Ketogenic Diet: Fat Melter or Microbiome Menace?

By Rachel Stuck, RDN

If the keto diet were an ice cream flavor, it would probably be pistachio—you either love it or you grimace when you see it listed on the ice cream parlor menu. Now imagine that pistachios start showing up on the morning news and talk shows, and that your Pinterest page is flooded with pistachio meal ideas and infographics detailing its so-called miracle properties. You can understand how the pistachio lovers would be thrilled to see their favorite flavor finally getting the recognition it deserves and the pistachio haters would start to loathe the mere mention of this flavor. This seems to be where keto currently stands. Either you love it or you despise another restrictive diet trend showing up everywhere you look.

What Is the Ketogenic Diet?

If you haven’t heard about keto yet, here’s a quick rundown. The ketogenic or “keto” diet is a high-fat style of eating; dietary fat accounts for a majority of daily calories, there’s a moderate intake of protein, and a very low intake of carbohydrates. While the definition of a ketogenic diet can vary, a typical macronutrient breakdown might look something like this:

  • 70–80% of calories from fat
  • 10–20% of calories from protein
  • 5–10% of calories from carbohydrates

Someone following a 2,000-calorie-per-day diet would have a caloric breakdown that looks like this:

  • 75% calories from fat = 215 grams of fat
    • Reference: 1 tablespoon of olive oil = 14 grams of fat
  • 15% calories from protein = 75 grams of protein
    • Reference: 5 ounces of chicken breast = 30 grams of protein
  • 10% calories from carbs = 50 grams of carbohydrates (For keto, 10% is the upper limit, but some suggest 5% is a true ketogenic diet.)
    • Reference: 1 cup of cooked pasta = 43 grams of carbohydrates

This means a keto diet will contain mostly high-fat foods like:

  • Avocado
  • Coconut oil
  • Olive oil
  • Butter
  • Cheese
  • Foods from animal fat (e.g. pork rinds)
  • Egg yolk
  • Nuts and seeds
  • Nut butter

Remember, a 2,000-calorie diet with 75% of calories coming from fat translates to 215 grams of fat per day. That’s almost 1 cup of olive oil or 8 medium avocados.

The idea behind the high-fat diet is to deprive the body of glucose, its main source of energy, and push it to use an alternative energy source—fat. Ketones are what your liver produces from fat when your body is deprived of adequate energy from glucose. This process is known as ketosis, which is the goal of the keto diet. Ketosis can also happen due to untreated type 1 diabetes, or during periods of starvation, low food intake, intense exercise, or alcoholism.

After just a few days of following a ketogenic diet, an individual may notice significant weight loss. This is because glucose, our main energy source, is stored as glycogen and water. When the glycogen stores have been depleted, the number on the scale will also go down because the body has not only depleted glycogen stores, but also the water that was stored with it. This leads dieters to believe the high-fat diet is quickly burning away their fat stores, which is not actually the case. If the ketogenic diet is continued, fat loss will follow, but unfortunately, the water and glycogen weight will return as soon as carbs are reintroduced and the body is out of ketosis.

Benefits of the Ketogenic Diet

Weight loss seems to be the most recent claim to fame for the ketogenic diet, but before becoming a popular diet trend, the ketogenic diet was well known to the medical world. Doctors found the ketogenic diet to be a beneficial way to manage the symptoms of neurological disorders like epilepsy, multiple sclerosis, Parkinson’s disease, Alzheimer’s disease, chronic headache, sleep disorders, and neurotrauma.(1)

Even dieters who don’t suffer from the above ailments have noted keto’s bonus effect of increasing mental clarity and reducing brain fog. Some studies have noted its positive impact on diabetes, metabolic disorders, and cholesterol. One study concluded that following a keto-style diet for sixteen to twenty-four weeks not only significantly reduced participants’ body fat and body mass index (BMI), it also decreased “bad cholesterol” (LDL cholesterol), triglycerides, and blood glucose levels.(2)

Where the Diet Is Lacking

After reading about the benefits of following the ketogenic diet, you might be thinking, “Hmm... maybe I should give this a try.” But, before you load your pantry with olive oil (you’ll need the big bottle), butter, and avocados, let’s talk about where the diet might be lacking.

The main shortcoming of the ketogenic diet is that it is extremely low in fibrous foods like fruit, whole grains, and legumes, and it even limits vegetables. These plant-based foods have, time and time again, has been proven to prevent disease, making them a crucial part of a balanced diet.(3) Reducing fruits, vegetables, and grains (and therefore fiber), not only reduces the amount of vitamins and minerals in a diet, it leads to constipation and uncomfortable digestion.

It is important to note that there is a rift in the keto community. The divide exists between “clean keto” and “dirty keto” camps, who disagree about which foods should be eaten to reach ketosis. The clean keto approach focuses on including fat from quality sources like olive oil, avocados, grass-fed meat, and nuts. The dirty version might include processed foods like pork rinds and bacon, and additional added fat from cheese and high-fat, commercially raised meat. Unfortunately, most of the research about high-fat diets does not distinguish between “clean” keto and “dirty” keto. Adding to the confusion, high-fat diet studies are often animal studies, making it challenging to draw a sound conclusion without further research.

How Does Keto Affect the Gut Microbiome?

