The question about whether one should supplement probiotics on a ketogenic diet requires a bit of a deeper dive as it touches on a point of hot controversy. In order to better answer the question, it’s important to not only understand what changes a ketogenic diet has on the gut microbiome, but also the health impacts of those changes. The truth is, we simply don’t yet know; however, we can glean a few insights.

A quick google search will return a host of articles that put forward a hypothesis which basically goes:

Gut bacteria feeds off of carbohydrates. A ketogenic diet is so low in carbs that it starves the good gut bacteria, therefore harming the gut microbiome. Furthermore, the starved microbes start to eat the mucus gel on the intestinal lining and may even start eating the intestinal lining itself.

It’s a plausible line of thinking; however it might turn out to be entirely too simplistic.

What doesn’t seem to be in doubt is that a ketogenic diet will shift the gut microbiome; however, what is unknown is whether the shift is ultimately negative or positive for human health. Dr. Eric Westman, author of Keto Clarity, noted on this very subject, “We don’t know if different means bad”.

If the impact on gut microbiome were indeed negative, it would be reasonable to expect ketogenic dieters to report increased occurrences of gastrointestinal issues, skin problems, flare ups of inflammatory conditions, and perhaps even depression. Yet, we see a complete lack of this anywhere. Most often the dieter self reports seem to be the exact opposite. In fact, Dr. Westman notes:

“By taking away the carbohydrate in the food, I can pretty much fix every gastrointestinal problem that affects people today.

So we’ve done studies on diarrhea predominate irritable bowel syndrome, That was done by Greg Austin, who we collaborated with when he was a fellow at UNC Chapel Hill. Austin also did a study on GERD, where heartburn went away, which was totally unpredicted in the research world, although, in the clinic, using a low-carb, high fat diet, I see that all the time. NASH or fatty liver which is a pretty common cause of cirrhosis today, actually goes away when you cut away the carbohydrates. The bowel gas or flatulence is greatly reduced or almost entirely resolves when you take away carbohydrate from the diet. Gluten which is found in carbohydrate containing foods is a well known cause of gastrointestinal problems including celiac disease or gluten intolerance. The signals that we get clinically are if someone has gastrointestinal disturbance you want to reduce or eliminate the carbohydrate, not the fat, so it’s almost the exact opposite of what is being discussed in the animal research.”

Source – Me and My Diabetes interview with Dr. Eric Westman

There are many voices on this issue and you’ll find a bunch of links at the end of this post pointing to both sides of the argument. Wading deeply into these debate waters is beyond the scope of this post and certainly beyond my ability to add any real value.

What is reasonable to posit is that other than causing a shift in the gut microbiome, the health impact of the ketogenic diet as a result of this shift is unknown and poorly studied. Furthermore, gut microbiome research in general is still at such an infancy that science cannot yet accurately describe what a healthy or normal gut microbiome looks like. Without this clear target, neither side of the debate can claim victory.

Given there’s so much we don’t yet know, a prudent approach for keto dieters is to invest in prebiotics and probiotics and eat as many probiotic rich foods that will fit into your daily macro allowances.


Personally, I’m deeply interested in this topic. Having a chronic inflammatory skin condition (Rosacea), my gut health is something I’m deeply concerned about. This debate was the source of my only real reservation before starting a keto diet. The last thing I’d want is to do anything that would harm my gut health. Ultimately, I started keto and sure enough my Rosacea symptoms (while already improving) disappeared. I don’t attribute this all to a keto diet, but I did notice a substantial drop in new papules and pustules.


Further research:

Sorry low carbers, your microbiome is just not that into you – Human Food Project

RHR: You Are What Your Bacteria Eat: The Importance of Feeding Your Microbiome – Chris Kresser

7 Lingering Myths Everyone Should Know About Low-Carb Ketogenic Diets (#2) – Livin La Vida Low Carb

Diet rapidly and reproducibly alters the human gut microbiome – Nature.com

Chowing Down On Meat, Dairy Alters Gut Bacteria A Lot, And Quickly – NPR

Microbiome Nonsense: response to “Chowing Down On Meat”  (An in depth rebuttal to Nature report and NPR report)

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates – Cell.com