The human diet has an enormous impact on the quantity and quality of bacteria in the gut. In 2013, a team of scientists showed that a change in diet can radically alter the microbiome after just four days 1. Will eliminating carbs have a direct impact on gut bacteria too? What are the consequences of that?

The best formula for showing the relationship of macronutrients and intestinal flora comes from the University of Washington in St. Louis 2.

yi = β0 + βcaseinXcasein + βstarchXstarch + βsucroseXsucrose + βoilXoil … etc.

In this formula, y stands for the total amount of species “i” given the addition of various macronutrients on the right side of the equation. This formula simplifies things. It turns out that all but two species of bacteria (E. coli and C. symbiosum) studied responded to a single variable. This means that if you introduce a specific protein, E. rectale, D. piger, and M. formatexigens begin to drop out of the picture, and species like B. hydrogenotrophica increase in number.

This formula seems simple enough, and when it is applied in a clinical trial 3, the total number of bacteria drops. This might explain the weight loss of low carbohydrate isocaloric diets (the same number of calories were consumed, but low carbohydrate diets showed greater weight loss) because the total number of bacteria in the gut is proportionate to weight gain 4.  Although the mechanism is clearly observed from lowering carbohydrates, to reducing total bacteria, to weight loss, there are negative biomarkers shown as early as the four-week mark. 5

There are many low-carb approaches, and they all have different traits that make them unique. Most of them give a carbohydrate limit and suggest that one should not exceed that amount for the diet to be effective. This number is not the same from diet to diet.  It could be 150 grams, 50 grams, or even 20 grams. In addition, the term “net carbohydrates” is thrown around. Some dietitians claim that only carbohydrates that can be used by the human metabolism should be counted toward the daily carbohydrate allowance, but when we refer to the formula above, common ingredients in low-carb foods, like fermentable fibers and sugar alcohols, give some bacteria a huge advantage. When the total number of bacteria are reduced, and “non digestible” carbs are consumed because people miss their sweets, this creates the perfect environment for bacterial subsets to become dominant.

vLow Carb + Sugar Alcohols: A Formula for Disaster

People on long-term, very low-carb diets should avoid sugar alcohols. When someone restricts their total carbohydrate intake to 20g or below per day, the bacteria responsible for forming short chain fatty acids (like butyric acid) reduce population. 6 A reduction of these fatty acids leads to a thinning of the lining in the gut that prevents unwanted compounds for entering into the bloodstream. 7 Sugar alcohols like xylitol, erythritol, and sorbitol feed bacteria that produce endotoxin. With both an excess of endotoxin in the gut and a weakened gut lining, endotoxins will enter the bloodstream dramatically increasing the risk of heart disease, insulin resistance, obesity, and cognitive dysfunction. Is it a coincidence that these are the same diseases the low carb critics always bring up?

Are Probiotics the Solution?

If the problem is that we do not have enough of the bacteria that produce short chain fatty acids, why not add them back using a probiotic? The presence of bacteria is not equal to their biome impact. Bacteria require carbohydrates to produce fatty acids needed by our guts. Supplementing with probiotics would be like trying to grow a rainforest in the Sahara Desert by sprinkling seeds into the sand. Rainforests do not exist because of the happenstance of seeds, they are there because of the environmental conditions, and the same is true for the microbiome.

Low Carb Solutions

There are a few ways to make carbohydrate restriction safer.  First, eat more carbs and increase the intensity of your workouts, which will increase your metabolic rate so that you can create more biological diversity in your gut and burn off the excess.  If exercise is not your thing, consider taking supplements to raise your NAD+ to NADH conversion rates. Raising the conversion rate will mimic carbohydrate restriction in the blood without disrupting gut function. Finally, add a “carb day” to your routine every three to seven days. Adding in “carb days” will give you a metabolic boost while providing the nutrients to your gut bacteria that will keep you healthy.

If you are on a low carb diet, please monitor your gut function very closely so that you do not cause yourself harm.


Written by Jason Hooper