Causes of Gut Dysbiosis and Leaky Gut

antibiotics Since one of the important functions of the gut microbiota is to regulate intestinal barrier function, gut dysbiosis and leaky gut are two conditions that go hand in hand. While both of these disorders long have been diagnosed by alternative health practitioners, it’s only in the last 5-10 years that the scientific research has made it clear that gut dysbiosis and leaky gut are real conditions that affect a lot of people. While our hunter-gatherer ancestors didn’t have to worry about their gut flora or intestinal health, changes in lifestyle have lead to alterations in the human microbiome and hyperpermeable intestines, two conditions which are associated with most of the chronic disorders we see in the world today.

What is gut dysbiosis and leaky gut?

Increased intestinal permeability (also called a leaky gut): The tight junctions of the intestinal lining have become hyperpermeable, allowing substances such as endotoxins and protein antigens to get into the bloodstream (1).

Gut dysbiosis: “Dysbiosis is a state in which the microbiota becomes altered as a consequence of an alteration in the composition of the microbiota, a change in bacterial metabolic activity, and/or a shift in local distribution of communities” Gut dysbiosis is primarily used to describe changes in the balance between “good” and “bad” microorganisms in the gut (2).

Dysfunctional gut flora is often used interchangeable with gut dysbiosis. The gut bacterial community is made up of hundreds of species of microorganisms, and these germs have different functions in the body (3). Especially in regards to digestion it’s clear that a diverse gut microbiome means better breakdown of complex polysaccharides and other fermentable substrates. A dysfunctional gut flora indicates a loss of diversity.

Causes of leaky gut and gut dysbiosis

Since there is still so much we don’t know about gut dysbisois and leaky gut, this is not a complete list of factors that have been linked to these disorders. However, it should give an overview of the most important ones.

– Drugs

While plenty of pharmaceuticals such as steroid drugs, analgesics and contraceptives have been linked to gut dysbiosis and/or leaky gut, most of the research has been done on antibiotics and NSAID’s.


Oral antibiotics (especially broad spectrum ones) disrupt the community of microbes, and several enteric pathogens get the opportunity to grow in the gut (4). Some studies indicate that the gut microbiota might never be able to recover after use of oral antibiotics (5).
“The potential for an antimicrobial agent to influence gut microflora is related to its spectrum of activity, pharmacokinetics, dosage, and length of administration” (6)


Non-steroidal anti-inflammatory drugs increase intestinal permeability, and long-term use has also been linked to bowel disease (7,8,9).

– Diet

Diet has a huge impact on both the gut microbiota and the permeability of the tight junctions of the intestinal lining. The following factors are especially important in regards to gut dysbiosis and leaky gut:

Limited intake of fermentable substrates

Fermentable substrates such as polysaccharides found in fruits and vegetables are digested by gut bacteria. In return, these bacteria produce short-chain fatty acids that fuel the cells lining the colon.
While it seems that some traditional societies maintain good health even with no fermentable substrates in their diets, feeding bacteria in the colon with dietary fiber and resistant starch has been linked to better colonic health. Consumption of fermentable substrates also seems to be especially important for maintaining proper bowel pH (10,11,12).

Sugar, refined flours, and highly processed food

While most of the bacteria in the human body are found in the large intestine, the small intestine also harbor complex microbial communities that are affected by the diet we eat. It’s likely that the increased consumption of westernized foods containing flours, sugar and refined fats produces an inflammatory microbiota in the upper gastrointesinal tract. Contrary to flour- and sugar-containing products, “ancestral foods” such as whole fruits, tubers and vegetables have lower carbohydrate densities (13).

High fat intake?

