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Dysbiosis and IBS


Are bacteria to blame for your symptoms of IBS?

“Recent findings suggest that IBS is linked to clearly detectable gut microbiota alterations. Thanks to new diagnostic insights and a rapidly growing knowledge about the role and function of the microbial communities living inside our guts, our view on IBS and its causes has changed considerably.”

President of the European Society of Neurogastroenterology and Motility (ESNM) Professor Giovanni Barbara

Your gut is home to a huge community of bacteria, some beneficial or ‘friendly’ and some potentially pathogenic or ‘bad’ bacteria. In a healthy balanced gut our friendly bacteria dominate and prevent the overgrowth of bad bacteria.

What is dysbiosis?

Intestinal dysbiosis is a condition in which the bacteria in your gut are out of balance, and pathogenic (bad) bacteria begin to dominate, creating symptoms of digestive disturbance.  There is more and more evidence accumulating that dysbiosis may play a key role in the development of IBS. (1, 2)

You are an ecosystem

We have over 100 trillion microbes living inside our bodies, most of them residing in our colon; these microbes are known as your microbiota.  Your gut is home to a complex ecosystem of 800 different species of microbiota, which include 7,000 different strains. Amazingly, our bodies contain 10 times more bacteria than we have cells!

The composition and balance of our gut microbiota differs a lot among people, but certain bacteria should dominate and act to suppress the overgrowth of harmful or pathogenic bacteria.

The Bad Guys

Although most of the bacteria in our gut are beneficial to us, some bacterial species, such as B.fragilis, C.difficle and Shigella, may colonise the gut and are potentially harmful. (3) These species, referred to as opportunistic bacteria, when in small numbers and under control actually fulfil some important functions in the gut, like assisting in the digestion of food, breaking down fats and bile acids.

In a balanced, healthy gut, the amount of these bacteria is limited and kept under control by the beneficial flora. (4) But if the beneficial flora are somehow weakened, for instance by antibiotics, poor diet and/or stress, the opportunistic bacteria can grow out of control and lead to a number of gastrointestinal symptoms including, bloating, abdominal pain, diarrhea and constipation. (5)

Your bacteria just ain’t that into you

Imbalances and disruptions in the gut microbiota are beginning to be recognised by the medical community as the missing link in understanding how IBS develops in the body.

Latest research has shown a clear distinction between the microbiota in the gut of patients with IBS and that of healthy people. Healthy individuals appear to have a more diverse gut microbiota than individuals who suffer from IBS. (6) Put simply, this means the composition of the bacteria in the gut of someone with IBS is different from that of someone without digestive symptoms.

Studies have found a distinct imbalance between beneficial and pathogenic bacteria in the microbiota of people with IBS, with:

  •        Decreased counts of bifidobacteria. (8)
  •        Increased levels of Clostridia spp.  (7)
  •        A decrease of coliforms, lactobacilli and bifidobacteria. (9)
  •        Reduced Bacteroides. (10)
  •        A 2-fold increase in the ratio of Firmicutes to Bacteroidetes. (11, 12)

What are the symptoms of dysbiosis?

  • bloating, abdominal pain and cramping.
  • constipation, diarrhea, or alternating.
  • indigestion, reflux, heartburn.
  • food intolerances.
  • fatigue, brain fog, lowered mood.
  • joint pain.
  • skin conditions.

What are the causes of intestinal dysbiosis?

Factors that may disrupt your gut microbiota include:

  •        Antibiotics
  •        Diet
  •        Chronic stress
  •        Gastrointestinal infections (food poisoning, travellers’ diarrhea,        gastroenteritis)
  •        Medications such as NSAIDs, proton pump inhibitors.
  •        C-section birth
  •        Exclusive bottle feeding
  •        Altered gastric secretions (gastric acid, pancreatic enzymes, bile)



The use of antibiotics is by far the most common and significant cause of intestinal dysbiosis. (16) The alteration and disruption of the normal level of flora caused by antibiotics has been known for a long time. Antibiotics do this by inviting a secondary infection by harmful yeasts and pathogenic bacteria to take hold. (17, 18)

Antibiotics kill all kinds of bacteria, both good and bad. They are indiscriminate in this regard and this causes many short-term as well as long-term side effects.

Studies have shown that, by taking a single course of antibiotics, you can lose the biodiversity and balance of your gut flora within as little as 3 – 4 days. Although broad-spectrum antibiotics are formulated to kill systemic infections, they also alter the gut flora. (30) A study was carried out showing that the use of broad-spectrum antibiotics was linked with the development of IBS. (19)

How do I know I have dysbiosis?

A comprehensive stool analysis  gives the most in depth analysis of bacteria, both beneficial and pathogenic, and their levels in your gut. Learn more about the test here.

How is dysbiosis treated?

Unfortunately, correcting dysbiosis is not as simple as just taking a probiotic. The goal of rebalancing the intestinal flora is to make the conditions in the intestine more hospitable for the friendly intestinal flora, but not for the pathogenic bacteria. Our protocols use diet, herbal medicines and nutritional supplements to restore balance to your gut ecosystem.

