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The Ketogenic Diet: What Happens In Your Body And Microbiome?

The Ketogenic Diet: What Happens In Your Body And Microbiome?

The ketogenic diet is a popular weight loss strategy. Read on to discover how it works, what it’s for, and why it has an impact on your gut microbes.

Wherever you look, you’re almost certain to find information about the ketogenic diet. Everyone’s talking about it. So much so that, in 2018, it was the most Googled diet! Yet, you could probably be forgiven for not really knowing what ketosis means, or even understanding the premise behind the diet itself.

Over the years, different versions of the ketogenic diet have emerged, like the standard ketogenic diet, the Atkins diet, Dukan diet, and the 4:1 diet. They all follow the same basic principle of high fat, moderate protein, and low carbohydrate intake, though the actual ratios of macronutrients may differ slightly.

Nowadays, the ketogenic diet is often considered a fad and is promoted as a weight loss aid. Nevertheless, it was originally developed for medical purposes until mainstream media marketed it for weight loss.

In this article, we'll explore the history, composition, and medical applications of this diet. Then we'll delve into how it may impact and disrupt the important work of your gut microbes for your health.

What is the ketogenic diet?

Keto is a low-carb diet, in which the body has to use fats as a replacement energy source. And it has medical applications for specific conditions.

A true ketogenic diet demands that the patient consume less than 50g of carbohydrates per day. The reduction in carbs and increase in fats means the body no longer uses glucose for energy, but utilises fats instead.

Since ancient times, it has been known that a fasting diet could be used to control epileptic seizures. In the 1920s, it was discovered that a diet high in fats and low in carbohydrates could mimic the effects of fasting, and so, the ketogenic diet was born.

The ketogenic diet was slowly put on the backburner for treating epilepsy following the advent of antiepileptic drugs, but rose again to prominence in the 1990s. Since then, the diet has been used to manage epilepsies that don't respond to treatment, as well as diabetes type II.

The composition of the ketogenic diet

Macronutrient Percentage of diet (%) Food sources*
Fat 60% Avocado, olive oil, butter, oily fish, nuts, seeds, dairy
Protein 30–35% Eggs, fish, meat, beans, lentils, tofu
Carbohydrate 5–10% Leafy greens, tomatoes, broccoli, courgette, mushrooms

These are some examples of food sources, but not an exhaustive list.

The diet promotes high fat, moderate protein, and low carbohydrate consumption. By doing so, it increases the body’s metabolism of fat, and reduces that of carbohydrates and proteins.

Carbohydrates are traditionally our main source of energy in the form of glucose, which provides essential fuel for the brain. When the intake of carbohydrates is restricted, the body secretes less insulin because blood sugar levels don’t rise as much, and the body enters a catabolic state.

Catabolism is a metabolic process where larger molecules, like fats and proteins, are broken down into smaller ones so they can be used for energy, heat, or to build new molecules.

Therefore, in the absence of carbs, the body breaks down its fat stores into smaller molecules called ketone bodies. The process is called ketogenesis, and when the resulting state of ketosis is reached, the body will continue to make energy from the ketones until carbohydrates are eaten again.

For many people, the issue with the diet is being able to stick to it. The Western diet is typically high in carbs, often approximately 50% of the overall intake, yet low in fiber because these carbohydrates are often refined.

As a result, the Western diet may seem more palatable, but research indicates that it is unhealthy and increases several chronic disease risks. Because the ketogenic diet demands high fat intake (and moderate protein), it usually consists of lots of meat, eggs, processed meat, dairy, fish, nuts, oils, seeds, and low carb vegetables.

The ketogenic diet is often criticised for the fact many people tend to eat too much protein, which can take the body out of ketosis. Some also consume too many poor-quality fats, like processed meats, and tend to not eat enough fruits and vegetables, thus limiting their intake of essential dietary fibers, vitamins, minerals, and other nutrients.

The side effects of keto

The diet is often associated with some transient side effects too, such as kidney stones, and vitamin and mineral deficiencies. But there are some minor side effects too, which collectively are often referred to as the “keto flu”. These include symptoms like nausea, vomiting, constipation, bad breath, and sleep issues.

Then there are those that affect our brain, like headaches, confusion, and brain fog. And the reason such symptoms develop is because the brain relies almost exclusively on glucose to function. So, when glucose is taken out from the diet (remember, glucose comes from carbs), these symptoms occur.