Multiple studies show that a high-fat diet is associated with increased intestinal permeability and low-level chronic inflammation. Fat seems to increase the systemic absorption of lipopolysaccharides, a pro-inflammatory bacterial toxin found in the outer-wall of gram-negative bacteria in the gut. However, while consumption of refined fats in itself negatively affects gut health, the problem with high-fat diets is often the lack of fermentable substrates, and not the fat itself (13,14).
The fact that some hunter-gatherer societies are virtually free from chronic disease despite the fact that they eat high-fat diets with limited consumption of fermentable substrates could indicate that other factors are involved.

Grains and legumes?

Even though whole-grains are a source of soluble fiber and resistant starch, they also contain a significant amounts of toxic or antinutritional substances such as phytic acid, protease inhibitors, amylase inhibitors, lectins, tannins, saponins, and goitrogens (15,16).
Although all plant foods have a chemical defense strategy, grains seem to be especially problematic since they contain so many potentially toxic compounds. The toxicity of these antinutrients seems to be dose dependent.

Studies indicate that lectins and gluten might be especially problematic. Wheat germ agglutinin, a type of lectin, has been shown to increase intestinal permeability and damage the gut lining (16). Gluten is a protein found in grains that often causes increased intestinal permeability and gastrointestinal problems even in patients without celiac disease (17,18). More data is needed before we can make any substantial claims regarding the possible adverse effects of most of the antinutrients found in grains and legumes.

Traditional food processing techniques such as soaking, sprouting and fermentation increase the bioavailability of many nutrients and reduce or eliminate many toxins and antinutrients. The fact that some healthy traditional societies relied on grains as staple foods could indicate that these preparation methods are important, but it also seems that changes in the human microbiome partially explains the rapid rise in gluten- and grain related disorders.

Excessive alcohol consumption

Alcohol abuse has been linked to growth of gram negative bacteria in the intestine and increased translocation of bacterial toxins (19,20,21).

– Other factors

Excessive hygiene and fear of “germs”

Even though hand sanitizers, soaps, food pasteurization and other measures of removing bacteria decrease exposure to rare pathogens, the fact is that humans have evolved for millions of years in a symbiotic relationship with trillions of microorganisms. This contact with both beneficial and potentially harmful germs is important in the development of a diverse microbiome and competent immune system. Hunter-gatherers routinely come in contact with bacteria from dirt, water, food and other humans and animals, and this is likely one of the reasons why these societies remain free of non-communiccable chronic disease. While it seems that early life exposure to microorganisms is especially important (22), adults will also benefit from reducing the use of soap and antibacterial gels and getting some more dirt into their diet.


Psychological and physical stress have been found to contribute to gut dysbiosis (23,24).

Infections and disease

Gut dysbiosis and leaky gut are considered disorders that contribute to the development of disease, but it’s often hard to determine cause and effect since disease in itself can alter the bacterial community in the gut and/or increase intestinal permeability.
Infectious diseases such as cholera and salmonella change the gut microbiota (25,26). Parasitic infections such as Helmith infection can also shift the composition of intestinal bacteria (27).

Dysfunctional gut flora passed on to the child

Microorganisms are passed on from mother to child during pregnancy, birth, and breastfeeding, and the newborn child also picks up germs from the rest of the family through kissing, pre-chewed food etc. It seems that gut flora is hereditary in the sense that children receive bacteria from their family.


Breast milk is not only a rich source of nutrients, but it also contains probiotics and prebiotics that help populate the gut of the newborn child with healthy gut flora. “Type of feeding in the first months of life appears as one of the most important determinants of the child and adult well-being, and its protective action seems to rely mainly on its ability to modulate intestinal microflora composition at early stages of life” (28).

Caesarean section

Some types of bacteria are naturally passed from mother to child during normal delivery, and it seems that Caesarean delivery affects the early biodeveristy of intestinal bacteria (12).


  1. […] by normal bacterial populations (1,9). However, antibiotics, increased carbohydrate consumption and several other factors  have made us prone to candida overgrowth. Decreased numbers of […]

  2. […] Several factors contribute to gut dysbiosis, and the following seems to be the most important in connection with acne: […]


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