There is not an extensive body of research about the effects of a clean ketogenic diet on the gut microbiome. We found that most of the research on a high-fat diet and the gut microbiome includes a small sample size or the high-fat diet is coupled with sugar or processed carbohydrates. This makes it challenging to form a clear understanding of how the ketogenic diet affects the health, diversity, and function of the gut microbiome.

To start, here are four studies that suggest gut microbiome diversity is altered after a shift toward a high-fat diet. Each article shows slightly different findings depending on how the study defines a high-fat or ketogenic diet. You will see that when the high-fat diet includes mostly animal-based fats and minimal plant foods, more negative outcomes are found than in a high-fat, low-carb eating style that includes a variety of plant fibers from non-starchy vegetables.

  1. Higher fat consumption appeared to be associated with unfavorable changes in gut microbiota, fecal metabolomic profiles, and plasma proinflammatory factors, which might confer adverse consequences for long-term health outcomes.(4)
  2. Short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression.(5) The animal-based diet increased the abundance of bile-tolerant microorganisms (bad bacteria) compared to the plant-based style of eating.(6)
  3. Researchers who created an in vitro human gut simulator found that gut bacteria are able to utilize dietary fats to sustain growth.(7) Unfortunately, a reduction in short-chain fatty acids and antioxidants was also noted, which might mean that a high-fat diet is detrimental to the gut microbiome.
  4. Healthy polyunsaturated fatty acids, specifically omega-3 fatty acids, were found to be beneficial to the gut microbiome and might even be considered a prebiotic in the future.(8) This finding could support the benefit of a “clean” ketogenic diet.

Ketogenic Diet and Athletes:

There are numerous ketogenic-adopting athletes who are excited to share their successes with keto, but are exercise and restrictive dieting a good match? Exercise puts stress on the body, and restricting energy sources can cause additional stress, leading to poor workouts or even injuries. If you are active, it’s best to follow a balanced diet that includes nutrients to replenish, build, and heal the body before and after exercise.

A small amount of research supports endurance athletes following a high-fat, low-carb diet, but athletes participating in high-intensity sports that require short bursts might see a drop in performance.(9) When athletes start a high-fat diet, there is an (often frustrating) seven- to nine-month period during which they may not be able to perform at a high level. That being said, it is safe to conclude that a varied diet with moderate carbohydrates might be the most realistic way for an athlete to reach peak performance without lost training time related to the adaption period.

The Ultimate Question: Is Keto Realistic and Sustainable?

Following a ketogenic diet takes a lot of dedication and can be challenging because it requires so much planning and willpower. It takes the body a few days to truly be in ketosis and then once you're in it, just one meal can sabotage your hard work. When you follow a ketogenic diet, holidays, parties, or nights on the town become obstacles instead of celebrations, especially if you are looking for long-term results.

Although the benefits of a ketogenic diet are valid, completely breaking up with carbohydrates is tough and, more importantly, can be detrimental to your gut bacteria. Following a varied diet with a balanced addition of carbohydrates from vegetables, fruits, whole grains, and legumes can help you achieve sustainable weight loss and ensure that the population and diversity of your gut bacteria is supported.

About the Author

Photo: Rachel Stuck, RDN

Registered Dietitian Nutritionist Rachel Stuck has a background in culinary arts and nutrition counseling. Rachel takes a positive approach to nutrition: she avoids recommending restrictive diets and instead focuses on helping people choose foods that promote health and well-being. She is passionate about empowering and assisting Ixcela members as they develop their unique, gut-healthy lifestyles.

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Interested in learning more about Ixcela? Check out Ixcela’s microbiome test, personalized nutrition and fitness plans, and other tools to help you optimize your health.


  1. Stafstrom, Carl E, and Jong M Rho. “The Ketogenic Diet as a Treatment Paradigm for Diverse Neurological Disorders.” Frontiers in Pharmacology, Frontiers Research Foundation, 9 Apr. 2012,
  2. Dashti, Hussein M, et al. “Long-Term Effects of a Ketogenic Diet in Obese Patients.” Experimental and Clinical Cardiology, Pulsus Group Inc, 2004,
  3. Tuso, Philip J, et al. “Nutritional Update for Physicians: Plant-Based Diets.” The Permanente Journal, The Permanente Journal, 2013,
  4. Wan, Yi, et al. “Effects of Dietary Fat on Gut Microbiota and Faecal Metabolites, and Their Relationship with Cardiometabolic Risk Factors: a 6-Month Randomised Controlled-Feeding Trial.” Gut, BMJ Publishing Group, 18 Jan. 2019,
  5. David, Lawrence A., et al. “Diet Rapidly and Reproducibly Alters the Human Gut Microbiome.” Nature News, Nature Publishing Group, 11 Dec. 2013,
  6. Amirault, Ben. “Bile-Tolerant Gram-Negative Bacteria.” Medicinal Genomics, Medicinal Genomics, 17 Dec. 2018,
  7. Agans, Richard, et al. Downloaded from Http:// on March 25, 2019 by Guest. American Society for Microbiology, 21 Sept. 2018,
  8. Costantini, Lara, et al. “Impact of Omega-3 Fatty Acids on the Gut Microbiota.” International Journal of Molecular Sciences, MDPI, 7 Dec. 2017,
  9. Radcliffe, Shawn. “Here’s Why the Keto Diet May Hurt Your Athletic Performance.” Healthline, 9 May 2018,