Can We Change Our Microbiome By Eating A Ketogenic Diet?

Lately, the ketogenic diet has been a hot topic in the fields of health and nutrition. This article will be about how the ketogenic diet can influence the gut microbiome, but first, we need to briefly cover what the ketogenic diet is if you are not familiar.

To be eating a ketogenic diet you need to be consuming specific macronutrients ratios: 70% fat, 25% protein, 5% carbohydrates.

The ketogenic diet restricts both simple and complex carbohydrates to typically around 15g/day to 50g/day or 5% of total dietary intake. There is a 50g/day cap on carbohydrates, which may seem high, but it’s difficult to stay away from carbohydrates completely. All the vegetables you are eating on a ketogenic diet contain some form of carbohydrates. For example, a cup of quinoa has 39g of carbohydrates,a cup of potatoes has 26g of carbohydrates, a cup of broccoli has 6g of carbohydrates, and a cup of zucchini has 3.5g of carbohydrates.

Carbohydrates are kept to a minimum on the ketogenic diet in order for the body to change its source of energy. On a regular diet, carbohydrate levels are high enough for the body to use them as its primary source of energy by converting the carbohydrates you eat into glucose, which is used as energy. If the body runs out of glucose for energy, it is capable of using ketones as energy which is primarily made in the liver from fat. The creation of ketones for energy from fat is called ketogenesis and is where the ketogenic diet derives its name.

If you want to learn more about the ketogenic diet, and how you can use it to improve your health and fertility, you can sign up at our resource center. The rest of this article will be on how the ketogenic diet influences the human gut microbiome.  

What’s The Gut Microbiome? And How Does It Influence Health And Behavior?

The gut microbiome is a term representing the collection of microorganisms within your digestive system. The microbiome begins right when food enters your mouth, and ends right when food leaves your system. The most intuitive function of the gut microbiome is that microorganisms help with the digestion of food, but they serve many other functions. For example, the gut microbiome is responsible for producing ~95% of the neurotransmitter serotonin production and influences the activity of brown fat (a type of fat that burns calories and white fat for temperature regulation). (1,2) The microbiome has been found to influence social behavior (Example: major depression), stress-induced behavior, memory, and learning ability, due to the microbiome changing gene expression, neurochemical metabolism, and other neurophysiological functions. (3) In future blog posts we will take a deeper dive into the human gut microbiome, but for now, we are going to stay on the topic of how the ketogenic diet influences the gut microbiome and what it means for you.

What Happens To The Gut Microbiome When You Eat A Ketogenic Diet?

The ketogenic diet has a history of being used for the treatment of epilepsy beginning in the 1920’s for its ability to reduce the frequency and intensity of seizures, and more recently the ketogenic diet has been shown to improve other disorders such as autism spectrum disorder, Alzheimer’s disease, metabolic syndrome, and cancer. (4, 5)

In a recent study published in Cell titled “The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet”, scientists found that the anti-seizure effects of the ketogenic diet are connected to how the ketogenic diet alters the gut microbiome. They found ketogenic diets in mice decrease raise seizure thresholds, alpha diversity of the microbiome, decrease the activity of gamma-glutamyl transpeptidase, decrease the total amount of gamma-glutamyl amino acids, increase the amount of two species of bacteria (A.muciniphila, and Parabacteroides), and increases the gamma-aminobutyric acid (GABA) to glutamate ratio. (6)

What Do Ketogenic Diet-Induced Changes To The Microbiome Mean For Your Health?

The study confirmed something we have already known for almost 100 years; the ketogenic diet reduces the frequency of seizures. The study also gave us further insight into how and why the anti-seizure effects of the ketogenic diet occur. Researchers were able to find a clear connection between ketogenic diet-induced changes to the gut microbiome and anti-seizure effects. This is good news.  

The effects of a ketogenic diet on the gut microbiome.

If you recall, the ketogenic diet reduced alpha diversity and increased the amount of two types of bacteria (A.muciniphila, and Parabacteroides). Previous research demonstrates that A.muciniphila, and Parabacteroides are associated with increased ketosis (the process of creating ketone bodies out of fat) and metabolic improvement in humans (less fat mass gain, less adipose tissue inflammation, increased levels of endocannabinoids, and improved insulin resistance). (7, 8)

The composition of the microbiome changes relatively quickly after adopting a ketogenic diet. The study showed that changes in the microbiome were complete after 4 days and stayed stable for the duration of microbial monitoring (14 days). For example, the relative abundance of A.muciniphila increased from ~3% to ~36% in four days after adopting a ketogenic diet. With the increase in relative abundance of A.muciniphila other species of bacteria get out competed — hence the decrease in overall alpha diversity.

A decrease in bacterial alpha diversity and increase in the relative abundance of A.muciniphila and Parabacteroides turns out to play a major role in anti-seizure effects and can produce other beneficial health effects such as increased GABA to glutamate ratios. The primary author of the study Christine Olsen said If we gave either species [of bacteria] alone, the bacteria did not protect against seizures. This suggests that these different bacteria perform a unique function when they are together.” (9) This means the ketogenic diet produces an environment within the gut microbiome that gives A.muciniphila and Parabacteroides an advantage (increased biological fitness) over other bacteria, and this produces anti-seizure effects.

One of the major changes that occur leading to anti-seizure effects is the change in the GABA to glutamate ratio. Eating a ketogenic diet increases GABA levels through changes in the gut microbiome. GABA is a calming neurotransmitter, and increasing levels of GABA by eating a ketogenic diet can be beneficial in many ways other than just reducing seizures frequency such as: alleviating depression, anxiety, insomnia, PMS symptoms, decreasing overall inflammation, improving focus, and increasing growth hormone levels. (10, 11, 12, 13, 14, 15)


Here is a quick recap of the top five things you should remember about how the ketogenic diet changes the gut microbiome and the consequences of those changes:

  1. Decreased alpha diversity of the microbiome
  2. Increased relative abundance of A.muciniphila, and Parabacteroides
  3. Increased levels of ketosis
  4. Improved metabolism
    1. Less fat mass gain
    2. Improved insulin resistance
    3. Less adipose (fat) tissue inflammation
    4. Increased levels of endocannabinoids
  5. Higher GABA levels
    1. Help alleviate depression
    2. Help alleviate insomnia
    3. Help alleviate PMS symptoms
    4. Reduce anxiety
    5. Decrease inflammation
    6. Improve focus
    7. Increase levels of growth hormone

If you have not already taken a look at our resource center we recently had ketogenic diet month where we explained in detail how to effectively integrate the ketogenic diet into your life for improving your health and fertility. You can sign up and get free, or paid, access now!


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