The Science Behind the Keto Diet and Gut Health: A Nutritionist’s Deep Dive (Extended Version)


You’re on the keto diet or considering it, but you’re not sure how it affects your gut health. If this is you, you came to the right spot.

In this article, I unpack the science behind keto and its impact on the gut, drawing from personal experiences and countless hours spent pouring over the latest research.

Whether you’re a keto fanatic, a keto skeptic, or are simply considering the keto diet but are wondering about its implications on the precious residents of the gut, this article is for you. And I guarantee (yes, guarantee) that after reading this article, you will know what the latest in scientific research has to say. 

So let’s dive in. 

Why You Should Trust Me & What You Will Learn

As the headline suggests, I’m a nutritionist as well as a NASM-certified personal trainer. In other words, while I’m still trying to figure out how to get my kids to school on time, when it comes to health and nutrition, I know my sh*t.

I’ve lived the keto lifestyle, helped countless others transition into ketosis and have read literally every study I could find on the ketogenic diet’s effect on gut health, and I will be unpacking that in the article below. Stick around, and you’ll learn:

  • How keto affects gut bacteria
  • The impact of keto on inflammation
  • Tips to optimize gut health on keto
  • Common digestive symptoms during keto adaptation
  • How to manage digestive symptoms on keto
  • Lifestyle factors that support gut health on keto
  • Potential risks and limitations of keto on gut health
nutritionist who has lived the keto lifestyle

Keto and Gut Bacteria: Your Gut’s Bacterial  Universe

First things first. Your gut is home to trillions of bacteria that play a vital role in:

  • Digestion
  • Immunity
  • Mental well-being
  • Hormone regulation
  • Nutrient synthesis

And guess what? Your diet is a major factor that shapes your gut microbiota.

Keto’s Impact on Gut Bacteria

Here’s the deal with keto and gut bacteria:

1. Boosting Beneficial Bacteria

Keto can promote the growth of specific gut bacteria that lead to better digestion.

Study 1: A study in Cell found that a high-fat, low-carb diet (like keto) increased the abundance of good bacteria like Akkermansia muciniphila [1], which is linked to improved metabolic health [2].

Study 2: Another study [3] discovered that a ketogenic diet enriched the gut microbiota with bacteria known for producing short-chain fatty acids (SCFAs). These SCFAs help maintain gut barrier integrity and reduce inflammation [4].

2. A Dip in Bacterial Diversity

But there’s a catch: Keto can also reduce gut bacterial diversity, which is generally considered good for overall health [5]. So, the key takeaway here is that keto must be done strategically to increase good bacteria and to find a balance that supports gut health.

Keto’s Anti-Inflammatory Superpowers

Keto diets have shown promise in reducing inflammation, including in the gut. How? It calls for the removal of known inflammatory foods and the mere existence of ketone bodies is anti-inflammatory.

While on the ketogenic diet, commonly known inflammatory foods like gluten-containing grains and sugars are off-limits.

Ketone Bodies: Inflammation Fighters

When you’re in ketosis, your body produces ketone bodies, like beta-hydroxybutyrate (BHB), which can help reduce inflammation.

Study 1: A study in PLoS ONE [7] found that BHB suppressed the production of inflammatory molecules called cytokines in the gut, leading to improved gut health[8].

Study 2: Another study in Nature Medicine [9] showed that a ketogenic diet reduced inflammation in the central nervous system (CNS) in mice. Since CNS inflammation has been linked to gut inflammation, this suggests that keto may have broader anti-inflammatory effects that benefit our gut. [10].

ketone production in body

Optimizing Gut Health on Keto: Dietary Strategies for a Happy Gut

Want to keep your gut happy while on keto? Try these tips:

Prebiotics and Probiotics:

Prebiotic and probiotic foods help maintain a healthy balance of gut bacteria. Prebiotics are non-digestible fibers that act as food for beneficial gut bacteria, while probiotics contain live beneficial bacteria.

