Colonic fermentation yields both gases (e.g., hydrogen, methane, and carbon dioxide) and short-chain fatty acids (SCFAs; e.g., acetic, propionic, and butyric acids), which exert several effects of major physiological and pathophysiological importance. The production and absorption of SCFAs facilitate the uptake of electrolytes and water and reduce the osmotic effect of unabsorbed carbohydrate molecules. Hence, diarrhea will ensue if colonic fermentation capacity is impaired (e.g., antibiotic-associated diarrhoea) or overwhelmed (e.g., lactase deficiency). Colonocytes rely mainly on nutrition from the colonic lumen (the “milieu extérieur”) and have a preference for using butyrate as an energy substrate. “Starvation colitis” may develop if access to SCFAs is hindered, and failure of β-oxidation of SCFAs has been proposed as a pathogenetic mechanism for ulcerative colitis. SCFAs, especially butyrate, display antineoplastic properties and may prevent the development of colorectal cancer. Furthermore, microbial fermentation products influence gastrointestinal motility and sensitivity and may play a role in the pathogenesis of irritable bowel syndrome.


A long history of:

  • Western lifestyles! A traditional Chinese diet, for example, does not include dairy products, gluten grains, alcohol and very modest amounts of fruit!
  • Failure to inoculate the gut at birth with the correct friendly bacteria - see Probiotics - we should all be taking these all the time and double the dose following antibiotics and gastroenteritis
  • A poor diet
  • high in sugar and refined carbohydrate
  • low in vegetables, pulses, nuts and seeds.
  • low in other micronutrients
  • Poor digestion of food - see Hypochlorhydria and Pancreatic exocrine function
  • An acid gut either because of fermentation of sugars or lack of bicarbonate from the pancreas
  • Modern medication
  • Antibiotics which kill bacteroides - especial care is needed with metronidazole. Other antibiotics are relatively benign and probably over-maligned as a cause of gut problems. Diet is a much bigger player.
  • Pill and HRT, which both suppress the immune system, encourage metabolic syndrome and are conducive to yeast overgrowth.
  • Acid blockers such as antacids, H2 blockers and proton pump inhibitors, which inhibit stomach acid production - Hypochlorhydria. Allergies to food may also result in this problem.


The medicines that can be thought of use are:-

  • Nux vomica
  • Pulsatilla
  • Phosphorus
  • Silicea
  • Sulphur