  1. Remove foods from your diet that cause inflammation, feed the wrong bacteria and irritate the gut wall, using our specialised eating plan.
  2. Stimulate production of and/or supplement stomach acid and enzymes.
  3. Reduce any overgrowth of pathogenic with herbal antimicriobials.
  4. Enhance the growth of beneficial flora with prebiotics, probiotics and fermented foods.
  5. Enhance gut immunity and repair the gut lining.

When conditions in your gut are improved then it naturally keeps an overgrowth of pathogenic bacteria at bay and healthy balance is restored.

What next?

To learn more about the testing and treatment options available to you we recommend you take a free 15 minute phone consultation with our Naturopath. During this call you can learn more about our treatments and have any questions you may have answered. This call is to determine if we are a good fit for one another rather than a history or complete consultation. There is no obligation, and no strings attached.

It is quick and easy to book your free 15-minute phone consultation using our online calendar. Just click the link below, choose a date and time convenient for you, enter your details, and our Naturopath will call you at your chosen time. Book here



  1. U. C. Ghoshal, H. Park, and K. A. Gwee, “Bugs and irritable bowel syndrome: the good, the bad and the ugly,” Journal of Gastroenterology and Hepatology, vol. 25, no. 2, pp. 244–251, 2010.
  2. Isolauri E. Probiotics in human disease. Am J Clin Nutr. 2001 Jun; 73(6):1142S-1146S.
  3. Cummings JH, Macfarlane GT (1997). Colonic Microflora: Nutrition and Health. Nutrition. 1997; vol.13, No.5, 476-478.
  4. McLaren Howard J. Intestinal dysbiosis. Complementary Therapies in Med 1993; 1:153. 13. Guarner, F; Malagelada, J (2003). “Gut flora in health and disease”. The Lancet 361 (9356): 512– 9
  5. Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S, de Vos WM. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1792-801.
  6. Codling C, O’Mahony L, Shanahan F, Quigley EM, Marchesi JR A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome. Dig Dis Sci. 2010 Feb; 55(2):392-7.
  7. Kerckhoffs, A. P., Samsom, M., van der Rest, M. E., de Vogel, J., Knol, J., Ben-Amor, K. & Akkermans, L. M. (2009). Lower bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol 15, 2887–2892
  8. Balsari A, Ceccarelli A, Dubini F, Fesce E, Poli G. The fecal microbial population in the irritable bowel syndrome. Microbiologica. 1982 Jul; 5(3):185-94.
  9. Paul J Kennedy, John F Cryan, Timothy G Dinan and Gerard Clarke. Irritable bowel syndrome: A microbiome-gut-brain axis disorder? World J Gastroenterol. 2014 October 21; 20(39): 14105-14125.
  10. Rajilic-Stojanovic M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S., de Vos W.M. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology. 2011;141:1792–1801
  11. Jeffery I.B., O’Toole P.W., Ohman L., Claesson M.J., Deane J., Quigley E.M., Simren M. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut. 2012; 61:997–1006.
  12. Malinen E, Rinttilä T, Kajander K, et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol. 2005; 100(2): 373-82.
  13. Chassard C., Dapoigny M., Scott K.P., Crouzet L., Del’homme C., Marquet P., Martin J.C., Pickering G., Ardid D., Eschalier A., et al. Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome. Aliment. Pharmacol. Ther. 2012;35:828–838
  14. Kim G1, Deepinder F, Morales W, Hwang L, Weitsman S, Chang C, Gunsalus R, Pimentel M Methanobrevibacter smithii is the predominant methanogen in patients with constipation-predominant IBS and methane on breath. Dig Dis Sci. 2012 Dec; 57(12):3213-8.
  15. Youn YH, Park JS, Jahng JH, et al. Relationships among the lactulose breath test, intestinal gas volume, and gastrointestinal symptoms in patients with irritable bowel syndrome. Dig Dis Sci. 2011 Jul; 56(7):2059–2066. Epub 2011 Jan 15.
  16. Gismondo MR. Antibiotic impact on intestinal microflora. Gastroenterol Int 1998; 11:29-30.
  17. Keefer, C. S. (1951) Alterations in normal bacterial flora of man and secondary infections during antibiotic therapy. American Journal of Medicine, 11, 665-666.95.
  18. Seelig, M. S. (1966) Mechanisms by which antibiotics increase the incidence and severity of candidiasis and alter the immunological defenses. Bacteriological Reviews, 30, 442-459.
  19. Villarreal AA, Aberger FJ, Benrud R, Gundrum JD. Use of broad-spectrum antibiotics and the development of irritable bowel syndrome. WMJ. 2012 Feb;111(1):17-20


The Digestive Wellness Clinic
12 Junction St Woollahra, NSW 2025 Tel: (02) 8001 6344