Gut – What are gut problems

Gut – What are gut problems

The human digestive track is inhabited by a staggering number of bacteria. Estimates put the number of bacteria at ten times higher than the number of cells in your body, and dead bacteria make up for about 60% of the fecal mass. Most of the bacteria reside in the colon, with the stomach and small intestine being relatively sterile. In the medical speak, these bacteria are often called gut microflora or microbiota.

For the most part, we coexist with these bacteria in a mutually beneficial relationship. The extent of our relationship with the gut bacteria is not yet known. But we do know they help in digestion of food, break down fiber humans couldn’t otherwise digest, synthesize certain nutrients, and keep the harmful bacteria and pathogens at bay. They also play a role in maintaining the gut barrier, allowing nutrients to pass and keeping harmful toxins out of the bloodstream. The microbiota also regulates the immune system, and disruptions in the gut microbiota can lead to autoimmune and other inflammatory problems.

Scientists are also starting to uncover the connections between gut microbiota and stress and other emotional problems. The bacteria seem to communicate with the nervous and immune systems, at least as far as gut health and immunity are concerned.

In addition to the probiotic, or beneficial bacteria, the gut also harbors pathogenic, or harmful bacteria.

Bacteria related problems

The gut is a battlefield. The different types of bacteria residing in the gut constantly fight for dominance. And the result of this ongoing battle can influence both your overall health and the health of your skin.

In a healthy gut, the so-called probiotic bacteria dominate. However, this balance can be disrupted (we’ll talk more about why that happens later in this section). Broadly speaking, there are three types of disturbances to the gut microflora:

  • Bacterial dysbiosis. The balance has flipped to favor the pathogenic bacteria.
  • Small intestine bacterial overgrowth (SIBO). The bacteria have moved in larger numbers to the otherwise relatively sterile small intestine.
  • Bacterial translocation. The bacteria migrate through the gut wall and into the bloodstream. In this situation, even the probiotic bacteria can be dangerous.

The first two are by far the most relevant for acne, and they will be our focus in here.


Humans have evolved to coexist with the healthy bacteria in the gut. Over time we’ve come to rely on them. Not only do they produce nutrients we can’t make, but they also help the immune system to recognize and deal with the ‘bad guys’.

The healthy bacteria cooperate with the immune system in a way that leaves the healthy bacteria alone. Think about it. If the immune system would also attack the healthy bacteria, your gut would quickly turn into a mess. This is sort of what happens in inflammatory bowel disease. Partially as a result of dysbiosis, the immune system attacks the bacteria in the gut wall. This results in toxic substances leaking through the gut wall (intestinal permeability) and reduces nutrient absorption. Not to mention causing frequent pain to the sufferers.

The bacteria in the gut have a metabolism. Much like you, they eat food and excrete waste products. For the most part, the metabolic by-products of the probiotic bacteria are good for us. For example, they create short-chain fatty acids (SCFA) that regulate inflammation in the gut and repair the gut lining.

On the other hand, the harmful bacteria produce toxins that, if leaked into the body, can have serious health consequences. In medical speak, the toxins produced by gut bacteria are called endotoxins.


That being said, even the so-called probiotic bacteria sometimes cause problems. The small intestine is relatively sterile compared to the large intestine. In some situations, the bacteria migrate from the large intestine ‘up’ to the small intestine. This is called small intestine bacterial overgrowth, or SIBO.

People who blindly recommend probiotics don’t realize that most SIBO cases involve an overgrowth of the probiotic bacteria. In other words, the supposedly beneficial bacteria have migrated to places where they aren’t supposed to be. In such a case, taking probiotics often makes the problem worse!

Many bacteria produce gasses as a result of fermentation. In simple English, they eat and produce gas. That gas isn’t supposed to be produced in the small intestine. It’s meant to be produced in the large intestine from where it’s easily eliminated (via the biological process called farting).

