Is Your Low-carb Diet Rages In Your Gut Microbes Group?

11 Sep

meatThere’s nothing inherently wrong with low-carbohydrate diets. A well-designed, low-carbohydrate diet can provide your body with all the raw materials it needs to function optimally and help you build a strong, robust physique. Not all low-carbohydrate diets are equally healthy though. A poorly constructed, low-carbohydrate diet can wreak havoc on your hormone levels, immune system, and athletic performance. Moreover, over the past decade, research has revealed that an improperly designed low-carbohydrate diet can inflict severe, long-lasting damage upon the gut microbiome.

We’re killing our symbionts

Your body consists of a complex mix of microbial and human cells. When things work as they should, the microscopic and macroscopic part of this superorganism live side-by-side in a peaceful, mutualistic relationship.

Unfortunately, life isn’t perfect; relationships change, friends lose touch with each other, and conflicts arise. These events don’t just occur between humans, but also between humans and microbes. If the human superorganism encounters stimuli that are novel or foreign, the balance between man and microbes may change, going from peace to war.

This perturbation of the harmonious state can occur as a result of many different behaviours, including antibiotic use and excessive cleanliness. The most important regulator of the human-microbe symbiosis, however, may be diet. While a prudent, fiber-rich diet can boost the diversity and resilience of the human superorganism, a highly processed diet, on the other hand, produces an ecosystem that is rid of diversity and prone to invading pathogens.

This is what is happening all over the world today. In the blink of an eye – on the evolutionary scale – humans have gone from eating bulky, fibrous diets comprised of wild plants and animals to eating highly processed, calorie-dense diets comprised of industrially produced food. This shift has been too profound and rapid for the human genome to adjust, and has thus produced a mismatch between the human microbiome – which rapidly changes in accordance with dietary alterations – and the human genome.

Suddenly, the human immune system is no longer receiving the microbial signals it needs to function properly and is opened up to attacks by pathogens. This has partly occurred because Short-Chain Fatty Acids (SCFAs) – produced in large quantities in the guts of our fiber-eating ancestors – have been replaced by starch, sugar, and saturated fats. The latter nutrients are primarily absorbed in the upper part of the gastrointestinal tract; SCFAs, in contract, are produced (via the fermentation of fiber) and absorbed in the colon. SCFAs are critical in that they mediate immunoregulatory signals and fuel the colonocytes.

Eating for trillions

This leads us back to low-carbohydrate diets. It isn’t just highly processed, western-style diets that can wreak havoc on the gut microbiome. Even a diet that is composed exclusively of whole foods may leave the microbiome in a sorry state if it contains an imbalanced proportion of carbohydrate (including fiber), fat, and protein.

I should know. For years I ate a whole foods diet that didn’t agree with me – or my microbial symbionts. At the time, the diet I ate was considered by most within the low-carb community to be a very healthy diet; it was rich in proteins and fats and contained little carbohydrate. I did eat some vegetables, but they were mostly non-starchy varieties.

Despite adhering to this “healthy” diet, I experienced declining health and athletic performance. Frustrated, I made a slew of further dietary changes over the following years. However, the idea that a low-carbohydrate diet is the optimal diet for humans had been deeply imprinted in my mind, so it took quite some time before I finally climbed out of the hole I had dug for myself.

In retrospect, I realise that the crux of the problem wasn’t low-carbohydrate eating per se, but rather my insufficient intake of fermentable carbohydrates. Today, I consume more non-fermentable carbohydrate than in the past, but still less than the average Standard American Dieter.

My experience is certainly not uncommon. Similar physiological processes likely occur in the body of all people who eat low-fiber diets.

A large body of evidence indicates that diets very low in fiber wreak havoc on the gut microbiome (1, 2, 3, 4). When it’s combined with a high intake of evolutionarily novel, high-fat foods such as cream, bacon, butter, and GHEE (all of which are an essential component of many low-carb diets), a low fiber intake is particularly problematic, and may result in dysbiosis, endotoxemia, and severe health problems.

Another worrisome consequence of decreased microbial biodiversity is its epigenetic effect. If you adopt a diet that is very low in fiber, the genetic diversity of your microbiome will likely decrease, and after a while, certain microbes may completely disappear from your gut. This will then affect the children you bring into life, who will receive a less diverse mix of bacteria than what would have been the case if you ate a more prudent diet.

Roughage to the rescue

So, what can you do about this problem? Is it sufficient add a couple of tomatoes to your standard bacon-and-eggs breakfast, eat an apple with your lunch, and include some lettuce, cucumber, and cooked onions with your high-protein, high-fat dinner?


The fiber content of these popular plant foods is quite low, because we humans have been selecting for fruits and vegetables that are large, low in fiber, and high in sugar. Not all domesticated plant foods are lower in fiber than uncultivated varieties, but many are (5, 6, 7). The potatoes and other starchy roots and tubers at your local health food store are markedly different from the underground storage organs hunter-gatherers such as the Hadza eat.

In other words, a person who adheres to a high-fat, low-fiber diet will not experience much health improvement from just eating a little more fruit and/or adding a small portion of non-starchy veggies to his dinner plate. Rather, he has to make a conscious effort to seek out and eat fiber-rich foods.

That said, it’s neither necessary nor wise to eat a lot of pasta, breads, and other cereal-based products. Good Paleo-friendly fiber sources of fiber include onions, leeks, roots, tubers, artichokes, and fennel; all of which are low in sugar and relatively high in fermentable fiber. Personally, I also include smaller amounts of non-gluten, low glycemic index whole grains in my diet, because they are a good source of fiber and starch – food for microbes and man.

Before we wrap up, let’s return to the statement I made in the beginning of the article: There’s nothing inherently wrong with low-carbohydrate diets. The fact is that the type of diet that we today classify as a low-carbohydrate diet actually isn’t that low in carbohydrate. A diet of 20-40% carbohydrate by calories is certainly low-carb compared to the typical grain-based, western diet; however, compared to a typical hunter-gatherer diet, its carbohydrate content falls well within the ancestral norm.

The difference is that our primal forebears generally ate a lot more fermentable carbohydrates than we do. In other words, their non-fermentable/fermentable carbohydrate ratio was lower. Since we don’t have access to the same foods as hunter-gatherers, we can’t perfectly replicate their diets; however, it is still instructive to study our distant ancestors’ dietary habits to learn from the broader nutritional patterns.

Key takeaways

It’s not just the human part of your body that you have to take into account when you plan your diet and food choices, but also the microbial part. Your intestinal microorganisms, just like your cells, need energy to survive. If you eat a diet high in fiber and low in evolutionarily novel foods, the beneficial bacteria in your gut get a chance to flourish; however, if you eat an imprudent, low-fiber diet, the gut microbiome can spin out of control, pathogens may get a foothold, and “health-promoting” microorganisms could disappear from the gut.