Diet microbiome
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The Effect of Different Diets on The Gut Microbiome

In the last couple of years, more and more scientific evidence has come up regarding the importance of our gut microbiome. Along with that, a lot of evidence has been provided, that what we eat, is a great influence on the health of our microbiome! But what are the effects of different diets on the gut microbiome? Should we be vegan? Doing keto? Just follow a standard diet?

Diet gut microbiome

The Gut Microbiome

If you’ve been reading more articles on my blog, you know by now that the gut microbiome is an essential part of health.

Your gut microbiome consists of trillions of bacteria that reside in your large intestine. There will always be a mix of healthy and unhealthy bacteria, and as long as this is balanced, we have a healthy gut.

Most of the food that we eat will be digested in our small intestine. Some of the food that we eat, mostly fiber, is indigestible and is the energy source for our gut microbiome.

When our gut microbiome breaks down fiber, they produce nutrients for us like vitamin K, Butyrate, and other Short Chain Fatty Acids (SCFA).

These are nutrients for us, but also nutrients for the cells in our intestinal wall. To keep our intestines healthy and functioning properly.

Apart from keeping our intestines happy, the gut bacteria also have an influence on our emotions, hunger and satiety, and body weight. (And many more!)

On the other hand, an unhealthy gut microbiome has been linked to numerous diseases. Such as cardiovascular disease, obesity, diabetes, cancer, Irritable Bowel Syndrome (IBS), and neurological disorders.

Diet and the Gut Microbiome

Our gut microbiome is massively important for our health and wellbeing. What we eat, determines how healthy our gut microbiome is. A healthy gut microbiome is identified by a great diversity of bacteria in the gut. And this is where diets can make a difference in overall health!

In a large review study in 2019, it became clear that different diets have different effects on the gut microbiome. Your gut microbiome is constantly shifting, depending on what you eat, if you’re stressed, how you sleep, physical activity, and so on. These small daily variations are not of any concern. Only if we change our diet (or lifestyle) drastically and for longer periods of time, will our microbiome react to it drastically too.

Changes in the gut microbiome are not necessarily bad. Some diets leave us with a healthier microbiome than before. While other diets leave us with an unhealthier microbiome and sometimes even gut issues! So it’s important to know what you’re getting yourself into before you start the latest fad diet.

Vegan/Vegetarian diet

Vegans and Vegetarians aim for a plant-based diet. Where vegetarians might still consume some dairy products, eggs, or fish. People who are vegan don’t eat any animal-based products at all (not even honey).

A vegetarian/vegan diet showed higher ratios of the healthy bacteria and a reduction of the less healthy gut bacteria. In another review study from 2020 this finding was confirmed, and they also found that there was an increase in the production of SCFA in the vegan diet.

Gluten-Free Diet

The Gluten-Free Diet (GFD) is a diet that is necessary to follow for a small amount of people that have Celiac Disease. An auto-immune disease where gluten (a protein) cause inflammation in the gut. Click here for more information about gluten and Celiac Disease.

Many people who do not need to eat gluten-free for health reasons (so people without Celiac Disease), still choose to eat gluten-free. Even though a gluten-free diet is not healthier than a diet containing gluten.

People who follow a gluten-free diet for 1 month have shown to have reduced amounts of healthy gut bacteria and increased amounts of unhealthy gut bacteria. This also leads to a reduction in the production of SCFA and overall gut health.

In my opinion, part of this can be explained by the poor quality of a lot of gluten-free products that are for sale. A gluten-free diet can be done well, with enough variety and then I would expect less effect on the gut microbiome. Nonetheless, don’t follow a gluten-free diet if you don’t have to. And if you do, talk to a dietitian to make sure you get enough fiber and diversity in your diet! Click here to schedule a free symptom assessment with the Positive Gut dietitian.

Ketogenic Diet

The ketogenic diet is a high-fat and low carbohydrate diet. It has shown some promising results in the treatment of epilepsy and a lot of people use it for weight loss (although long-term results aren’t very promising).

The study showed an increase of unhealthy bacteria and gut inflammation on the ketogenic diet. And a reduction of the healthy gut bacteria and less production of SCFA. There are concerns about the health of the gut lining when the diet is being followed for a longer period of time.

A common side effect of a ketogenic diet is constipation, which is due to a lack of dietary fiber.

For me, this is reason enough to not consider the ketogenic diet as a healthy way to eat or lose weight.

The low FODMAP Diet

The low FODMAP diet, is used in the treatment of IBS. For an extensive explanation about the diet, click here. It is an elimination diet that shows promising results in the reduction of IBS-symptoms. During the diet, multiple food groups are being cut out of the food pattern for a short period (preferably 2-6 weeks) before reintroducing them back and finding your triggers. Because a lot of food groups are being cut out, the diet shows an effect on the microbiome.

A prolonged low FODMAP diet has shown to reduce bacterial diversity in the gut and can result in a reduction of the SCFA. For more information on the FODMAP diet long term, click here.

The FODMAP diet can be a great way to figure out triggers for your IBS symptoms, but always do it under the guidance of a specialized dietitian! Click here to find out how I can help.

Western Diet

The Western diet (WD) is the diet that many people grow up to follow. It’s the average diet in developed countries and consists of a lot of meat, refined sugar and processed foods.

The combination of these foods leads to a reduction in the diversity of the microbiome and inflammation in the intestines, an alteration of the gut barrier. Creating an unhealthy gut.

Mediterranean Diet

The Mediterranean diet refers to the diet that was followed in the early 1960’s by the people in Greece and Southern Italy. The diet consisted mostly of fruit, vegetables, olive oil, nuts, legumes and whole grains. It had a low intake of animal products. This diet has been linked to numerous health benefits and it also shows its result in the gut microbiome.

On the Mediterranean diet the total diversity of the microbiome was increased and there was increased production of SCFA. And I daresay, this is the healthiest diet you can follow. Another benefit of the Mediterranean diet, is that it’s not a hard diet to follow. Just stick to low-processed foods, eat anything nature has given us and not too much meat.


The picture below shows an overview of the diets and their different effects on the gut microbiome and gut health. If you want to eat as healthy as possible, try the Mediterranean Diet or go for a vegetarian/vegan diet with mostly whole-food plant-based products.

If you want to do a low FODMAP diet or gluten-free diet, always check in with a dietitian. Make sure you get all your nutrients and don’t stick to it for too long. Click here to schedule a free symptom assessment with the Positive Gut dietitian.

Diet and microbiome
Source: Rinninella E, Cintoni M, Raoul P, et al. Food Components and Dietary Habits: Keys for a Healthy Gut Microbiota Composition. Nutrients. 2019;11(10):2393. Published 2019 Oct 7. doi:10.3390/nu11102393

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