The ketogenic diet is one of the fasted growing diet trends these days. It is a high fat diet where about 70% of the calories come from fat, 25% from protein and only 5% from carbohydrate. Through this way of eating, the body goes into a state of ketosis and utilizes fat to produce ketone bodies, which than provide an alternative energy for the body
The ketogenic diet was originally used as a treatment for epilepsy but by now, there are thousands of research articles on the ketogenic diet, showing positive effects on weight loss, mental performance, and a variety of modern diseases.
However, the effects of a ketogenic diet and our gut microbiome are less well understood. We know that the microbiome is extremely important for our overall health and well-being, which is why it is so important to understand how certain diets impact the microbiome.
Problems with most studies using high-fat diets
One reason high-fat diets are frowned upon is that in animal studies those diets are used to make the animals sick and studies on the microbiome are no different. Whenever you want to induce a gut dysbiosis in animals you put them on a “high fat diet”. [2, 3]
However the problem is that while animal research is certainly valuable in many areas, the results don’t necessarily apply to humans, especially in the case of a high-fat diet. 
Additionally, in animal and human research, the most common high-fat diets use highly processed and refined fats like corn and soybean oil. Nothing you would find in a ketogenic diet. 
What is most striking, however, is that in most studies, a high-fat diet usually still includes about 40% carbohydrates, which is not even close to a low-carb diet where the carbs are usually restricted to less than 20% of the calories. [5, 18]
So, let’s look at some studies where a proper ketogenic diet was used without high amounts of unhealthy fats or processed carbohydrates.
In a 2018 study, Olson and colleagues found the beneficial effects of a ketogenic diet on epileptic seizures are mediated by the gut microbiome. They found that specific microbes are increased on a ketogenic diet and that those species are necessary for an improvement of the neurotransmitter ratio of GABA to Glutamate, which protects against epileptic seizures.
What is most fascinating about this study is that researchers took antibiotic-treated mice and found that they are not protected against seizures even when fed a ketogenic diet but the protection could be restored via a transplantation of these beneficial bacteria. 
Another 16-week study looked at effects of a ketogenic diet on the gut microbiome composition and possible benefits on cognition in mice and found that the ketogenic diet could increase the relative abundance of beneficial gut bacteria (Akkermansia muciniphila and Lactobacillus), and reduced that of pro-inflammatory microbes (Desulfovibrio and Turicibacter). 
On the downside, the ketogenic diet decrease the overall microbial diversity, probably due to the low fiber intake.
Studies on Humans
Even though bacterial composition can adapt rapidly to new eating patterns, it sometimes can take little bit to fully adjusted. 
This was also seen in a study published in 2017. Researchers analyzed the microbiome of patients with Multiple Sclerosis and found that it was overall reduced in diversity compared to healthy people and since the ketogenic diet shows promising results in reducing the severity of MS, they placed half the patients on a ketogenic diet. The researcher found that “the effects of a ketogenic diet were biphasic. In the short term, bacterial concentrations and diversity were further reduced. They started to recover at week 12 and exceeded significantly the baseline values after 23–24 weeks on the ketogenic diet.” 
“The ketogenic diet for 6 months completely restored the microbial biofermentation mass (in MS patients) and is an interesting interventional tool for prospective clinical studies.” 
Another study on children with epilepsy found that those children with epilepsy have higher amounts of pathogenic bacteria and that those harmful species could be pretty much replaced with beneficial bacteria after just a week on a ketogenic diet. 
On the other hand, a different study also revealed some potential negative effects of a ketogenic diet on the gut microbiome. A 2009 study by Brinkworth and colleagues found that people on a ketogenic diet produce significantly less short-chain fatty acids, which are putatively beneficial molecules, produced via the fermentation of fiber by bacteria. 
However, the participants on a ketogenic diet were only consuming 13 grams of fiber per day and while it is true, that it is easier to consume high amounts of fermentable fiber on high-carb diets, a ketogenic diet can still include a decent amount of fiber from vegetables, nuts and seeds.
When it comes down to the microbiome, we cannot yet be completely sure about the effects of a ketogenic diet. However, a ketogenic diet excludes all processed foods, refined carbohydrates and sugars and this by itself can have positive effects on the gut microbiome. [12-17]
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Anya Ellerbroek, The effects of ketogenic diets on the gut microbiome, JEN, 2018
Murphy et al., Influence of high-fat diet on gut microbiome: a driving force for chronic disease risk, Curr Opinion Clin Nutr Metab Care, 2015
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Magnussion et al., Relationship between diet-related changes in the gut microbiome and cognitive flexibility, Neuroscience, 2015
Olson et al., The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet, Cell, 2018
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