What’s Your Beef With The Ketogenic Diet? Dr. Chutkan Explains

Lindsay: I saw a compelling study linking the ketogenic diet to reducing inflammation in the gut and improving microbial parameters. I realize you’ve been against keto diets in the past. To me, ketones seem to be beneficial for gut health. Can you elaborate on the study and your take on it?

Dr. Chutkan: Lindsay, the study you’re referring to, Ketogenic diets alter gut microbiomes in humans, mice, was published in May of this year and was conducted by researchers at the University of California, San Francisco. Probably the trendiest diet of 2020, the ketogenic diet is a very low carb, high fat way of eating, which keeps the body in a metabolic state called ketosis, in which the body burns fat for energy instead of carbohydrates and transforms fat cells into ketones in the liver, which act as an energy source for the brain.

Some preliminary scientific evidence shows that a ketogenic diet may help in managing some difficult-to-treat diseases, such as multiple sclerosis, epilepsy, cancer, diabetes, and Alzheimer’s, not to mention its ability to ignite weight loss – hence it’s mainstream popularity.

In the May 2020 study published in Cell, researchers were motivated by one question: Why do high fat diets promote negative shifts in the microbiome, as well as disease, while a ketogenic diet (which is even higher in fat than the historic high fat diets like Atkins) seems to protect against disease with beneficial microbial shifts? To answer this question, scientists took 17 overweight or obese, non-diabetic adults and enrolled them into a metabolic ward for 2 months while controlling and monitoring their dietary intake and exercise. Participants were split into two groups and received either a keto (5% carbs, 15% protein, 80% fat) or standard (50% carbs, 15% protein, 35% fat) diet for the first 4 weeks, then the groups switched diets. Microbial DNA via stool samples were measured throughout the study to track the impact the dietary shifts had on the gut microbiome.

Results showed dramatic shifts in 19 different bacterial communities, including in the beneficial bacteria phyla, Bifidobacteria, which showed the greatest decrease. To take the study further, researchers then took mice and injected them with microbial components observed when humans adhere to a ketogenic diet. A reduction in bacterial populations that reduce the number of Th17 immune cells (a T cell that fights off infectious disease, and has also been implicated in triggering inflammation – a precursor to autoimmune disease) was observed. Researchers also fed rodents different diets, consisting of a low fat, high fat, and a ketogenic diet. Interestingly, they found that high fat and ketogenic diets have opposite effects on the gut microbiome, suggesting that a high fat diet that promotes ketone production has a very different impact on the gut microbiome than simply a high fat diet. When mice were fed ketones, while not on a ketogenic diet, similar microbial shifts were observed.

So, what does this all mean? Based on their findings, the researchers who conducted the study are hopeful that the research will lead to positive findings in administering ketone bodies in humans to induce microbial change, without individuals needing to follow the incredibly challenging restrictions of a ketogenic diet.

What I find interesting is that although the ketogenic diet resulted in dramatic shifts in the gut microbiome in this study, the shifts observed weren’t necessarily beneficial, especially when considering microbial protection against diseases associated with autoimmunity. Lower Bifidobacteria and Th17 immune cells can actually increase risk for infection in some cases. In addition, 2 months is a very short duration when looking at the dietary effects on the microbiome. Because of the incredible lack of fiber content of a ketogenic diet, I would expect to observe harmful effects when assessing the impact of a long-term ketogenic diet on the gut microbiome.

While, if done correctly, a ketogenic diet can be filled with healthful fats and vegetables, because of the restrictions on carbohydrate intake, there is no way that a ketogenic diet can contain enough MACs (microbiota accessible carbohydrates – the very fiber that feeds your gut microbes) in quantity and diversity to result in a rich gut microbiome that promotes lifelong health. In fact, the most beneficial fibers for the gut microbiome, resistant starches and non-starch polysaccharides, are found in foods eliminated from most ketogenic diets – fruits, legumes, and grains. Studies have shown that the single most determining factor in gut bacteria diversity (the leading microbial pillar associated with overall health) is the diversity of plant foods eaten throughout any given week.

While ketone bodies might have positive effects on the gut microbiome (they’re the body’s way of producing short chain fatty acids in the absence of fiber), the diet itself, with such low fiber content (specifically MACs), would not be beneficial in the long-term. This isn’t to say there’s not a time and a place for the ketogenic diet. For those suffering from certain diseases, under the supervision of a healthcare practitioner, a shorter-term ketogenic diet has shown promise as a successful treatment. But to assume that a long-term ketogenic diet is a beneficial vehicle for microbial health – a diet that eliminates the very things that make the gut microbiome thrive – is just not something we’ve seen as of yet in the scientific literature.