Woman sitting and eating a meal as part of her Ketogenic diet plan to address her autoimmune disease

Here’s the #1 secret to getting the autoimmune benefits of a Ketogenic diet without wrecking your good gut bacteria in the process

The Ketogenic diet has been gaining popularity among people struggling with autoimmunity over the past several years. This is mostly due to the diet’s high concentration of polyunsaturated fatty acids (when done right) and its ability to facilitate the production of anti-inflammatory ketones (also when done right). But do the benefits of the ketogenic diet really outweigh the risks? And if not, are there ways to secure the anti-inflammatory benefits that are coveted by people suffering with lupus, Crohn’s disease, ulcerative colitis, rheumatoid arthritis, Hashimoto’s thyroiditis, Grave’s disease, psoriasis, and other autoimmune diseases without taking on the additional health risks that are associated with following a classical Ketogenic diet long-term? In this article, I’ll discuss the basics of Keto, how it leads to its anti-inflammatory effects, what the research is saying about the long-term effects of this type of diet, and how you can secure the benefits of a Ketogenic diet without wrecking your gut microbiome (specifically your good gut bacteria) and while avoiding the other negative consequences associated with this diet.

What is the Ketogenic diet and does it actually help with autoimmune disease?

The Ketogenic diet is basically a way of eating that includes lots of fats and very few carbohydrates. People essentially replace carbohydrate-containing foods with fats in their diet. Here are some examples of foods that are permitted and foods that are typically avoided on the Keto diet:

Foods that people typically avoid on the Ketogenic diet:

  1. Grains and starches, including breads, pastas, cereals, other grains
  2. Beans and legumes, including black beans, garbanzos, lentils, kidney beans, peas, etc.
  3. Sugary foods: fruit juices, candy, ice cream, sodas, smoothies, pastries, cakes, etc.
  4. Fruit, except very small amounts of low-sugar berries like raspberries and blackberries
  5. Most root vegetables, including potatoes, sweet potatoes, carrots, beets, etc.
  6. Low-fat condiments, including low-fat mayonnaise, low-fat salad dressings, etc.
  7. Artificially sweetened foods, including most “sugar-free” candies, syrups, pastries, sweeteners, and desserts
  8. Sweetened condiments and sauces, including honey mustard, barbecue sauce, teriyaki sauce, ketchup, etc.
  9. Unhealthy fats, including processed vegetable oils, mayonnaise, etc.
  10. Alcohol, including wine, beer, liquor, and mixed drinks

Foods that people typically eat on the Ketogenic diet:

  1. Fatty fish, including salmon, trout, tuna, and mackerel
  2. Other types of meat, including turkey, chicken, red meat, etc.
  3. Eggs, including pasture-raised eggs (which are a better choice than free-range, cage-free, and caged)
  4. Butter and cream, including grass-fed butter (which is nutritionally a better choice than regular butter) and heavy cream
  5. Cheese, including unprocessed cheeses like cheddar, blue, or mozzarella
  6. Nuts and seeds, including almonds, flax seeds, chia seeds, walnuts, pistachios, etc.
  7. Healthy oils, including avocado oil, extra virgin olive oil, and coconut oil
  8. Avocados, including whole avocados or homemade guacamole
  9. Low-carb vegetables, including green vegetables, peppers, zucchini, etc.
  10. Condiments, including salt, pepper, herbs, and spices

So as you can see, this diet is actually pretty restrictive, and the reason for this is that the anti-inflammatory benefits associated with this diet depend on your body entering into a metabolic state called ketosis.

Here’s the breakdown on ketosis: basically, most of your body’s cells prefer to use carbohydrates as their main energy source; however, when you significantly limit carbohydrates (grains, sugars, and other starches) in your diet, your body begins to convert your stored fat into ketone bodies. These ketone bodies are then released into the bloodstream and your body uses them to produce energy. This, in a nutshell, is the process known as ketosis. This diet relies on this process.

