Danone-led research uncovers how certain diets impact the gut microbiome

By Mary Ellen Shoup

- Last updated on GMT

Photo Credit: GettyImages /  MARHARYTA MARKO
Photo Credit: GettyImages / MARHARYTA MARKO

Related tags Danone microbiome Gut health

Low-carb diets such as keto and paleo have exploded in popularity among consumers and brands that formulated products to fit the nutritional guardrails of each, but how does drastically eliminating carbs impact the diversity of good bacteria in gut microbiome?

New findings published in the American Journal of Clinical Nutrition​ from an international research team at Danone Nutricia Research in France and the University of California San Diego (UC San Diego) found that out of the five dietary patterns studied, those low in carbs and high in fats, animal products, 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 citizen science microbiome project.

Additionally, individuals following a flexitarian diet, which is rich in plant-based foods but also includes meat and dairy products, presented one of the most diverse gut microbiomes, especially compared to a standard American diet.

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

Study methods

The research team examined the dietary patterns of 1,800 adults in the American Gut Project – an ongoing research initiative that is studying the microbiome composition of citizen volunteers.

Using food consumption surveys, the researchers divided study participant into five predominant groups based on their long-term dietary intakes: (1) plant-based; (2) flexitarian; (3)‘health-conscious’ American diet (diet rich in nuts, whole-grain cereal, dairy food, but also high in added sugar, refined grains, and low in vegetables); (4) a standard American diet (the poorest diet quality of all groups, including the highest consumption of sugar-sweetened beverages and processed foods and the lowest diversity in plant-based foods consumed, as well as the lowest intake of dietary fiber); and (5) exclusion diet (restrictive diet low carbohydrates and highest in fats and animal products compared to the other eating patterns examined).

Results: Flexitarian diet comes out on top

The analysis (done through collection of stool samples of the gut microbiome) revealed that the alpha diversity of the gut microbiota (a measure of the different kinds of bacteria), was significantly lower in the standard American diet compared to the flexitarian pattern, which included a mix of plant and animal foods, including high amounts of dairy products.

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

Altogether, 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 some animal foods, such as meat and dairy products in the plant-based dietary pattern.

‘Evaluating diet as a whole is important when studying the gut microbiome’

“This study showed that the flexitarian eating pattern that includes larger amounts of plant foods, yet doesn’t totally eliminate animal foods, was associated with better overall diet quality and one of the approaches resulting in the most nourished gut,”​ said Miguel Freitas, PhD, vice president of health and scientific affairs at Danone North America. 

“This study together with previous research reinforce that a healthy gut microbiota is supported by a balance between all food groups, without restricting fiber-rich grain foods or animal products, like fermented dairy products entirely. At Danone, this approach is completely in line with our portfolio offerings of both plant-based and animal products.”

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

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