Keto and Your Gut: How the Ketogenic Diet Affects the Microbiome

Originally published at courtneyholmbergnd.ca

The Ketogenic diet is an extremely popular diet amongst the weight loss community. Originally brought to light for its promising research in epilepsy management, it quickly became a hopeful solution for those looking to quickly shed pounds without massive caloric restrictions. But like any trend, we must weigh all the pros and cons while simultaneously accounting for the long-term impacts on our health.

First off, let’s break down what the ketogenic diet actually involves. The premise of the diet focuses on reducing carbohydrates to shift the body toward greater fat breakdown and the production of ketones, a process known as ketogenesis. Ketogenesis is a metabolic process our bodies enter when sources of glucose (both dietary and stored) cannot meet our metabolic needs, forcing the body to produce ketone bodies from adipose tissue (aka fat) to use for energy in place of sugar. As you can imagine, this is favorable for weight loss for several reasons. In addition to fat now being used as fuel, the blood sugar staying so low sharply drops insulin secretion, which further reduces the stimulus for fat and sugar storage. As long as the body remains deprived of carbohydrates, ketosis is sustained, and weight loss continues. There’s also the concept of something called ‘super fuel’, meaning ketone bodies produce more usable ATP molecules (aka energy) to the heart, muscles, and brain than glucose, resulting in the additional energy and mental focus many people report while in ketosis.⁽¹⁾

Studies are showing very promising results for epilepsy and have been well documented and proven to be effective for rapid weight loss, with initial weight loss of up to 10 lbs in 2 weeks or less.⁽¹⁾

However, literature exceeding 2 years of use is lacking, and some studies show that red flags are raised within 3 months into ketosis that may have more concerning long-term health implications. Let’s dive further into what those risks are.

1. Vitamin and mineral deficiencies.

While the ketogenic diet does help to eliminate certain unhealthy foods, like refined sugars and carbohydrates, it also eliminates fruits and other vegetables that contain carbs. It’s no surprise that fruits and vegetables provide a primary source of the vitamins and minerals the body needs for optimal health, in addition to being high in antioxidants. Now, there are also two ways to approach ketosis – one that maintains a high low-carb vegetable intake and a balanced amount of saturated fats, and one that involves eating bacon and hamburger patties at every meal.

All that aside, Harvard Health highlights that the most common nutrients depleted on a ketogenic diet are electrolytes like sodium and potassium, magnesium, calcium, and B vitamins ⁽²⁾. Supplementation is an option, but no concrete evidence shows supplementing vitamins and minerals provides the same health outcomes as getting them from nutritious food, so I always suggest food first.

2. Ketosis, digestive health, and the microbiome.

Beyond constipation that comes from a lack of grains & fiber that result from a keto diet, the impacts of a long-term high fat/low carb diet on the microbiome are of my greatest concern. Without dietary fiber, people on the Keto diet can experience either diarrhea or constipation, as well as bloating. Sometimes these are transient side effects, and other times not.

However, dietary fiber is the key ingredient to a microbiota-accessible carbohydrate (or MAC) diet. Fiber is what feeds our flora, which then converts it into short-chain fatty acids like butyrate that provide us with the endless health benefits we hear about surrounding probiotics. Without fiber, our flora suffers, which is demonstrated in the literature looking at all fiber-deficient diets, including FODMAP and gluten-free diets. ⁽³⁾

Even short-term ketosis reveals a “statistically significant increase in Desulfovibrio spp., a bacterial group supposed to be involved in the exacerbation of the inflammatory condition of the gut mucosa associated with the consumption of fats of animal origin”. ⁽⁴⁾

To vastly oversimplify the research, it seems the benefits of the ketogenic diet on the microbiota as a whole are unclear. Some studies show a favorable increase in beneficial flora, while others show the opposite. In summary, the take-home seems to be that an overall decrease in microbial diversity is seen in those following a ketogenic diet. ⁽³⁾

3. The Keto diet can worsen athletic performance, and maybe even long-term weight loss

Losing fat sounds great when you want to get fit. However, recent research found that in a ketogenic state, study participants performed worse on running and high-intensity cycling tasks after being on the Keto diet for four days, compared to participants who spent the same four days following a high-carb diet. ⁽⁵⁾

The conclusion of the study suggests “short-term low-carbohydrate, ketogenic diets reduce exercise performance in activities that are heavily dependent on anaerobic energy systems. These findings have clear performance implications for athletes, especially for high-intensity, short-duration activities and sports”. ⁽⁵⁾

Therefore, you may wish to again if you’re considering using the ketogenic diet to fuel your HIIT workouts every morning.

Recent studies have also highlighted that “ketogenic diets impair glucose and lipid metabolism in mice” ⁽⁶⁾, suggesting that long-term use may actually alter metabolic activity. There may also be concerns around the “yo-yo” effects of the Keto diet (where people lose fat, only to gain it back, and oftentimes more) on long-term metabolism.

4. Following the Keto diet long-term can increase the risks of chronic diseases.

Since fat consumption is essential to fueling ketogenesis, participants need to consume foods with high-fat content to maintain a ketogenic state. As a result, a rise in cardiovascular risk factors is often seen. Some literature shows an increase in blood pressure and cholesterol levels in ketogenic states, which is something I also see demonstrated in blood work for my current patients on a ketogenic diet.

A study from the American College of Cardiology found that people following the Keto diet long-term had a higher risk of developing atrial fibrillation, a common heart rhythm disorder that also increases the risk of heart disease and strokes.⁽⁷⁾ Other literature also highlights adverse effects including hepatic steatosis, hypoproteinemia, and kidney stones.1

In conclusion, it’s safe to say the use of a ketogenic diet needs to be evaluated on a case-by-case basis, and there calls for a collection of better long-term safety research before the diet can be considered as an ongoing intervention. With your microbiome always at the forefront of my mind, short-term ketosis may result in some favorable shifts in weight and metabolism, but offsetting the long-term impacts should be discussed with your ND.

To find out more about the right dietary adjustments for your gut and metabolism, please feel free to contact Toronto naturopathic doctor, Dr. Courtney Homberg at 647-351-7282 to schedule your appointment today.

About Dr. Courtney Holmberg, ND

Dr. Courtney Holmberg, BSc, ND, is a licensed Naturopathic Doctor, speaker, entrepreneur, and yoga enthusiast based in Toronto. With more than a decade of experience, her practice focuses on complex hormonal, digestive, and autoimmune concerns.

Her work is also informed by her own experience navigating PCOS and digestive issues. Dr. Holmberg takes a functional medicine approach that emphasizes thorough testing and assessment, looking beyond individual lab numbers to better understand the factors that may be contributing to a patient’s concerns.

You can learn more about Dr. Holmberg and her work through her official website, follow her on Instagram, or connect with Holmson Health on Facebook.

Read More: Scientists Find High-Fat Diet Could Help Maintain Brain Health