How a Healthy Diet Benefits the Gut Microbiome


Adults who scored higher on the Healthy Eating Index were found to have higher gut microbiota diversity, as well as a higher exercise frequency and lower BMI.

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It has long been acknowledged that better nutrition can promote health and prevent diseases. Diet directly affects the gastrointestinal microbiota (commonly called “the gut”), which is increasingly understood to impact one’s health.

The microbiota is made up of trillions of microorganisms that live in the gastrointestinal system. A diverse gut is a healthy gut, as it boosts the body’s resilience to disruptions that can cause disease. The dangerous pathogen Clostridioides difficile, for example, germinates when antibiotics or other agents disrupt the gut microbiota, killing off the competition and allowing the pathogen to flourish uncontested.

One study, recently published in The Journal of Nutrition, investigated the relationship between diet quality and the gut microbiota to better understand how nutrition impacts human health.

The investigators studied how adults’ adherence to the Dietary Guidelines for Americans affects their fecal microbiota composition. The conducted a cross-sectional analysis of 432 healthy adults, ranging from 18-60 years of age. Participant data were obtained from the American Gut Project, a crowdsourced database that included fecal samples from thousands of Americans.

Participants collected fecal samples at home and mailed them to the American Gut Project laboratory at the University of California San Diego School of Medicine. There, the V4 region of the 16S ribosomal RNA gene was amplified and sequenced.

The study cohort was 65% female and 89% white, with an average age of 45.4 years. Using the Healthy Eating Index-2015 (HEI), the investigators assessed participants’ compliance with Dietary Guideline recommendations. The cohort was sorted according to their HEI scores and the investigators compared microbiota diversity between high and low scorers.

The average HEI score was 58.1 among the adults classified as low scoring, which was comparable to the 56.7 score of an average American adult. Compared to the adults who scored high on the HEI, the low scoring participants consumed less dairy, whole grains, refined grains, greens and beans, total vegetables, and whole fruit; they consumed more fatty acids. Total vegetables and refined grains were the categories investigators found to be the biggest differentiators between the participants with low HEI scores versus high HEI scores.

HEI high scorers had the highest gut microbiota diversity, including a larger presence of bacteria capable of fermenting fiber and metabolizing complex carbohydrates. Additionally, high scorers tended to have a higher exercise frequency and a lower body mass index (BMI).

Because the adults who scored low on the Healthy Eating Index had scores similar to the general American adult population, the investigators emphasized the significance of eating healthy and promoting a highly diverse gut microbiota. “As there is growing interest in the diet and microbiota,” the study authors wrote, “these novel findings demonstrate the utility of the HEI in differentiating the fecal microbiota composition of those who more closely adhere to the guidelines compared with those who do not.”

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