Part 3: Gut bacteria - what’s on the menu? Fermented foods

Part 3: Gut bacteria - what’s on the menu? Fermented foods

Fermented foods, such as yoghurt, sauerkraut, kimchi and kombucha, are foods that contain live bacteria. These foods are growing in popularity due to an increased awareness into the microbiome and its influence on human health.


The process of fermentation involves the conversion of sugars and starches by bacteria present in the food, into alcohol and various acids (these give fermented foods a specific flavour). Some bacteria also produce beneficial bioactive molecules and vitamins, such as vitamin B12 and folate, thereby increasing their concentration in fermented foods.

Fermentation has been used for centuries to increase the shelf life of fruit, vegetables and dairy products during times of scarcity. The process also makes the food more easily digestible and increases its nutritional properties. This, combined with the presence of beneficial micro-organisms, results in a food that may confer a range of health benefits

such as improved immune function and digestive health. (1) However, the number and type of micro-organisms present is important, and this can vary depending on how the food is manufactured and stored. Many canned or bottles products such as pickled vegetables, lose their bacterial content through pasteurisation. Other foods are preserved with vinegar rather than by fermentation, making them void of microorganisms.

Foods that contain live bacteria will have it listed in the ingredients and there have been studies that have looked at the viability of their contents.

A review published in Frontiers of Microbiology in August 2018, looked at 400 studies that characterised the content of microorganisms in certain retail products such as yoghurt, kimchi and sauerkraut. This review found that lactic acid bacteria were the most common strains identified, with most products containing between 105 - 109 colony-forming units (CFU) per mL. (1) Other studies have shown that certain strains of lactic acid bacteria, when present at these levels of CFUs, are able to survive the conditions of the gastrointestinal tract. (2, 3)

Bacteria found in fermented foods only colonize the gut temporarily, however they have been shown to help improve the diversity of commensal gut microbiota and can therefore provide longer-lasting health benefits. (4)

This is good news. However, not everyone can tolerate fermented foods.

Histamine Intolerance and Fermented Foods

Fermented foods are high in histamine and this poses a problem for individuals with histamine intolerance.

Histamine is a molecule that is produced, stored and released by immune cells, called basophils and mast cells, in response to injury, allergy or inflammation. These cells are prominent in tissues that are associated with symptoms of allergies such as the nasal passages, sinuses, mouth and internal surfaces of the body. Histamine is the compound that produces swelling and itching in allergic reactions.

Histamine is also found in cells that line the stomach where it is released in response to trigger molecules that enter the gut.

In the brain, histamine is a neurotransmitter released by neurons and is known to influence sleep, appetite and hormonal regulation.

For this reason, people who have allergies or food intolerances may experience a range of symptoms ranging from the typical allergic symptoms of rash, runny nose, sneezing and itchiness, to gut symptoms and alterations in brain function.

Once released, histamine produces an immune response and is then broken down by an enzyme called diamine oxidase (DAO). This is important as it helps to reduce histamine and prevent prolonged or excessive damage by the immune response.

Histamine intolerance occurs when the levels of histamine exceeds the ability of DAO to break it down. There are a number of reasons why this can occur:

  • Eating foods that are high in histamine such as fermented foods and beverages (including wine), dried fruits, avocados, tomatoes, eggplant, spinach, processed meats, shellfish, vinegar and tomato sauce.

  • Eating foods that block DAO such as black and green tea, alcohol.

  • Eating foods that trigger the release of histamine in the body such as alcohol, bananas, beans, citrus fruits, chocolate, certain nuts, papaya, pineapples, strawberries, tomatoes, legumes, seafood, egg whites and certain food additives

  • Gastrointestinal disorders such as irritable bowel syndrome, leaky gut or inflammatory bowel disease.

  • Medications that block DAO including certain anti-inflammatory medications, anti-depressants, antibiotics, anti-diabetic, anti-arrhythmic drugs, analgesics, muscle relaxants and sedatives.

The severity of symptoms related to histamine intolerance depends of the degree of exposure to histamine. It is important to note that almost all foods contain some level of histamine and low levels may be well tolerated. However, individuals with gut issues may find that their symptoms worsen when they include fermented foods (or any of the foods listed above) in their diet. In these cases, it is best to avoid these foods until gut issues are managed, after which a slow reintroduction of these foods may be trialled.


1. Rezac S, Kok CR, Heermann M, Hutkins R. Fermented Foods as a Dietary Source of Live Organisms. Front Microbiol. 2018;9:1785. Published 2018 Aug 24. doi:10.3389/fmicb.2018.01785

2. Derrien M & van Hylckama Vlieg JE (2015). Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends in Microbiology 23(6):354-366. PMID 25840765

3. Marteau P, Minekus M, Havenaar R, & Huis in’t Veld JH (1997). Survival of lactic acid bacteria in a dynamic model of the stomach and small intestine: validation and the effects of bile. Journal of Dairy Science 80(6):1031-1037. PMID 9201571

4. Uyeno Y, Sekiguchi Y, & Kamagata Y (2008). Impact of consumption of probiotic lactobacilli-containing yogurt on microbial composition in human feces. International Journal of Food Microbiology 122(1-2):16-22. PMID 18077045