Including keto-friendly prebiotic and probiotic foods in your diet, like asparagus, artichokes, and fermented foods like kimchi and sauerkraut are great ideas. [11]. They are delicious and will also help you digest all your foods more effectively. 

Ensuring adequate fiber intake

Dietary fiber is vital for maintaining a healthy gut microbiota and promoting regular bowel movements. You should be having at least one healthy bowel movement a day. Message me privately if you want to discuss further the definition of “healthy!”  

Although keto diets can be low in fiber, you can still consume high-fiber, low-carb vegetables, nuts, and seeds to meet your fiber needs while remaining in ketosis [12].

Common Digestive Symptoms During Keto Adaptation

It’s not uncommon to experience digestive symptoms during the initial stages of keto-adaptation. They are not fun and may include:

  • Constipation
  • Diarrhea
  • Bloating
  • Stomach cramps

While these symptoms can be uncomfortable, they’re often temporary and can be managed with a few simple strategies. 

Most people experience one or more of these due to the change in bacterial composition, but it usually only lasts a few days as the previous gut bacteria die off and are replaced by new bacterial residents. 

The glucose-consuming bacteria are different strains of bacterial species than those that consume ketones. [19]  

common digestive symptoms during keto adaptation

How to Manage Digestive Symptoms on Keto

If you’re experiencing digestive symptoms while adapting to keto, consider these tips:

  • Stay hydrated: Drinking plenty of water can help alleviate constipation and bloating [13].
  • Gradually increase fiber intake: To minimize digestive discomfort, slowly increase your fiber intake from low-carb sources.
  • Pay attention to electrolytes: Ensure you’re getting enough sodium, potassium, and magnesium, as imbalances can contribute to digestive issues [14].

Almost everyone that I have counseled into ketosis has been dehydrated and low on electrolytes. Find a tasty electrolyte supplement and drink up!

Lifestyle Factors That Support Gut Health on Keto

In addition to dietary strategies, consider these lifestyle factors:

  • Exercise: Regular physical activity can promote healthy bowel movements and support a healthy gut microbiota [15].  Even a walk will help!
  • Manage stress: Chronic stress can negatively impact our gut bacteria, so consider incorporating stress-reducing practices like meditation or yoga into your routine [16]. Deep breathing can do wonders. 
  • Prioritize sleep: Not groundbreaking, but adequate, high-quality sleep is essential for overall health, and our guts need it to function properly. Deep and restorative sleep can solve most of your problems. 

Potential Risks and Limitations

As with any diet, there are potential risks and limitations to consider. They are as follows:

Individual Variability: Not a One-Size-Fits-All Solution

Every gut microbiota is unique and this isn’t some unhelpful cliche that I’m parroting. The research shows that many people see improvements in their gut health on keto, while others might experience negative effects. 

Long-Term Effects: The Verdict Is Still Out

Most studies on keto and gut health focus on short-term outcomes. More research is needed to understand the long-term effects of keto on gut health and how they impact overall well-being[18].

potential risks of keto

FAQ: Other Commonly Asked Questions On Keto & Gut Health

Is the keto diet good for gut health?

The keto diet can have both positive and negative effects on gut health, such as promoting beneficial gut bacteria and reducing inflammation, but there is potential for it to reduce bacterial diversity. Individual responses to the diet may vary, so it’s essential to monitor your gut health and adjust your diet as needed.

How do I heal my gut after keto?

To heal your gut after keto, gradually reintroduce a diverse range of nutrient-dense, fiber-rich foods like whole grains, fruits, vegetables, and legumes. Prioritize prebiotic and probiotic foods to support a healthy gut microbiome, and maintain a balanced diet for overall gut health.

Can a keto diet cause digestive problems?

Yes, the keto diet can cause temporary digestive problems, especially during the initial adaptation phase. Common symptoms include constipation, diarrhea, bloating, and stomach cramps, which can usually be managed through hydration, gradually increasing fiber intake, and monitoring electrolyte balance.

Are carbs necessary for gut health?