Gas in the small intestine causes all kinds of problems. The most obvious being that it makes you look and feel bloated. The gasses also affect motility, which is a scientific term for the time it takes for food to pass through the digestive track. Some gasses, such as methane, slow motility, i.e. they cause constipation. Some increase motility – they cause loose stools or diarrhea.

SIBO has also been linked to intestinal permeability.

Intestinal permeability

Your digestive system is a very long and thin tube with extremely thin walls that, in some places, are only a single cell thick.

This gut lining forms a vital barrier between what’s ‘in’ and ‘out’ of your body, because, if we don’t split hairs, the contents of your digestive system are not yet part of your body. Substances that don’t pass through the intestinal barrier, and thus technically do not enter the body, have a much smaller influence on your health than the substances that do pass through the intestinal barrier. The barrier, and the bacteria that reside on it, actively seek out nutrients and keep out bacterial toxins and other undesirables.

The intestinal barrier is composed of cells that are joined together very tightly. Under certain conditions, these tight junctions can loosen; such conditions include exposure to bacterial and/or diet-derived toxins, stress, certain medications, and inflammation in the gut. This compromises the intestinal barrier and allows ‘toxins’ to pass through to the bloodstream. In medical speak, this is described as increased intestinal permeability, or colloquially as the leaky gut syndrome.

The term leaky gut syndrome has been abused by alternative medicine practitioners and quacks. To the point where many people don't take it seriously anymore. When I talk of leaky gut, I specifically refer to the scientific meaning of it, intestinal permeability. At the time of writing, a PubMed search for 'intestinal permeability' brings up 11452 published scientific papers. Intestinal permeability, unlike leaky gut syndrome, is a valid medical concern and an active area of research.

A 2014 review concluded:

> In summary, intestinal permeability, which is a feature of intestinal barrier function, is increasingly recognized as being of relevance for health and disease, and therefore, this topic warrants more attention.

Bischoff, S. C. et al. Intestinal permeability--a new target for disease prevention and therapy. BMC Gastroenterol14, 189 (2014).

The toxic substances that pass through the intestinal wall increase systemic inflammation as they leak into the bloodstream. One such substance is called bacterial lipopolysaccharide (LPS), which are cell wall components found in harmful bacteria. LPS are toxic molecules known to trigger inflammatory reaction in the body.

The immune system must actively hunt down and clean these substances. In some cases, even live bacteria can pass through the gut wall, which may lead to serious infections.

Some researchers believe increased intestinal permeability plays a part in the development of food allergies. As incompletely digested food particles enter the circulation, they train the immune system to see harmless food proteins as invaders. So when you later eat those foods, the immune system recognizes the undigested proteins as invaders and attacks them.

In medical speak, this leakage of toxins from the gut is called metabolic endotoxemia. Scientists believe that metabolic endotoxemia plays a role in diabetes, heart disease, and many other chronic health problems, including acne.


We covered a lot of ground on this page. Most of this was FIY-type of information. Background information that helps you to better understand the links between your gut and skin. However, in practice you just have to remember these three things:

  • Bacterial dysbiosis. Imbalance of bacteria in the gut. Results in the production of toxic substances in the gut.
  • Small intestine bacterial overgrowth (SIBO). Bacteria have migrated up from the large intestine into the small intestine where they shouldn’t be. This results in fermentation and gas production in the small intestine. Makes you feel bloated, can cause constipation/loose stools, and increases intestinal permeability.
  • Intestinal permeability, or leaky gut. The tight junctions between cells in the intestinal wall have loosened. This allows bacterial toxins and other ‘foreign’ substances to leak into the bloodstream. Results in systemic inflammation.

About Me

Hi, I am Acne Einstein(a.k.a. Seppo Puusa). I'm a bit of a science nerd who is also passionate about health. I enjoy digging through medical journals for acne treatment gems I can share here. You can read more about my journey through acne and how I eventually ended up creating this.