What are gut problems and what causes them

What are gut problems and what causes them

A staggering number of bacteria inhabits the human digestive track. 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 the 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 or symbiosis. The bacteria help in digestion of food, break down fiber humans couldn’t otherwise digest, synthesize certain nutrients, and keep 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 regulates the immune system, and disruptions in gut microbiota can lead to autoimmune and inflammatory problems.

What do we mean with gut problems

Bacterial problems

Gut problems are often linked to a disruption of the gut microbiota. Broadly speaking, there are three types of disturbances to the gut microflora:

  • Bacterial dysbiosis. The balance or helpful and harmful bacteria has flipped to favor the ‘bad’ bacteria.
  • Small intestine bacterial overgrowth (SIBO). The bacteria have moved in larger numbers to the relatively sterile small intestine.
  • Bacterial translocation. Refers to bacteria migrating through the gut wall into the bloodstream and organs. In this situation, even the probiotic bacteria can be dangerous.

I’ll go over these in more detail in the in-depth section.

Intestinal permeability

The gut is a long tube that runs from the mouth to the anus. In many places, this tube is only a single cell thick. This incredibly thin gut wall is the most important barrier between you and the outside world. It must absorb nutrients from the food while keeping bacterial toxins and other harmful substances out.

When everything is in balance, the cells in the gut wall and the healthy bacteria in the gut work together to achieve this goal.

Harmful bacteria produce substances and toxins that are ‘corrosive’ to the gut wall, which can lead to a situation where tiny gaps open between the cells forming the intestinal wall. Substances that typically stay in the gut leak through the gaps and into systemic circulation. In medical speak, this is called intestinal permeability.

Intestinal permeability is not the same thing as ‘leaky gut syndrome’. Leaky gut syndrome is a disease invented by the alternative medicine proponents. While the concepts are similar, the term leaky gut syndrome has been ‘contaminated’ by quackery to the point where it’s difficult to take seriously; whereas intestinal permeability is a legitimate medical concern and an active research topic.

Among the substances that pass through the gut wall are lipopolysaccharides (LPS), which are toxic molecules found in the outer membranes of harmful bacteria. LPS cause systemic inflammation and exposure to larger quantities leads septic shock – even death. In medical speak, LPS are called endotoxins, i.e. poisons from within.

Some studies covered on the previous page have found that people with acne have much higher levels of LPS in the blood as compared to people without acne. I believe this is one potential cause of acne.


Certain drugs

Many drugs have been linked to gut problems. The main ones are:

  • Antibiotics kills both good and bad bacteria in the gut. Unsurprisingly, they have been associated with many gut problems. For example, studies have shown that people who have taken tetracyclines for acne have 65% to 75% higher risk of inflammatory bowel disease than the population average.
  • Nonsteroidal anti-inflammatory drugs (NSAID) can cause damage to the gut wall. NSAID are your everyday painkillers and fever reducing drugs; such as aspirin, ibuprofen, and naproxen. Brand names include Advil, Motrin, Celebrex, Aleve, and Naprosyn. Paracetamol (Tylenol) is much safer. Studies show it causes little to no damage to the gut.
  • Proton pump inhibitors (PPI) suppress stomach acid production and are used to treat GERD and acid reflux. However, stomach acid kills bacteria in the food and reducing stomach acid production allows the bacteria to survive the stomach and enter the small intestine.

The combination of NSAIDs and PPIs is especially problematic.

After taking NSAIDs and PPIs for two weeks, >50% of subjects had small intestine injuries.

Fujimori, S. What are the effects of proton pump inhibitors on the small intestine? World J. Gastroenterol. 21, 6817–9 (2015). https://www.ncbi.nlm.nih.gov/pubmed/26078557


What you eat largely determines the type of bacteria residing in your gut. The bacteria that digest fats are different from those that feed on fiber. So it’s not surprising that over 50% of the variation in gut microbiota comes down to diet.

The main diet-related causes of gut problems include:

  • ‘Crappy’ food diet – Or your typical Western-style diet with lots of processed foods and not a lot of fiber. One study showed that 4 weeks of such diet increased endotoxin levels by whopping 71%.
  • Fructose – Consuming too much fructose has been shown to increase endotoxin levels. In one study, teenagers were asked to drink 3 12-oz (350 ml) cans of fructose-sweetened beverages a day. After 2 weeks their endotoxin levels shot up by 19%.
  • Excess fat – Eating too much fat, especially dairy fat, increases the number of bacteria that produce toxic gasses in the intestines. Fat also seems to increase intestinal permeability. I don’t mean to suggest you have to avoid fat – not at all, but it seems a high-fat diet with little fermentable fiber isn’t good for the gut.
  • FODMAPs – FODMAPs are poorly absorbed and rapidly fermented sugars found in many fruits and vegetables. Because they are poorly absorbed and rapidly fermented, they generate a lot of gas in the intestines. Low FODMAP diets have been shown to be effective in people with irritable bowel syndrome. See the in-depth section for details on which foods contain FODMAPs and which are safe to eat.
  • Gluten – Zonulin is a protein that regulates intestinal permeability. It opens gaps between intestinal cells and allows nutrients to pass through. Exposure to gliadin, which is a part of gluten, causes intestinal cells to release zonulin and leads to intestinal permeability. In people with celiac disease, and possibly gluten intolerance, exposure to gliadin triggers a massive zonulin release and consequent intestinal permeability. However, this doesn’t mean everyone has to avoid gluten. Many people with acne I’ve talked to say going gluten-free did nothing for their skin. But it’s a possibility you should keep in mind.
  • Lectins – Lectins are proteins plants use for defense, and they are toxic to intestinal cells. That being said, proper cooking eliminates most lectins, and most people have no problems with the small amounts of lectins left in cooked foods. A tiny minority of people are sensitive to lectins, but I want to emphasize that it’s a small minority. The in-depth section explains which foods contain lectins and how to do a lectin elimination diet.


Stress is a factor in most, if not all, of the gut-related problems. A 2015 paper titled “Stress induces endotoxemia and low-grade inflammation by increasing barrier permeability” reviews the many effects stress has on the gut, including:

  • Increases intestinal permeability. In a 2014 study, researchers measured intestinal permeability before and after public speaking stress – the participants were asked to give an impromptu speech. Their results showed that stress caused about 50% increase in intestinal permeability.
  • Alters the bacterial balance in the intestines. Animal studies show stress reduces the numbers of probiotic bacteria and supports the growth of harmful bacteria in the gut.
  • Causes inflammation in the gut wall. Stress has long been known to cause inflammation in the gut and aggravate inflammatory bowel conditions.
  • Stress reduces ‘motility’ (the time it takes for food to move through the gut), which in turn encourages SIBO and the growth of pathogenic bacteria.
  • Stress reduces secretion of stomach acid secretion, which in turn allows live bacteria to slip through to the small intestine.

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.