when genetic sequencing of gut microorganisms became feasible. Studies in mice and humans have now linked the microbiome to brain development and behavior (possibly because microbiota influence the production of neurotransmitters and brain synapses); overweight and obesity (perhaps partly because some microbes help extract more nutrients from food); food allergies and inflammatory bowel diseases (possibly because the immune system is compromised by lower microbiome diversity in people with these conditions) and colorectal cancer (perhaps due to pro- and anti-carcinogenic compounds produced by different gut bacteria). Diet also appears to influence the makeup of the microbiome: Some small studies in humans have shown that the microbiota of people whose diets are primarily plant-based are significantly different than those of people whose diets are primarily animal-based.

A major caveat here is that research on the microbiome is still in its infancy, and science hasn’t pinned down the precise role microbiota play in the development of disease. Changes in the microbiota might turn out to be merely a side effect of obesity or other health conditions, not a causal factor in these conditions.

But with that caveat in mind, here are some ways you might alter your diet for better gut health. If the microbiome does turn out to be a major factor in the development of disease, you’ll be ahead of the curve. And if not, these changes certainly couldn’t hurt (you may notice that the recommendations for gut health are surprisingly similar to what most nutrition experts have been recommending for years!).

-     “Eat food. Not too much. Mostly plants.” These three simple lines (coined by Michael Pollan in his wonderful book In Defense of Food) apply as much to gut health as they do to overall nutrition. Eating adequate amounts of food keeps intestinal microbiota alive and kicking but not overwhelmed with nutrients (which could lead to imbalances in the species of organisms). And eating mostly plants, as opposed to mostly animal products, helps reduce the particular microbial species that are associated with obesity.

-     Take probiotics. These beneficial bugs help improve the diversity and makeup of the microbiome. In clinical trials, both supplemental and food forms of probiotics have been found to be associated with improved outcomes for conditions like diarrhea and eczema, and for overall health maintenance. Probiotic microbial strains won’t flourish in your gut without continued supplementation, so a daily dose is recommended.

-     Consume adequate fiber. It can help prevent colonization by harmful microbes and reduce inflammation (which has been linked to many chronic conditions, including inflammatory bowel disease, cancer, and even allergies and respiratory illness). It’s most beneficial if the fiber comes from whole plant foods rather than supplements, since whole foods contain a host of other nutrients that may contribute to gut and overall health.

-     Encourage diversity. A more diverse microbiome is associated with leanness, as well as protection from many of the diseases mentioned above. To ramp up the diversity, eat a wide variety of foods, particularly (you guessed it) high-fiber plant-based ones: There is thought to be a particularly large variety of microbes associated with these foods. Another study shows that exercise may also help increase diversity in the microbiome.

-     Expose yourself (and your kids) to germs. OK, so this isn’t a dietary recommendation per se, but it appears to be an important component of gut health. If you’re able to give birth via normal delivery rather than C-section, do it; if you’re able to breastfeed, do it. These exposures in the first few days of life give your child a head start on developing a diverse microbiome and may help protect against allergies.

Christy Harrison, MPH, RD, is a registered dietitian nutritionist specializing in chronic disease prevention, weight management and eating disorders. She writes about food and nutrition for various publications and hosts Food Psych, a podcast about the psychology of eating. Find her at

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