Carbohydrates, particularly those found in fiber-rich foods like whole grains, fruits, vegetables, and legumes, can be beneficial for maintaining gut health. 

They provide fuel for beneficial gut bacteria, support regular bowel movements, and promote a diverse and balanced gut microbiome. 

Some of these fibers are ketogenic. Some are not. 

In any case, you may want to explore keto cycling. 

Keto cycling includes intentionally increasing carbohydrates to get out of ketosis for a period of time. (This might be done for various reasons.) 

The time and frequency of higher carbohydrate meals or days should be strategic and may be used to enable you to incorporate these foods. 

A healthy well-designed carb cycling plan can provide the benefits of ketosis while also allowing you to take advantage of the benefits of fiber-rich foods that contain carbohydrates.

Conclusion: How Does Keto Affect Gut Health

If we were to summarize the above, it would be the following 3 things:

  • Keto can boost beneficial gut bacteria – Positive
  • It may reduce bacterial diversity – Negative
  • The diet has anti-inflammatory effects – Positive

Studies have shown that the ketogenic diet can boost beneficial gut bacteria and demonstrate anti-inflammatory effects, which contribute to improved gut health as well as overall health!

However, it’s important to note that the diet may also reduce bacterial diversity, which is generally considered beneficial for overall health, but if you focus on a whole-foods keto diet with prebiotics, probiotics, and fiber, you can mitigate this potential negative risk 

Further research is needed to understand the long-term effects of keto on gut health and how these findings translate into overall well-being, so continue to do your research and listen to your body.

References we mentioned in the article:


[2] Cani PD, et al. (2016). Next-generation beneficial microbes: The case of Akkermansia muciniphila. Frontiers in Microbiology. Retrieved from 

[3] Xie G, et al. (2017). Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy. Retrieved from 

[4] Ríos-Covián D, et al. (2016). Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health. Frontiers in Microbiology. Retrieved from 

[5] Lozupone CA, et al. (2012). Diversity, stability and resilience of the human gut microbiota. Nature. Retrieved from

[7,8] Youm YH, et al. (2015). The ketone metabolite β-hydroxybutyrate blocks NLRP3 inflammasome-mediated inflammatory disease. Nature Medicine. Retrieved from

[9] Kim DY, et al. (2012). Inflammation-mediated memory dysfunction and effects of a ketogenic diet in a murine model of multiple sclerosis. Retrieved from

[10] Braniste V, et al. (2014). The gut microbiota influences blood-brain barrier permeability in mice. Science Translational Medicine. Retrieved from

[11] Scott KP, et al. (2015). Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro. FEMS Microbiology Ecology. Retrieved from

[12] Makki K, et al. (2018). The impact of dietary fiber on gut microbiota in host health and disease. Cell Host & Microbe. Retrieved from

[13] Popkin BM, et al. (2010). Water, hydration, and health. Nutrition Reviews. Retrieved from

[14] Bothe G, et al. (2017). The impact of water intake on energy intake and weight status: a systematic review. Nutrition Reviews. Retrieved from 

[15] Monda V, et al. (2017). Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxidative Medicine and Cellular Longevity. Retrieved from

[16] Karl JP, et al. (2017). Effects of Psychological, Environmental, and Physical Stressors on the Gut Microbiota. Frontiers in Microbiology. Retrieved from

[18] Paoli A, et al. (2019). Beyond weight loss: a review of the therapeutic uses of very-low-carbohydrate (ketogenic) diets. European Journal of Clinical Nutrition. Retrieved from

[19] Paoli A, et al. (2019). Ketogenic Diet and Microbiota: Friends or Enemies? Genetic and Epigenetic Modulation of Cell Functions by Physical Exercise. Retrieved from

Nolwen Cameron

Nolwen Cameron has had a lifelong passion for exercise and nutrition. She loves to educate and coach people to help them feel and look healthy inside and outside. She is an ISSA Certified Specialist in Fitness Nutrition and NASM Certified Personal Trainer.

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