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Chronic Diarrhea

Chronic diarrhea is one of the more crippling symptoms I see in clinic, with sufferers experiencing anxiety about accidents and not being able to find a bathroom if urgency hits. This can really impact your work and social life, as you may have to plan activities around where the nearest bathroom is, or even miss out altogether.

Having diarrhea predominant irritable bowel syndrome (IBS-D) means you are chronically affected by frequent abdominal pain and urgent/frequent episodes of diarrhea (loose/watery stools). Often times you may experience gas and bloating as well.

Living with this is not normal, there is something going on in your gut and you need to find the cause:

Causes of Chronic Diarrhea

When diarrhea continues for longer than 4 weeks it is categorised as chronic, in the clinic these are the most common causes I see for chronic diarrhea:

  • Gut Dysbiosis
  • Small Intestine Bacterial Overgrowth (SIBO)
  • Bile Acid Malabsorption
  • Parasites
  • Intestinal Permeability (Leaky Gut)
  • Food intolerances/malabsorption
  • Pancreatic enzyme insufficiency

Gut Dysbiosis

Gut dysbiosis refers to an alteration or imbalance of the microbes in your digestive tract. (Learn more about dysbiosis here).

Dysbiosis has been repeatedly reported in IBS-D patients, and it has been shown that IBS-D patients have a lower level of microbial diversity compared to healthy individuals. (1)

A number of studies have found lactic acid-producing bacteria such as Lactobacillales were decreased significantly in IBS-D patients. The decrease or elimination of lactic acid buildup will impair the intestinal defense barrier and increase osmotic load in the intestine, leading to more water staying  in the bowel and diarrhea.

Another study found that butyrate-producing bacteria such as Ruminococcaceae and Lachnospiraceae were decreased dramatically in diarrhea patients. Butyrate is a short chain fatty acid produced by certain gut bacteria when they ferment carbohydrates and is a preferred energy source for cells of the gut wall to maintain normal barrier function and also maintains balance in the gut through anti-inflammatory actions. (2)

Decreased populations of beneficial bacteria in IBS-D patients, allows for a proliferation of more pathogenic species such as proteobacteria, streptococci and clostridia. These bacteria can damage the gut lining and alter anion secretions leading to more water entering the colon.

Bile Acid Malabsorption (BAM)

Bile acids are known as endogenous laxatives (endogenous meaning originating from within the body) because they trigger propulsive contractions in the bowel and bring water into the colon. (3)

In fact, a condition called bile acid malabsorption (BAM) is known to cause chronic diarrhea. This condition is caused by excess bile salts entering the colon rather than being absorbed in the small intestine, increasing the reabsorption of water and colonic movement, which results in diarrhea.

Studies show that bile acid malabsorption (BAM) accounts for at least 30% of patients diagnosed with functional diarrhea and IBS-D. (4)

In healthy people, the primary bile acids are dehydroxylated in the colon by your microbiota. In people with bile acid diarrhea, dehydroxylation is decreased and the concentration of bile acids in the colon is markedly elevated leading to increased motility, water excretion and diarrhea.

A study of fecal samples from people with IBS-D found a significant increase in fecal primary bile acids compared to healthy controls. Researchers in this study also found dysbiosis, characterised by an increase of E.coli, a decrease in bifidobacteria, and a decrease in bacteria from the Leptum group. The Leptum group contains the bacteria responsible for the dehydroxylation of bile acids. (5)


Small Intestine Bacterial Overgrowth (SIBO) is, as its name implies, an overgrowth of bacteria in the small intestine, and studies implicate it as a potential cause of IBS-D. (Learn more about SIBO here)

A study on the role of SIBO in 87 patients with chronic diarrhea reported that SIBO was present in 33% of patients compared to 0% in healthy controls. (6)

The causes of diarrhea in patients with SIBO include de-conjugation of bile salts, increased small intestinal permeability and low grade inflammation resulting from immune activation in the small intestinal mucosa. (7,8,9)

