Intestinal flora after colonoscopy: How to rebuild it

With the help of a colonoscopy, changes in the bowel can be detected early on. During the examination, the doctor inserts a small camera into the intestine so that the intestinal mucosa can be examined visually. However, this is only possible if the bowel has been thoroughly emptied. In the short term, this radical evacuation of the bowel can lead to a change in the microbiome of the bowel mucosa. However, it is possible to rebuild the intestinal flora after colonoscopy.

Stress for the intestinal flora: colonoscopy

Before a colonoscopy it is necessary to empty the intestine with the help of a laxative. You should start purging a few days before the treatment: you must drink a saline solution that removes water from the intestinal wall. This liquefies the stool, increases the stool volume and activates the evacuation process. You can support this process and prevent dehydration by drinking plenty of water. You must avoid solid food until the examination. This procedure burdens the intestinal flora and can lead to a short-term change in the microbiome. The gentle build-up of the intestinal flora after the colonoscopy is therefore a sensible measure.

The microbiome: important for your health

The microbiome describes the totality of all microorganisms in your intestine. More than 400 different types of intestinal bacteria live alone in your colon. In total, the intestinal flora comprises several trillion bacteria. They support your digestion, produce enzymes, amino acids and vitamins (B2, B12 and K). In addition, intestinal bacteria are extremely important for your immune system, as they effectively protect you from pathogens. A stable and species-rich microbiome is therefore important for your health and well-being.

The intestinal flora after colonoscopy

A healthy intestinal flora is based on a complex interaction of bacteria and microorganisms. Various factors can disturb this sensitive balance. These include, for example, persistent stress, an unbalanced diet or the intake of antibiotics. However, even the intensive intake of laxatives can change the composition of the intestinal flora in the short term. Studies1 have shown that taking laxatives reduces the bacterial species Lactobacillus plantarum, Gemella, Clostridium cellulosi and Ruminococcus callidus.

Other genera such as proteobacteria and Dorea formicigenerans, on the other hand, occur in greater numbers immediately after intestinal cleansing. Consequently, the intestinal flora after colonoscopy may have a similar bacterial composition as in people suffering from irritable bowel syndrome or chronic inflammatory bowel disease. This imbalance can be alleviated by taking the laxative in two doses.2 In addition, you can gently rebuild your intestinal flora after the colonoscopy with a healthy diet and probiotic foods.

Building of the intestinal flora after colonoscopy with a balanced diet

Immediately after the colonoscopy low-fat and easily digestible foods spare the still empty digestive tract. Tea, still water and vegetable juices are well suited to compensate for the loss of fluid. As soon as your bowel movements have normalised, you can start eating more varied foods again to rebuild your intestinal flora after a colonoscopy.

A balanced, vitamin-rich and fibre-rich diet is particularly suitable for this. Wholemeal products, fruit and vegetables, nuts, legumes and dairy products provide valuable nutrients and minerals that serve as a nutritional basis for beneficial intestinal bacteria. Finished products, alcohol, simple carbohydrates and sugar, on the other hand, support the growth of undesirable bacterial strains. It is therefore advisable to avoid such foods or replace them with nutrient-rich, unprocessed alternatives.

Rebuild the intestinal flora after colonoscopy: Prebiotics and probiotics

Psyllium, garlic, artichokes, chicory or black salsify are examples of prebiotic food: they contain indigestible food components which are an important source of food for beneficial bacteria. Prebiotics are fermented in the digestive tract, which produces useful metabolic products: Short-chain fatty acids serve intestinal cells as an energy source and, like lactic acid, ensure a low pH value in the large intestine. This acidic environment makes it difficult for harmful intestinal bacteria to settle, while it can increase the number of useful intestinal bacteria.

Among the useful intestinal bacteria are lactic acid bacteria and bifidobacteria. These strains of bacteria strengthen the immune system and support the absorption of nutrients. Probiotic foods such as natural yoghurt or kefir contain live lactic acid bacteria that can multiply in the intestine and thus displace unwanted organisms.

A balanced diet with prebiotic and probiotic foods can thus contribute to the development of a healthy intestinal flora after colonoscopy.

Intestinal bacteria after colonoscopy: gain clarity with BIOMES

Do you want to check if your intestinal bacteria are in balance after the colonoscopy? With the modern intestinal analysis3 INTEST.pro from BIOMES you can get an overview of the bacterial composition of your intestinal flora. To do this, you send a small stool sample to our laboratory. The detailed analysis of the stool sample will tell you about your intestinal health, the bacterial balance of your intestinal flora and your immune strength. In addition, you will receive information about the vitamin synthesis of your intestinal flora and find out whether you suffer from intolerances. In addition, you will receive personalized recommendations with numerous nutritional suggestions that serve the health of your intestine. With concrete tips we help you to effectively rebuild and strengthen your intestinal flora after a colonoscopy.
Analyze your intestinal flora.
Find out what your body needs.


1. Jalanka J, Salonen A, Salojarvi J, Ritari J et al. Effects of bowel cleansing on the intestinal microbiota. Gut 2015:64(10), 1562-8. https://www.ncbi.nlm.nih.gov/pubmed/25527456

2. Ibid.

3. Cho I, Blaser M J. The human microbiome: at the interface of health and disease. Nature Reviews Genetics 2012:13, 260-270. https://www.nature.com/articles/nrg3182