Now, this article isn’t about trying to persuade you to go Keto; instead, it’s about educating you about the benefits, risks, and alternatives associated with using this diet to address your autoimmune symptoms. I want you to have the best outcome possible, so if you’re going to try a Ketogenic diet, I want you to do it correctly; I don’t want you to be uninformed and end up wasting your time on a diet that won’t help you reach your wellness goals.

That being said, it’s important to note that the benefits of the Ketogenic diet are highly dependent on the ketosis process, so if you’re sneaking carbohydrates or if your fat-to-protein ratio is not ideal, you will likely not enter into ketosis and you won’t experience the anti-inflammatory benefits associated with following a classical Ketogenic diet. In all honesty, you’ll probably experience pro-inflammatory effects and an increase in your autoimmune disease symptoms.

The truth is that this diet isn’t something you can “sort of do” and still get some of the benefits; it’s more of an all or nothing type of deal. There is a threshold of carbohydrate availability that your intake must be below and there are specific guidelines that you must follow regarding your ratio of fat to protein in order for you to actually enter into ketosis. Furthermore, if you’re eating, but you’re not consistently adhering to these narrow guidelines for at least 2 to at least 14 days, [1] it becomes less likely that you’ll begin to produce the ketones which lead to the anti-inflammatory effects that are associated with this diet. Every time you sneak carbs, you set yourself backwards and have to start all over until you get to the place (again, within that 2- to 14-day window, where your body begins to produce ketones).

To summarize, when done correctly, the Ketogenic diet can reduce the immune system dysregulation and symptoms that we see with various autoimmune diseases, but it is a diet that takes a lot of work and is very difficult to get right. Also, it isn’t without its risks and the potential for long-term complications.

What are some of the problems associated with the Ketogenic diet?

In light of the fact that the Ketogenic diet can help improve autoimmunity symptoms, it’s also important to consider the drawbacks associated with this diet. There are multiple problems associated with the long-term use of the Ketogenic diet, and these center around the diet being restrictive and acidic, as well as around the diet’s effect on your gut bacteria and vagus nerve function. I’ll discuss each of those in this section.

The Ketogenic diet is restrictive

In order to properly follow a classical Ketogenic diet, you would need to completely eliminate multiple food groups. This results in a diet that is low in fiber (which is typically found in a wide array of fruits and vegetables) and oftentimes low in micronutrients (which are also plentiful in appropriate quantities in a variety of fruits and veggies).

The fact that the Ketogenic diet is low in fiber is the main reason why people who adhere to this diet oftentimes report gastrointestinal concerns like bloating and extreme constipation, and it’s also been cited as the main reason why people have a difficult time staying on the diet long-term.

As far as micronutrient status is concerned, there are a few nutrients that those who adhere to high-fat, minimal-carbohydrate-containing diets are significantly more likely to be deficient in. These include potassium, magnesium, vitamin C, and folate. Some researchers have argued that people adhering to a true high-fat, low-carb diet need less of these nutrients; however, this remains to be seen in the scientific research.

In fact, nutrient deficiencies are the main reason why children who have to be on a Ketogenic diet to manage their seizures need to be seen by their providers within one month of starting the diet and every three months thereafter for evaluation. [2] If they aren’t supplementing appropriately, the micronutrient deficiencies can significantly impair their health and lead to problems with their growth. Of note is the fact that children who were placed on this diet for 3-15 months to address their seizures saw a decline in their growth and tended to be shorter than their healthy peers who were on a more standard diet. [3]

The Ketogenic diet is acidic, which can negatively affect bone health

Research suggests that low-carbohydrate, high-fat diets are highly acidic, especially when compared to diets that contain more plant-based foods. [4-5] In fact, it’s a well-known fact that the Ketogenic diet leads to metabolic abnormalities that increase our risk for kidney stone formation. These metabolic abnormalities may also contribute to increased risk for osteoporosis and poor bone health in both the short- and long-term. [6-9]

The Ketogenic diet wrecks your gut bacteria, endangers gastrointestinal health, and impairs your vagus nerve’s ability to sense and modulate inflammation levels

The title of this section is a mouthful, but these characteristics of the diet are all related. I’ll share some background physiology to catch you up to speed and then I’ll explain why each of these negative consequences of the Ketogenic diet is relevant to you as a person diagnosed with an autoimmune disease.

