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Your gut microbiome — a collection of trillions of microorganisms inhabiting your intestinal tract — has wide-ranging effects on your health. Your unique mix of bacteria, fungi, parasites and viruses reflects your genes, your age, the medications you take — but most of all, what you eat.

Over the past two decades, numerous studies have explored how gut microbes and their breakdown products (metabolites) affect factors linked with heart disease. For the most part, the findings support the same basic advice health experts recommend: Follow a mostly plant-based eating pattern and cut back on highly processed foods. Doing so can help promote a more diverse, healthier microbiome.

“The standard American diet — appropriately called SAD — features a lot of processed foods that are high in sugar, artificial sweeteners and unhealthy fats,” said Dr. Uma Naidoo, director of nutritional and metabolic psychiatry at Harvard-affiliated Massachusetts General Hospital.

This nutrient-poor diet can lead to dysbiosis, an overgrowth of harmful microbes. When bad microbes thrive in the gut, they form pro-inflammatory breakdown products and toxins, Dr. Naidoo explains. The resulting low-grade, body-wide inflammation contributes to obesity, poor mental health, diabetes and cardiovascular disease.

Animal vs. plant-based foods

One metabolite of interest is trimethylamine (TMA), which is created when gut microbes feed on choline, a nutrient found in red meat, fish, poultry and eggs. In the liver, TMA gets converted to trimethylamine N-oxide (TMAO).

While some research suggests a link between TMAO and artery-clogging plaque, the evidence isn’t consistent. Still, the advice to limit red meat consumption — the main source of TMA in the diet — makes sense.

But according to Dr. Naidoo, there’s no need to avoid those animal-based foods, which is something most Americans aren’t especially keen on doing. Instead, people should focus more on what they’re not eating — namely, fruits, vegetables and whole grains.

Diversify your diet

A woefully small percentage of adults — only about 10% — eats the recommended daily amount of fruit (one-and-a-half to two cups) or vegetables (two to three cups).

Don’t limit yourself to only a few favorites like apples or broccoli, said Dr. Naidoo. “Eat a wide variety of different fruits and vegetables on a regular basis to bring biodiversity to your microbiome,” she said.

Despite a recent uptick, whole grains make up less than 16% of the average American’s total grain intake. Whole grains such as oats, quinoa, spelt and barley are healthier choices than most “whole-wheat” bread, which isn’t always made with 100% whole grains. Other foods that promote gut health include beans, lentils, nuts and seeds.

Fruits, vegetables, beans and whole grains are good sources of fermentable or prebiotic fiber, which gets broken down by bacteria in your colon to form short-chain fatty acids. These compounds then circulate through the bloodstream and interact with receptors on cells that quell inflammation. The fatty acids also appear to play a role in keeping blood sugar, blood pressure and cholesterol levels in check.

You can also increase good gut bacteria levels by consuming probiotics, which are found in fermented foods (see box). “Try adding a little bit of these foods to your meals and then grow from there,” Dr. Naidoo suggested.

© 2023 by Harvard University