Plants can be good sources of protein too, not just eggs and meat

There are certain carbohydrates the body needs to keep the gut microbiome healthy. Unrefined carbohydrates from plants contain dietary fibers and resistant starches that can’t be digested in the body. Instead, they travel through the gut to the colon where they are fermented and increase the growth and activity of healthy bacteria.

Prebiotics provide nourishment for gut bacteria and are turned into vitamins and short-chain fatty acids - something we'll discuss a bit later. Yet, some of these are limited in the keto diet, and this can cause imbalances in the microbiome, referred to as dysbiosis by doctors.

Equally, in the Western diet, the majority of people consume less than 50% of the recommended daily allowance of dietary fibre. So, if you're thinking about switching from a Western diet to keto, maybe you should consider replacing refined carbohydrates for more natural sources of fiber like fruit, vegetables, legumes, seeds, and nuts instead.

Therapeutic applications for the ketogenic diet

Despite huge promotion in the media, the ketogenic diet didn’t start its life as a weight loss craze. Instead, it was initially used because of its ability to limit epileptic seizures.

A therapeutic application is the use of a product, medication, or intervention which can prevent or treat an illness or injury. They are usually licensed for their particular use and prescribed by doctors for the treatment of a condition.


The ketogenic diet was originally designed for a medical purpose: to treat epilepsy. Today, this is still the case. Approximately 30% of epileptic patients have what is known as refractory epilepsy, in which seizures do not respond to medication.

Recent research has shown that the ketogenic diet can be a beneficial option for both adults and children with refractory epilepsy. In fact, the ketogenic diet can control seizures in up to 50% of children with the condition, and the benefits may even last long after the diet has stopped.

However, two of the major reasons why patients don’t stay on the classic ketogenic diet are that it is restrictive and unpleasant. It is put together mathematically, based upon the individual, and medically monitored. It is also calculated so as to provide the patient with enough vitamins and minerals to reduce the risk of deficiencies.

Interestingly, it is not fully understood how the ketogenic diet helps with epilepsy. Many theories suggest that the diet alters the excitability of the nerves, as well as their metabolism, reducing the frequency of seizures. Metabolic changes in the blood, like a reduction in blood sugar levels and an increase in ketone bodies, are also related to the reduction in seizures.

Diabetes type 2

The ketogenic diet can also be used to manage type II diabetes, in which high blood glucose and insulin resistance are major underlying metabolic factors. A key feature of insulin resistance shows that muscle cells are unable to take up the glucose circulating in the blood and use it for energy.

Instead, a body experiencing insulin resistance redirects much of its circulating blood glucose to the liver where it is converted to fat rather than used for energy. Therefore, if carbohydrate intake is restricted, insulin resistance tends to improve, or even disappear completely.

However, it is important to know that the restriction of carbohydrates needs to be calculated individually. This is because it needs to be limited to an amount where the carbs aren’t excessively converted to fat, and this figure isn’t the same for everyone.

Just like in the case of epilepsy, the ketogenic diet must be well formulated for individuals with metabolic syndrome, like insulin resistance or type II diabetes.

Is the ketogenic diet good for weight loss?

The diet is promoted for its weight loss attributes even though there are no long-term studies on potential health benefits or risks.

In short, no, the ketogenic diet shouldn’t be promoted for weight loss. The ketogenic diet is reliant upon consuming lots of meat and little fibre, both of which have consequences for human health. Plus, there is very little scientific evidence showing that the diet significantly increases weight loss.

Research has shown that individuals who follow a very low carbohydrate diet have much lower dietary fibre intakes compared to those consuming a regular UK diet. A diet low in fibre not only has consequences for the health of the gut microbiome, but also increases the risk of cardiovascular disease (CVD).

Fibre has been suggested to have a cardioprotective role because it is able to reduce low-density lipoprotein cholesterol (LDL-C). Plus, not eating enough fiber causes constipation, a major side effect of the ketogenic diet.

Equally, ketogenic diets which are high in saturated fat increase blood cholesterol levels as well as the risk of developing CVD. In rodents, non-alcoholic fatty liver disease (NAFLD) and insulin resistance have developed because of following a ketogenic diet.

The long-term consequences of the ketogenic diet have not yet been fully established. Plus, diets which promote rapid weight loss are often associated with increased mortality.

If you are looking to lose weight, eating a diet which is healthy, balanced, and has little or no processed foods is likely to be healthier than a short-term, quick-fix alternative.

A diet rich in fruits, vegetables, lean meats, fish, whole grains, seeds, nuts, and olive oil, like the Mediterranean Diet, is backed by plenty of scientific evidence for better health and reduced mortality.