OK, we all have bacteria in our gastrointestinal tracts and these bacteria serve multiple functions. Through a mechanism known as the gut-brain axis, our gut bacteria can communicate with and influence our brains. This mainly happens through the bacteria’s effects on a nerve called the vagus nerve.

The vagus nerve plays a critical role in inflammation control, autoimmunity, and even mood control, but it’s hampered by the Ketogenic diet

The vagus nerve is the longest nerve in your body; it’s a cranial nerve, meaning that it originates in our brains, and it descends all the way down to our gastrointestinal tracts. It serves various functions, but its roles in modulating inflammation levels, mood regulation, and controlling the parasympathetic (“rest and digest,” so the opposite of “fight or flight”) nervous system are the most relevant to our discussion here.

The vagus nerve controls inflammation through what’s known as the inflammatory reflex. Basically, the vagus nerve senses where our bodies’ inflammation levels are, it communicates that information to the brain, and then it receives feedback from the brain and makes changes in our internal environments based on that feedback. [10]

But there are multiple factors that can impair our vagus nerves’ ability to sense what’s going on in the environment. When this happens, the vagus isn’t able to provide the brain with the necessary feedback (at least not as efficiently), and our inflammation levels may be permitted to rise outside of the normal range.

One of the factors that can impair the vagus nerve’s ability to sense the inflammation levels in the environment is chronic stress, not only stress in adulthood but also childhood stress. This is because when we experience chronic stress during childhood, it changes our brains and bodies, alters how our bodies respond to chronic stress, and leads to alterations in our vagus nerve function as well. [11] These changes then increase our risk for a host of chronic conditions, including increasing our risk of being diagnosed with and hospitalized with symptoms due to multiple autoimmune diseases. [12] But, this is another topic for another day. If you haven’t yet and you’re intrigued by this topic, I recommend checking out my article on childhood stress and autoimmune disease risk.

To stay on topic, animal research demonstrates that in the short-term, high-fat diets may actually help the vagus afferents to do their job of controlling inflammation more efficiently. [13] But in the long-term, and by long-term I mean after 24 hours or more, the effect is the exact opposite. After as little as one day, high-fat diets impair important functions of the sensing portion of the vagus nerve.

Remember, if our vagus nerve has a harder time sensing our inflammation levels, it can’t relate that info to the brain, and the result is that the inflammatory reflex is interrupted and our inflammation levels are more likely to go beyond what the brain considers to be normal. This, of course, would be associated with an increase in autoimmune disease symptom severity.

Furthermore, there’s actually an overwhelming amount of research that demonstrates that high-fat diets lead to significant changes in our gut bacteria. [14-15] In fact, after fewer than 5 days on a high-fat diet, we see a significant increase in inflammatory, gram-negative bacteria like Bilophila wadsworthia and Desulfovibrio spp.  [16-18]

Now here’s why you don’t want these guys in your gut. These bacteria are composed of something called lipopolysaccharides or LPSs, and if they’re in your gut, they can release LPSs there. The LPSs interact with your vagus nerve and the result is an increase in inflammation. [19] To make matters worse, high-fat diets are known to facilitate intestinal permeability. [20]

This basically means that whereas the barrier in your gut was solid like a bowl, after being on a high-fat diet, it becomes more like a colander or a sieve. The LPSs can then go through the little holes in your gut barrier and they can enter your bloodstream where they cause your body to have low-grade, chronic inflammation. [21] In addition to worsening your autoimmune disease symptoms, these LPSs can also negatively impact your mood and contribute to depression and other mental health concerns.[22-24]

If the Ketogenic diet destroys your good bacteria, why would anyone even recommend it to treat autoimmune disease?

