5 Signs Your Gut Microbiome is Out of Balance

diverse-e.coliYou are a superorganism! Your body is home to trillions of microorganisms (the human microbiota) that co-exist side by side with your human self. The collective genome of these microorganisms – the human microbiome – can be thought of as an extension of our own genome, in the sense that our microbial inhabitants carry out vital functions that we lack the genetic capability to perform ourselves. Our microbial symbionts break down some of the food we eat (in particular non-starch polysaccharides), protect us against invading pathogens, and regulate our immune system, among many other things.

Given the complexity and wide-ranging effects of the microbiota, it doesn’t come as a surprise that perturbations of the microbial rainforest found within us can have widespread effects on our health and well-being. A Western diet and lifestyle selects for a microbiota that is very different from the ones our primal ancestors co-evolved with. Broad-spectrum antibiotics, caesarean sections, highly processed foods, and inadequate exposure to biodiversity from the natural environment are just some of the many elements of a modern lifestyle that upset the man-microbe relationship that was shaped through eons of time. Some (including myself) would say that it’s likely that few, if any, people in contemporary, industrialized societies have a truly healthy gut microbiota.

This may lead you to ask: How do I know if I harbor an unhealthy or healthy gut microbiota, and hence, whether I need to take steps to change the composition of the microbial community in my gut? You can certainly do a stool analysis to find out what’s living in your bowels; however, simply assessing your current health condition can often be more telling, and may be sufficient to give you the answers you are looking for.

Here are 5 signs that you carry a gut microbiome that is out of balance…

1. Cravings for sugar and highly processed foods

In the ancestral, natural environments in which our Paleolithic ancestors evolved, calorie-dense foods high in sugar and/or fat were hard to come by. Honey was only seasonally available in certain areas of the world, and getting a hold of animal source foods often required hours of hunting or scavenging.

This is in stark contrast to how things are like in modern, industrialized societies. Today, we can simply drive down to the local grocery store, where we can choose from a wide selection of foods that contain an evolutionarily novel, potent combination of fat, salt, sugar, and starch.

From an evolutionary perspective, it makes complete sense that humans have evolved a taste/preference for foods that are calorie-dense and high in sugar or fat. However, that doesn’t mean that it’s normal to go around craving doughnuts, candy, and ice cream every day. Rather, strong cravings for highly processed, unhealthy foods are a sign of a deeper problem.

Studies have shosw that gut microbes can exert a strong regulatory effect on our dietary preferences and appetite (1, 2). For example: If you eat a diet high in refined sugar, certain proinflammatory microorganisms can get a chance to flourish in your gastrointestinal (GI) tract (3). These gut bugs may then produce compounds that affect your brain in such a way that you crave more of the foods that these critters depend on for their survival and reproduction.

Cravings for processed foods high in refined sugar and/or fat are a typical sign of gut dysbiosis!

2. Food intolerance

The human body, excluding its associated microorganisms, possesses the genetic capability to break down mono- and disaccharides, starch, fats, and protein (of the major nutrients we get from our diet). Some exceptions do exist; for example, about 70% of the world’s population loses the ability to produce the enzyme lactase after infancy, and they therefore can’t break down the disaccharide lactose.

Most non-starch polysaccharides, as well as certain other compounds we get through the food we eatr are broken down by our microbial symbionts. That is, if we harbor microorganisms that are able to degrade these compounds.

A lot of people experience symptoms of food intolerance because they harbor a gut microbiome that is poorly matched with the diet they’re eating. If you don’t possess a microbiome that is adapted to break down the fermentable compounds you’re eating, you’re not going to experience the promised health benefits associated with fiber consumption, but rather gastrointestinal distress and a leaky gut.

We now know that it’s not just the non-starch complex carbohydrates we get from our diet that are broken down by gut bacteria. For example, some microbes are able to degrade gluten, phytic acid, and lactose, meaning that if we harbor these gut bugs in our GI tract, many of the adverse effects associated with the consumption of these compounds could potentially be avoided.

As for lactose, several studies have shown that consumption of yoghurt, kefir, and certain probiotics improves symptoms of lactose intolerance (4, 5, 6). This makes sense, as when we consume these products, we’re also eating bacteria that are able to break down lactose. These bugs can potentially colonize our gut or transfer genetic material to bacteria living in gut biofilms, meaning that we essentially add genes to our microbiome that are needed to break down lactose.