How keto affects gut microbes

What you eat influences gut microbiome diversity, and the ketogenic diet is no exception. In fact, studies show that it can decrease microbiome diversity.

The gut microbiome plays an important role in our health and protection from excessive inflammation and chronic disease. Beneficial microbes feed on prebiotics from dietary fibers and other complex carbohydrates, without which this ecosystem can become unbalanced.

Heart health

Research has shown that short-term use of the ketogenic diet may improve blood risk factors for cardiovascular disease development.

However, 20-year studies have shown that the quality of the diet, as well as fat and protein sources, are important determinants in overall health outcomes when following a low-carb diet.

Eating large amounts of animal protein and fat increases the risk of developing atherosclerosis and cardiovascular disease. Atherosclerosis is a condition where plaques made up of fat, cholesterol, and calcium build-up inside your arteries, causing them to narrow over time.

The narrowing of the arteries increases the risk of coronary heart disease, angina, stroke, and heart attacks. The condition is related to lifestyle, particularly a diet high in fat. The ketogenic diet increases the risk of atherosclerosis risk. This is because it promotes the consumption of many animal-based foods, including eggs and red meat.

For many followers of keto, eggs (and often red meat) are a major part of their diet, but these foods contain choline, which can be metabolised by the gut microbiota into trimethylamine (TMA). TMA is delivered to the liver where it is converted to trimethylamine N-oxide (TMAO).

Why is this significant? Well, TMAO has been linked to the development of atherosclerosis, inflammation, and obesity. Plus, the precursors to TMAO, like choline found in eggs and red meat, have also been linked to an increase in cardiovascular disease.

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However, prebiotics, many of which are restricted in the ketogenic diet, have a beneficial impact on the gut microbiota because they can stimulate the growth and activity of beneficial bacteria.

Prebiotic fibers

The ketogenic diet is known for its limited carbohydrate intake (50 g/day) and this includes vegetables and legumes, as well as fruits. The restriction of plant-based carbohydrates and fiber can have significant effects on the gut microbiota.

The gut microbiota needs different types of prebiotic fibers found in carbohydrates because it provides nourishment for lots of different types of bacteria. This is what scientists call “diversity”, and it’s an essential marker for microbiome health.

Prebiotics make it possible for bacteria to do important jobs. For example, the microbes that feed on dietary fibers produce vitamins and short-chain fatty acids like butyrate that support gut and whole-body health.

The gut microbiome plays an important role in the gut-brain axis, and dysbiosis (imbalances in this ecosystem) has been reported in many neurological diseases, including refractory epilepsy in infants. In these individuals, the ketogenic diet is thought to fix the imbalance in their gut microbiota.

Research has shown that the gut microbiome in epileptic infants is significantly different from those who are healthy. Yet after the ketogenic diet, commensal bacteria such as Bacteroides increased and opportunistic microbes like Proteobacteria were reduced.

However, the evidence for the keto diet and the gut microbiome in epileptic patients is also conflicting. Although research agrees that there is a change in the microbiome, changes to the fecal microbiome may not be so beneficial for gut health.

For example, essential probiotic microbes called Bifidobacteria were reduced, which means their health-promoting activities were also blunted. Prebiotic supplements may help reduce such undesirable changes, but there's still a lot to be learned about phytonutrients in actual plant foods, which may not be present in prebiotic supplements.

The bacteria residing in our gut is also involved in maintaining a healthy weight, managing blood glucose levels, as well as keep the gut healthy. However, they can only do this by fermenting the dietary fibers they need for their own sustenance.

These fibers, which are severely restricted in the ketogenic diet, improve the growth and activity of beneficial and probiotic bacteria. Therefore, if you’re looking to achieve all round health and maintain a healthy weight, the ketogenic diet is probably not for you.


The long-term health consequences of following a ketogenic diet are still not understood, but its use in a clinical setting is well-founded. There is even new, emerging evidence for the diet's benefits in controlling other conditions.

Yet, the diet needs to be well formulated and medically monitored to make sure it is working appropriately and is safe for each individual. Changes brought about by this diet in the gut microbiome alone can lower our defenses against serious diseases like cardiovascular disease, diabetes, inflammatory bowel disease, and obesity.

That's why it's important to first evaluate your current diet and health, and see what changes you can make that are less drastic, like cutting out refined carbohydrates and processed foods. After all, a diet that is healthy and balanced is more beneficial for overall health, your gut microbes and, as a result, even weight loss.

Leanne Edermaniger
Leanne Edermaniger Science writer who enjoys laughing which is proven to help you live longer.

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