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How Your Microbiome May be Affected by a Ketogenic Diet

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In brief, there is no singular ketogenic diet. It’s really a function of the macronutrient composition of the diet (low-carb being a key factor), not specific foods. That is why there are no actual 'keto foods'.

However, the foods you choose to eat on a ketogenic diet will influence the composition and functional attributes of your gut biome.

In this article, I’d like to demonstrate that an amount of starchy carb-rich foods that would be prohibitive of nutritional ketosis is not necessary for a thriving ‘biome.

Why is Gut Microbiome Important?

Some people are convinced we know nothing about the ‘biome, and dietary fibre is useless. I’m not one of those people nor am I trying to convert anyone.

There are plenty of examples in the literature of certain microbial strains consistently low in the sufferers of certain gut symptoms and higher in people without those symptoms. There are even some strains associated with mood and cognitive function. And don’t even get me started on the studies on probiotics!

How Your Microbiome May be Affected by a Ketogenic Diet

The Role of High-Fibre Foods

I will use the term fibre to broadly mean “microbiota-accessible carbohydrate,” or, carbohydrates that are resistant to digestion by human enzymes but are digestible to microbes (1). Technically, cellulose, for example, is a fibre that is inaccessible to both humans & microbes so that definition isn’t entirely accurate, but it’s easier to type than “microbiota-accessible carbohydrate.”

In one study, patients with multiple sclerosis (MS) were recruited and put on a ketogenic diet consisting of <50 grams net carbohydrates, >160 grams of fat, and <100 grams of protein per day. They instructed the patients on low-carb, non-starchy plant foods like almonds, leeks, mushrooms, onions, Brussels sprouts, broccoli, cauliflower, avocados, asparagus, zucchini, eggplant, etc.

They wanted to assess microbial diversity and abundance as these metrics seem to be frequently associated with robust health among healthy human populations who also eat high fibre diets ( 2,  3).

Compared with health controls at baseline, patients with MS showed significantly lower microbial diversity and abundance. When the patients initiated a ketogenic diet, at first their ‘biome got worse but it soon began to recover and eventually reached the levels of healthy controls. That is, their microbiome improved beyond where they were at baseline.

Starchy carb-rich foods are not necessary for a thriving biome. A whole foods based ketogenic diet that includes high-fibre foods has shown to improve gut microbiome.

What may have happened is this that living with MS is difficult so the convenience of low-fibre fast foods may make life less burdensome. We aren’t given those data so this can be regarded as speculation.

The patients were given workshops by an experienced nutritional coach about the diet, how to handle/prep keto-friendly foods, etc. This, also, makes life less burdensome.

Their ‘biomes may have declined at first because they were just learning how to prepare ketogenic foods/meals, likely, for the first time in their lives. It may have taken a while to learn how to prepare the recipes in ways they found palatable, so maybe they ate less at first (that would also be harmful to the ‘biome). But when they got in their groove, they would’ve been eating a diet healthier than they were at baseline and possible healthier than the healthy controls.

This proves one thing: Starchy carb-rich foods are not necessary for a thriving ‘biome.

How Your Microbiome May be Affected by a Ketogenic Diet

In another study, the gut ‘biome was assessed in infants with refractory epilepsy before and during a period of ketogenic dieting ( 4). An interesting nuance on doing a study with 2-year olds is that it is very easy to control food intake. In most cases, they have little say in the matter. In this study, the diet consisted of ketogenic liquid formulas and set-meal packages. The diet was supplemented with prebiotic fibres.

As with the above study, the ‘biome in epileptic infants was less healthy than that of healthy controls and I suspect the reason may be the similar. Either these two conditions exert diet-independent effects on the ‘biome or these two conditions influence the patients’ diets.

In this study, diversity wasn’t as influenced as abundance in the patients. And after just one week on the fibre-supplemented ketogenic diet, the ‘biome started improving and was nearing that of healthy controls.

The speed of which this took effect is not surprising because after a marked dietary alteration, the ‘biome rapidly evolves within days. It took longer in the former study because, as mentioned, I suspect it took a while to ease into the diet so the ‘biome just followed along.

The Potential Effect of Nutritional Ketosis

One other thing to speculate on is the possible non-dietary effect of nutritional ketosis. I’m speaking specifically about ketones.

Intestinal cells are exposed both to the intestinal lumen but also the blood supply. The ‘biome may be releasing fuels that are used by intestinal cells, but these cells also love to use ketones.

With the added input of ketones, it’s possible that some of the symptomatic improvement on a ketogenic diet may be due, in part, to some of those ‘biome-derived factors escaping usage by the intestinal cells to influence something in the periphery. Maybe!

The Role of Fermented Foods

Lastly, low-carb non-starchy fibre-rich foods is a big part but not the whole part of the picture. It’s good to include fermented foods like sauerkraut, kimchi, yogurt, kefir, pickles, etc. to ensure abundance of the beneficial microbes ( 5,  6). Note that you may need to limit your consumption of fermented foods if you suffer from Candida.

How Your Microbiome May be Affected by a Ketogenic Diet

Take Home Message

I't a myth that humans need to eat starchy carb-rich foods in order to keep their microbiome healthy. In fact, studies have shown that people who follow a whole foods based ketogenic diet that includes high-fibre foods have a thriving gut microbiome.

Other than high-fibre foods, nutritional ketosis may potentially have a direct impact on the biome.

Finally, fermented foods like sauerkraut or kefir play a significant part in a keeping our gut microbiome healthy.

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Bill Lagakos, Ph.D.
Nutritional sciences researcher, consultant and blogger

Bill Lagakos

Hi, I’m Bill. I have a Ph.D. in Nutritional Biochemistry and Physiology from Rutgers University where my dissertation focused on fatty acid-binding proteins and energy metabolism. I studied inflammation and diabetes at UCSD. And most recently, I studied circadian biology at the Mayo Clinic. I have a broad range of knowledge about health, wellness, sickness, and disease... and I’m learning more every day!

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Comments (2)

Loved the article. I am a nutritionist so it is great to keep for my practice!

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Thanks Toni!

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