Now, you may be saying, “Wait a minute, Dr. Janelle. I thought you said the Ketogenic diet was anti-inflammatory; what’s all this? And if it really can destroy my microbiome, hamper my vagus nerve function, and negatively affect my mood, why on earth would I, or anyone for that matter, even try it?!”

Here’s my explanation: All of what I’ve just described does take place in the body on a Ketogenic diet, but in spite of that, the diet still has a net anti-inflammatory effect. In other words, as I mentioned in my introduction, the anti-inflammatory effects of the ketones and the polyunsaturated fatty acids that typically comprise the diet are so powerful that they can overcome the inflammatory effects, to a certain degree. So to summarize, the anti-inflammatory effects outweigh the pro-inflammatory effects in this case, but that doesn’t mean the diet is devoid of negative potential long-term complications.

So if you’re actively thinking as you’re reading, then you’re probably wondering “Is there a way then to secure the anti-inflammatory benefits of ketosis without the bone-depleting, gut-wrecking, and mood-destroying effects of a high-fat diet?”

And if this is your question, then boy do I have an answer for you!

Enter time-restricted eating.

How does time-restricted eating help with autoimmunity and help my body produce anti-inflammatory ketones without the negative effects associated with the Ketogenic diet?

Time-restricted eating is a manner of eating that supports optimal circadian rhythm function [25] (which, by the way, is a critical part of wellness for people diagnosed with autoimmune disease). It essentially limits your daily eating times to 6-12 hours per day and allows for a period of fasting every day. Research demonstrates that this type of time-restricted eating has powerful anti-inflammatory effects on the body, as well as other benefits.

These benefits are partially due to the fact that this type of fasting has been shown to actually lead to the production and metabolism of ketone bodies. [26] In other words, by implementing this type of time-restricted eating, we can produce ketones on a daily basis, while enjoying a much less restrictive diet than the Ketogenic diet (and not to mention avoiding the unwanted potential complications and the increased all-cause mortality—or likelihood of death—that is associated with high-fat, low-carbohydrate-containing diets). [27-28]

In order to help the high-performing women I work with who’ve been diagnosed with autoimmune disease to improve their symptoms while simultaneously addressing the underlying causes of their conditions, I typically recommend a much more sustainable diet that is centered around whole foods and that includes complex carbohydrates, moderate protein, and healthy fats. I make these recommendations in the context of time-restricted eating in order to support optimal vagus nerve and circadian rhythm function. I have them have their last meal by 6pm for the latest and fast overnight until 12-16 hours later, so if they finish eating by 6pm, they have breakfast between 6 and 10 a.m. To further support circadian function, I recommend that they follow a schedule and have their meals at the same time each day.

Because stress is a significant contributor to both autoimmune disease risk and symptom severity, I also work with my clients to help normalize their chronic stress response (which is controlled in the body by the hypothalamic-pituitary-adrenal or HPA axis, and which can get out of whack and increase our risk for autoimmune disease and many other chronic disorders if we experience high stress in adulthood or even comparatively small amounts of stress in childhood).

I’ve found that this three-pronged approach to addressing autoimmune disease—an approach that emphasizes optimal HPA axis function, vagus nerve health, and circadian rhythm function—leads to amazing results in helping my clients significantly reduce their autoimmunity so that they can truly thrive.

If you’d like to learn more about my unique and comprehensive approach to addressing autoimmunity, you can click here to watch the replay of a webclass I did for my audience a while back.

I wish you nothing but the best as you progress along your wellness journey!


To see a list of references associated with this blog post (and any of my other posts where I reference an extensive list of scientific sources), click here.

Article highlighting the risks and benefits of a ketogenic diet for autoimmune disease and what to do instead