Treatment of Dysbiosis

Treatment depends on the type of dysbiosis being treated.

Putrefaction dysbiosis

 increasing the amount of soluble and insoluble fiberPutrefaction dysbiosis is usually managed through diet by increasing the amount of soluble and insoluble fiber and decreasing the amount of animal protein and fat. Fermented dairy products such as fresh yogurt can sometimes be helpful, though most of the bacteria are killed by the stomach’s acid. These changes to diet are aimed at lowering the concentration of Bacteroides and at increasing the concentration bacteria that produce lactic acids, including Streptococci, Lactobacillus, and Bifidobacteria. Addition of soluble fiber to the diet increases the bacterial concentration and enzyme activity of beneficial bacteria raising the levels of short-chain fatty acids. Addition of insoluble fiber to the diet decreases the concentration of pathogenic bacteria and decreases their enzyme activity. This is the reason why addition of insoluble fiber to the diet of the patient is linked to a decrease in the likelihood of colon cancer. Another food supplement which raises levels of Bifidobacteria and lowers stool pH is fructose-containing oligosaccharides. These compounds can be found in vegetables such as asparagus and onion.

Fermentation dysbiosis

carrot juiceIn contrast, soluble fiber and starch may exacerbate the problem in patients with fermentation dysbiosis. When the duodenum and jejunum are involved in the process, simple sugars are also contraindicated. This means that the diet should exclude sugars and cereal grains. Tolerance of fruits, starchy vegetables and fat is variable in different cases. Oligosaccharides, on the other hand, improve the condition of the patient by inhibiting the ability of enterobacteria to bind to intestinal mucosa. Carrots in particular are rich in oligosaccharides, which is why concentrated carrot juice has been used as a treatment of bacterial diarrhea in Europe for over a century.

Administration of benign bacteria has been shown to produce a positive effect in this condition reducing the concentration of pathogenic bacteria.

  • Administration of lactobacillus has been used for a long time to improve the microbial ecology. Regular drinking of acidophilus milk is also helpful, as it decreases the concentration of urease-positive organisms and bacterial enzymes within the stool. Lyophilized Lactobacillus preparations and fermented dairy products have been proven to be useful in treating shigellosis, salmonellosis, antibiotic-induced diarrhea, and decreasing the likelihood of colon cancer. However, the main problem of this treatment is that lactic acid-producing bacteria very poorly survive the influence of hydrochloric acid within the stomach and bile within duodenum. Also, they have trouble adhering to the mucosa of the large intestine. This is the reason why the use of fermented milk products is questionable at best. In order for benign bacteria to survive the stomach acid they either have to be placed in special capsules that dissolve only in large intestine, or they have to be ingested in a very high concentration. Only then a sufficient amount of bacteria will be able to reach the large intestine and adhere to its walls.


  • Administration bifidobacterium brevum has been shown to decrease the fecal concentration of Enterobacter and Clostridia, bacterial enzymes (tryptophanase and beta-glucuronidase), and ammonia.
  • Administration of E. coli and Enterococcus has been popular in Europe; however, there is little evidence that this is a valid treatment of dysbiosis.
  • Bacillus laterosporus, is a new type of bacteria which has been used in food supplements in the United States for about 10 years. These bacteria have anti-tumor, antibiotic, and immune modulating properties, and are a good adjunctive treatment of small bowel dysbiosis.
  • A type of yeast, Saccharomyces boulardii, has been thoroughly researched and used for decades in Europe. Controlled studies have shown its effectiveness in treating Clostridium difficile colitis and antibiotic associated diarrhea. Lab experiments have also shown that it increases secretory IgA, which may be contraindicated in people with reactive arthritis and diseases associated with exaggerated intestinal immune response.

Antimicrobial therapy

Antimicrobial therapy can be useful in some cases. For example, contamination of the small intestine by anaerobes is treated using tetracyclines and metronidazole. When the main cause of the disease is enterobacterial overgrowth, ciprofloxacin is used, especially since it spares anaerobes.

Moreover, since bacterial overgrowth syndromes often require prolonged use of antibiotics, herbal antibiotics can be used, since they provide a greater margin of safety.

citrus seeds extract

  • This includes citrus seed extract due to its broad spectrum of anti-fungal, antibacterial, and anti-protozoan effects. Studies have shown no adverse effects of this treatment except for intestinal irritation (which causes diarrhea) even if very large doses of citrus seed extract are used. The usual dosage is 600-1600 mg/day.
  • Bayberry leaf, which contains alkaloid berberine, can suppress the growth of enterobacteria, amoebae, and yeasts. Usually several grams per day are required to control the symptoms.
  • Artemesia annua is primarily used to treat protozoan infection. Its main ingredient is artemisinin, which is a strong pro-oxidant, whose potency is increased by polyunsaturated fats (e.g cod liver oil) and decreased by vitamin E. This medicine has been shown to have no side effects except for increasing the risk of spontaneous aborting, which is why it is contraindicated for pregnant women.