If you’re making resolutions for a healthier new year, consider a gut makeover. Refashioning the community of bacteria and other microbes living in your intestinal tract, collectively known as the gut microbiome, could be a good long-term investment in your health.

Trillions of microbial cells inhabit the human body, outnumbering human cells 10-1 according to some estimates, and growing evidence suggests that the rich array of intestinal microbiota helps us process nutrients in the foods we eat, bolsters the immune system and does all sorts of odd jobs that promote sound health. A diminished microbial ecosystem, on the other hand, is believed to have consequences that extend far beyond the intestinal tract, affecting everything from allergies and inflammation, metabolic diseases like diabetes and obesity, even mental health conditions like depression and anxiety.

Much of the composition of the microbiome is established early in life, shaped by forces such as your genetics and whether you were breast-fed or bottle-fed. Microbial diversity may be further undermined by the typical high-calorie American diet, rich in sugar, meats and processed foods. But a new study in mice and people adds to evidence that suggests you can take steps to enrich your gut microbiota. Changing your diet to one containing a variety of plant-based foods, the new research suggests, may be crucial to achieving a healthier microbiome.

Altering your microbiome, however, may not be easy, and nobody knows how long it might take. That’s because the ecosystem already established in your gut determines how it absorbs and processes nutrients. So if the microbial community in your gut has been shaped by a daily diet of cheeseburgers and pepperoni pizza, for example, it won’t respond as quickly to a healthy diet as a gut shaped by vegetables and fruits that has more varied microbiota to begin with.

“The nutritional value of food is influenced in part by the microbial community that encounters that food,” said Dr. Jeffrey Gordon, the senior author of the new paper and director of the Center for Genome Science and Systems Biology at the Washington University School of Medicine in St. Louis. Nutritional components of a healthy diet have to be viewed from “the inside out,” he said, “not just the outside in.”

One of the questions the study set out to answer was how individuals with different diets respond when they try to improve their eating habits. The scientists harvested gut bacteria from humans, transplanted them into mice bred under sterile conditions, and then fed the mice either American-style or plant-based diets. The scientists then analyzed changes in the mice’s microbial communities.

Of interest, the scientists harvested the gut bacteria from people who followed sharply different diets. One group ate a fairly typical American diet, consuming about 3,000 calories a day, high in animal proteins with few fruits and vegetables. Some of their favorite foods were processed cheese, pepperoni and lunch meats.

The other group consisted of people who were devotees of calorie restriction. They ate less than 1,800 calories a day and had meticulously tracked what they ate for at least two years, sticking to a mostly plant-based diet and consuming far less animal protein than the other group, a third fewer carbohydrates and only half the fat.

This calorie-restricted group, the researchers found, had a far richer and more diverse microbial community in the gut than those eating a typical American diet. They also carried several strains of “good” bacteria, known to promote health, that are unique to their plant-based diet. “Their choices as adults dramatically influenced their gut community,” said Nicholas W. Griffin of Washington University, the paper’s lead author.

The study, published in Cell Host & Microbe, is not the first to report findings suggesting dietary shifts can induce persistent changes in a gut microbial community, said Dr. David A. Relman, a professor of medicine, microbiology and immunology at Stanford University, who was not involved in the current research. He noted that other studies had found even more profound effects.

After the human microbiota was transplanted into the mice, the mice got to eat either like typical Americans or like the calorie restrictors.

Mice that had a microbiota conditioned by the typical American diet had a weaker response to the plant-based diet. Their microbial communities didn’t increase and diversify as much. “They all responded in a predictable direction, but with not as great a magnitude,” Griffin said.

Another aspect of the study suggests the company you keep may also enrich your gut microbiota — at least in mice. At first the animals were kept in separate cages. Then, when they were housed together, the microbes from the communities conditioned by plant diets made their way into the American-diet microbiome.

It’s not clear how that translates to humans: Mice eat one another’s droppings when they live together, so they easily share the bacterial wealth. Still, it’s possible humans have other ways of sharing bacteria, Griffin said. “We know from previous work and other studies that spouses who live together will develop microbial communities that are similar to each other,” he said.

Perhaps the best way to cultivate a healthier microbiome is to eat more fiber by consuming more fruit, vegetables, whole grains, legumes, and nuts or seeds, said Meghan Jardine, a registered dietitian who was not involved in the current study but has published articles on promoting a healthy microbiota. (She is also affiliated with the Physicians Committee for Responsible Medicine, which recommends a plant-based diet.) She urges people to aim for 40-50 grams of fiber daily, well above levels recommended by most dietary guidelines.

“When you look at populations that eat real food that’s high in fiber, and more plant-based foods, you’re going to see they have a more robust microbiota, with more genetic diversity, healthier species and fewer pathogenic bacteria living in the gut,” she said.

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