How to improve your gut microbiome today by going keto

May 29, 2020

No guts no glory is what they say. And although improving your microbes in the gut is not the first thing that comes to mind when adopting the diet, it may lead to severe changes to your allies down below.

For other articles related to the ketogenic diet, check out:

A diverse intestinal flora is very important for health and with a ketogenic diet you are well on your way to a healthy microbiome. Because of the limited amount of sugars and processed products, you minimize the risk of unwanted bacteria. The consumption of grains and beans is also low, which reduces the risk of damage to the intestinal wall. Gluten and phytic acid in particular can damage the intestinal wall in large quantities and can lead to blood clots. In addition, consuming healthy fats and Omega 3 leads to an increased microbial diversity.¹

It is not always known that your microbia can provide support for goals that are pursued through a ketogenic diet. Research is still in its infancy here, and in recent years in particular more and more has become known about the role of bacteria, viruses and yeasts in our body. Thus it has so far become clear that a diversity of these micro-organisms does the following:

1. It helps your body to absorb fats and nutrients

There are certain bacteria that can aid digestion. For example, there are strains of bacteria that increase the production of digestive enzymes that are required for the absorption of certain fats in the intestinal tract. It has recently been shown in mice that a specific microbiome can help to absorb fats well.²

2. Provides support for weight loss

Several studies show that an unbalanced microbiome can undermine your basal metabolism (these are the calories you burn at rest). Nowadays there are several biotech companies that offer this, so I recently sent a sample myself and got results about the bacteria that contribute to healthy weight.

Gezond gewicht bacteriën

3. Has effects on blood sugar regulation

In general, it is known what benefits ketosis has on blood sugar regulation and the associated positive effects. Without the carbohydrate peaks, people are generally less affected by mood swings, the afternoon dip or potential problems with insulin. And although minimizing carbohydrates has a positive contribution to this, the microflora also plays an important role in this.³

What should I pay attention to for a healthy microbiome?

Make sure your food is of high quality

For a healthy bacterial balance, it is important that you do not only look at your macronutrients. It is possible to eat ketogenic according to the letter of the rule, but if you do that with low quality food, you run the risk that you eat food with antibiotics or pollutants that can disturb the balance.

Watch for adequate intake of magnesium and potassium

It is sometimes difficult to get enough magnesium and potassium in a keto diet, as it is mainly found in beans, bananas and potatoes. But both are very important; for example, a magnesium deficiency can affect your gut flora composition which can lead to unwanted mood swings.⁴ A potassium deficiency can also lead to changes in your digestive system. Keto-friendly alternatives to meet these requirements include spinach, cabbage, pumpkin seeds, salmon and avocados.

Get enough prebiotics

One of the disadvantages of a keto diet may be that it is more difficult to get enough prebiotic fiber. This can lead to problems because your gut bacteria need fiber to break down fats into short chain fatty acids. It is therefore worth taking a good look at the carbohydrates you do consume, and whether those 30-50 grams of carbohydrates also contain fiber-rich products. Low-starch vegetables, nuts, seeds and soft fruits can complement your diet.

If you are struggling to include carbohydrates in your keto diet, it's worth checking out what prebiotic supplementation can do for you. GOS and XOS in particular are popular commercially available supplements that can have positive effects on digestion, immune system and bowel movement. I would always recommend testing how your nutrient metabolism currently looks like.

Final thoughts

My expectation is that there will be much more research in the coming years about the role the microbiome plays and how these bacteria operate as 'small medicine factories'. There is an enormously complex and dynamic ecosystem in our body that is connected to our entire biological evolution. By paying attention to this you can ensure that you can carry out your ketogenic lifestyle more efficiently and more happy overall.


1. Menni, C., Zierer, J., Pallister, T., Jackson, M. A., Long, T., Mohney, R. P., Steves, C. J., Spector, T. D., & Valdes, A. M. (2017). Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women. Scientific Reports, 7(1).

2. Martinez-Guryn, K., Hubert, N., Frazier, K., Urlass, S., Musch, M. W., Ojeda, P., Pierre, J. F., Miyoshi, J., Sontag, T. J., Cham, C. M., Reardon, C. A., Leone, V., & Chang, E. B. (2018). Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids. Cell Host & Microbe, 23(4), 458–469.e5.

3. Simon, M.-C., Strassburger, K., Nowotny, B., Kolb, H., Nowotny, P., Burkart, V., Zivehe, F., Hwang, J.-H., Stehle, P., Pacini, G., Hartmann, B., Holst, J. J., MacKenzie, C., Bindels, L. B., Martinez, I., Walter, J., Henrich, B., Schloot, N. C., & Roden, M. (2015). Intake ofLactobacillus reuteriImproves Incretin and Insulin Secretion in Glucose-Tolerant Humans: A Proof of Concept. Diabetes Care, 38(10), 1827–1834.

4. Winther, G., Pyndt Jørgensen, B. M., Elfving, B., Nielsen, D. S., Kihl, P., Lund, S., Sørensen, D. B., & Wegener, G. (2015). Dietary magnesium deficiency alters gut microbiota and leads to depressive-like behaviour. Acta Neuropsychiatrica, 27(3), 168–176.

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