Danone research reveals the impact of certain diets on the gut microbiome


New findings published in the American Journal of Clinical NutritionAn international research team from Danone Nutricia Research in France and the University of California, San Diego (UC San Diego) found that of five exclusion diets studied, those low in carbohydrates and high in fat, produced d animal and non-starchy vegetables had the greatest negative impact on the gut microbiome.

The study was funded by Danone Nutricia Research and supported by The Microsetta Initiative, the world’s largest microbiome citizen science project.

Additionally, people following a flexitarian diet, high in plant-based foods but also including meat and dairy, had one of the most diverse gut microbiomes, especially compared to a standard American diet.

“The association between habitual diet and gut microbiota is of major interest, yet to our knowledge this is the first study to use this type of approach and identify dietary patterns that offer the best associations with the intestinal microbiota, ”said study lead author Patrick Veiga, PhD, director of health and microbiome sciences at Danone Nutricia Research.

Study Methods

The research team looked at the eating habits of 1,800 adults as part of the American Gut Project, an ongoing research initiative that studies the makeup of the microbiome of volunteer citizens.

Using food consumption surveys, researchers divided study participants into five predominant groups based on their long-term dietary intakes: (1) plant-based; (2) flexitarian; (3) “health-conscious” American diet (diet high in nuts, whole grains, dairy products, but also high in added sugars, refined grains and low in vegetables); (4) a standard American diet (the poorest diet quality of any group, including the highest consumption of sugary drinks and processed foods and the lowest diversity of plant-based foods consumed, as well as lower dietary fiber intake); and (5) exclusion diet (restrictive diet low in carbohydrates and high in fats and animal products compared to other dietary habits examined).

Results: the flexitarian diet comes out on top

The analysis (performed by collecting stool samples of the gut microbiome) revealed that the alpha diversity of the gut microbiota (a measure of the different types of bacteria) was significantly lower in the standard US diet compared to the flexitarian model, which included a mixture of plant and animal foods, including large amounts of dairy products.

But, the low-carb eaters on the exclusion diet had the lowest relative abundance of Bifidobacterium, a type of beneficial bacteria found in the gut.

Overall, this highlights that some diets may be more microbiota-friendly than others, noted researchers, who also found that the gut microbiota alpha diversity of the plant-based diet and the standard American diet was similar, which may be explained by the depletion of certain animal foods, such as meat and dairy in the plant-based diet.

“Assessing the diet as a whole is important when studying the gut microbiome”

“This study showed that the flexitarian dietary pattern that includes greater amounts of plant foods, but does not totally eliminate animal foods, was associated with better overall diet quality and a approaches resulting in the most nourished intestine”,​ said Miguel Freitas, PhD, Vice President of Health and Scientific Affairs at Danone North America.

“This study, along with previous research, reinforces that a healthy gut microbiota is supported by a balance of all food groups, without entirely restricting fiber-rich grain foods or animal products, such as fermented milk products. At Danone, this approach is perfectly in line with our portfolio offerings of both plant and animal products.

“These results confirm that assessing the diet as a whole is important when studying the gut microbiome,” Veiga said. “It will also facilitate the design of more personalized dietary strategies in general populations.”


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