Microbiota management in the gut

Our gut is home to more than 1014 (billion) bacteria, known as the gut microbiota. That means there are at least as many cells inside our gut, or gastrointestinal tract (GIT), as there are in our entire body. Figure 1 shows the distribution of the different bacteria inside the GIT. The stomach is populated mainly by Helicobacter pylori. The presence of other species here, mainly originating in the mouth or the duodenum, is temporary.1 As we get further into the GIT, pH goes down and bacterial diversity goes up. The largest concentration of bacteria is found in the colon. Our stools give a reasonable impression of the composition of the microbiota in the colon, and,  since stools are relatively easy to examine, this is what we know most about. For that reason, the term gut microbiota usually concerns the colon.

Figure 1: Distribution of bacteria inside the gastrointestinal tract.

Research has shown that many chronic diseases are linked to imbalances in the colonic microbiota. The most obvious are bowel conditions, including ulcerative colitis (UC) and Crohn's disease. Other conditions to which microbiota imbalances are linked include obesity, metabolic syndrome, diabetes (types I and type II) and certain types of cancer.2 Less obvious conditions that have also been linked to microbiota imbalances are allergies and neurological conditions such as MS, autism and ADD.3 A similar link has been shown in psychological conditions, such as chronic depression and anxiety. See the “Indications” for more details on these indications in relation to the microbiota.

References to the use of faeces-based preparations for the treatment of severe bowel complaints such as persistent diarrhoea and food poisoning can be found in Chinese medical writings dating back to the 4th century CE. This treatment was rediscovered in 1958 in the USA, when Ben Eiseman and colleagues successfully treated four severe cases of pseudomembranous colitis, now known to be caused by Clostridium difficile (recently renamed Clostridioides difficile), through faecal transplants by means of enemas.4 More recently, researchers at the Amsterdam Medical Centre (AMC) unequivocally proved the effectiveness of this treatment in a randomized controlled trial (RCT).5 In fact, the trial was so successful that it was terminated early, because researchers considered it unethical to withhold treatment from the control group.  Eiseman's trial gave rise to a wide range of trials into the effectiveness of faecal transplants for a multitude of conditions. Initially, they focused on clearly bowel-related conditions such as UC.6 7 A number of clinical trials are currently underway looking into the therapeutic effect of Fecal microbiota transplant (FMT), mainly in connection with irritable bowel syndrome (IBS), obesity, metabolic syndrome and non-alcoholic fatty liver disease.

The health-promoting effect of probiotic bacteria was recognized by Russian microbiologist Ilja Mechnikov in the early 20th century8. Since then Probiotics have been the focus of many studies. Their use is associated with and has produced good results in indications including various forms of diarrhoea, food allergies, atopic eczema, IBS, inflammatory bowel disease (IBD) and various forms of cancer.9 More recently, the influence of probiotics on the gut-brain axis was recognized as well, and since then many studies into the use of probiotics in mood-related conditions such as stress, anxiety and depression have been initiated.10

It is important for care providers and doctors to be aware that, despite the good results achieved with probiotics, they should not be thought of as a miracle cure, and this should be communicated to patients. Probiotics are usually not capable of effecting a complete cure or disease reversal. However, they do contribute to a healthy intestinal flora, which makes them an important factor in the improvement of patients’ quality of life. Furthermore, the use of probiotics is not known to cause any severe side effects. This means probiotics can be recommended without risk for conditions in which they can be expected to have an effect, and recommended in addition to standard therapies in applicable cases.


  • 1. Zilberstein, B. et al. Digestive tract microbiota in healthy volunteers. Clinics (Sao Paulo) 62, 47-54 (2007).
  • 2. Shreiner, A. B., Kao Jy Fau - Young, V. B. & Young, V. B. The gut microbiome in health and in disease. Curr Opin Gastroenterol 31, 69-75 (2015).
  • 3. Principi, N. & Esposito, S. Gut microbiota and central nervous system development. LID - S0163-4453(16)30251-1 [pii] LID - 10.1016/j.jinf.2016.09.010 [doi]. J Infect http:// dx.doi.org/10.1016/j.jinf.2016.09.010 (2016).
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  • 7. Borody, T. J., Warren Ef Fau - Leis, S., Leis S Fau - Surace, R., Surace R Fau - Ashman, O. & Ashman, O. Treatment of ulcerative colitis using fecal bacteriotherapy.
  • 8. metchnikoff, E. Etudes sur la flore intestinale. Ann Inst Pasteur Paris 22, 929-955 (1908).
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  • 10. Mangiola, F. et al. Gut microbiota in autism and mood disorders. World J Gastroenterol 22, 361-368 (2016).