3. Depression

There’s solid evidence to show that chronic depression is an inflammatory disorder (7, 8). The question scientists are now asking themselves is: Where does the low-grade inflammation that accompanies depression stem from? Emerging evidence shows that our microbiome may be the key to answering this question.

Some 70% of our immune system is located in and around the gastrointestinal tract, and the microorganisms found in our gut play a key role in regulating this system. Also, having a healthy gut microbiota is absolutely crucial for the prevention of chronic inflammation, as a resilient and diverse community of gut bugs keeps proinflammatory bacteria at bay and protects the intestinal barrier.

The bacteria in our gut also affect our brain function and mental health, and recent studies suggest that microbes may play a crucial role in inducing anxiety and depression (9, 10, 11). While certain gut bugs can contribute to making you depressed, others have antidepressive effects. For example, the soil bacterium Mycobacterium vaccae has been shown to mirror the effect on neurons that drugs like Prozac provide, which has led some authors to suggest that probiotics may one day replace – or at least supplement – antidepressive drugs (12).

In the coming decade I suspect that we will see a whole range of new microbiome modulators and probiotics on the market that are specifically designed for the treatment of mental health disorders such as chronic depression, ADHD, and autism.

4. Gas, bloating, bad breath, coated tongue, loose stools, constipation, and other problems associated with irritable bowel syndrome

If you go to your general health practitioner and say you’re struggling with gas, bloating, and/or other gastrointestinal issues, he will likely have little good advice to offer you. He may run a couple of tests to check for food allergies (which most likely come back negative), advice you to eat more fiber-rich whole grains, recommend that you take steps to reduce your stress levels, and then send you on your way with a prescription for a bottle of pills that does nothing to improve your underlying problem, but rather just help mask the symptoms.

From listening to your doctor and reading online, you may get the impression that irritable bowel syndrome is a condition without any clear causes or good treatment options. However, this is simply not the case.

A proportion of patients with irritable bowel syndrome have an abnormal gut microbiota that lacks biodiversity and resilience (13, 14). This sets the stage for food intolerance, elevated intestinal permeability, decreased protection against pathogens, and gastrointestinal issues such as gas, bloating, loose stools, and/or constipation. A dysfunctional gut microbiota isn’t the only cause of IBS, but it’s definitely an important one.

5. Acne vulgaris

If you ask your dermatologist whether there’s a connection between diet and acne, he’ll most likely pass on what he learned when he studied for his medical degree, which is that the food you eat has little, if any, impact on your skin health. This is unfortunate, because as those who’ve kept up with the science in this area will tell you, diet and lifestyle changes may actually be the key to preventing and treating acne vulgaris.

Studies looking into the health condition of hunter-gatherers and traditional, non-westernized people have shown that acne vulgaris is rare or nonexistent in these populations (15, 16). This is in stark contrast to the situation in today’s industrialized world, where virtually everyone gets acne some time during their life. For some it’s just a couple of pimples during adolescence, for others it turns into debilitating cystic acne.

Why is acne vulgaris such a common and widespread disorder in the modern world, whereas it’s almost unheard of among hunter-gatherers and certain non-westernized societies? Many theories have been proposed, most of which revolve around the mismatch between our modern way of life and our ancient genome.

Personally, I believe that chronic inflammation, gut dysbiosis, and increased intestinal permeability are largely to blame for the epidemic of acne vulgaris in Westernized nations. To keep this article from getting very long I won’t get into the science supporting this statement, other than to say that this view is supported by a growing body of research that links acne vulgaris to a dysfunctional gut microbiota and supports the use of probiotics, prebiotics, and dietary interventions in the treatment of this skin condition (17, 18, 19).


Gut dysbiosis and lack of microbiota diversity set the stage for increased intestinal permeability, systemic low-grade inflammation, and chronic disease. The five problems described above are just some of the many health issues that start in the gut. Chances are, if you suffer from a chronic health disorder of some sort, your gut microbiome is partly to blame, and hence, you should take steps to change the composition of the microbial communities that live “in” and on your body.


  1. Thanks again Eirik – well thought out post.
    “We now know that it’s not just the non-starch complex carbohydrates we get from our diet that are broken down by gut bacteria. For example, some microbes are able to degrade gluten, phytic acid, and lactose, meaning that if we harbor these gut bugs in our GI tract, many of the adverse effects associated with the consumption of these compounds could potentially be avoided.
    … and, might I add, potentially get benefit from these foods. This is why I have left strict “paleo”.

  2. Eirik this is a really good post, and the kind of issues I talk about on my blog. High fives!

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