Researchers have found that patients with SIBO had significantly elevated unconjugated bile acid levels in their stools (10), and another study found a predominance of bacteria in the small intestine that metabolise bile salts to unconjugated bile salts in patients with diarrhea. (11)

In addition, due to this overgrowth in the small intestine, particles of food that would normally be fermented by the bacteria in the large intestine begin to ferment in the smaller confines of the small intestine, producing excessive quantities of hydrogen and/or methane gas. The gases also have an effect on bowel motility, with excessive hydrogen production having a strong link to diarrhea. (12)


A chronic parasite infection can mimic many of the same symptoms of IBS-D. Medical investigators in Australia have found the parasite D. fragilis in patients suffering from IBS like symptoms. (13)

Many of the clinical symptoms associated with IBS are non-specific and have also been reported in patients infected with D. fragilis and B. hominis.  Anecdotal evidence suggests that many patients infected with these parasites are indeed being misdiagnosed as having IBS”. (14)

A study carried out in Norway on 82 patients that had been infected with Giardia showed that 66 of them (81%) had symptoms of IBS 12 to 30 months after they initially got the Giardia infection. The most common symptom subtype was diarrhoea-predominant IBS (47%). (15)

Intestinal Permeability (Leaky Gut)

The lining of our gut serves as a protective layer and controls the unrestrained movement of pathogens and toxins from the gut to the underlying tissue.

Compromised intestinal barrier function has been associated with low-grade inflammation in the gut mucosa of diarrhea patients, sustained inflammation and damageto  barrier integrity promotes “leakiness” in the gut, where the absorptive capacity of the colon is significantly compromised resulting in excessive loss of fluid in the stool. A positive association between increased intestinal permeability and severity of diarrhea has been recently demonstrated in IBD patients. (16)

IBS-D patients with increased intestinal permeability have more severe symptoms and hypersensitivity to stimuli than healthy people (17)

Food Intolerance/Malabsorption

Some diarrhea sufferers may have an inability to fully absorb particular types of carbohydrates. When they arrive in the lower small intestine and colon, these poorly absorbed carbohydrates exert an osmotic effect, which means more fluid is drawn into the bowel.

The most common culprits are: lactose, sorbitol, fructose, and starches.

Pancreatic enzyme insufficiency

The pancreas secretes pancreatic enzymes into the small intestine, which breaks down proteins, fats and carbohydrates in preparation for absorption into the bloodstream.

Symptoms of insufficient pancreatic enzymes include:

  • Bloating or painful stomach cramps after meals
  • Loose, greasy, foul-smelling stools
  • Deficiency of fat-soluble vitamins A, D, E and K
  • Diarrhea

Exocrine pancreatic insufficiency (EPI) is a condition that results when the pancreas doesn’t secrete enough enzymes. Someone with EPI who doesn’t have enough pancreatic enzymes cannot properly digest the nutrients in foods such as protein, fats, and carbohydrates. In one study, EPI was found to exist in 6.1% of patients with IBS-D.

How do I find out what’s causing my diarrhea?

As you can see, the cause of your chronic diarrhea can be complex and may involve a number of factors. To find an effective solution it is vital to find its root cause. Based on your presenting symptoms and history, there are a number of lab tests we may use to find the cause of your symptoms, including:

  • A Comprehensive Stool Analysis which tests your stool for overgrowths of bacteria, yeasts, and parasites and also the levels of beneficial bacteria such as bifido, lactobacillus, F.praunitzii plus other digestive markers
  • Lactulose Breath Test for SIBO
  • Lactulose Mannitol test for intestinal permeability

How is it treated?

Once we have a better idea of what’s causing your diarrhea, we begin a treatment plan using diet, herbal medicines, nutritional supplements,  and lifestyle changes. This plan works by:

  • Removing foods from your diet that cause inflammation and feed bacterial/yeast overgrowths. Learn more about the eating plan here.
  • Removing any overgrowths of bacteria and/or yeasts in your gut with herbal medicines..
  • Restoring beneficial bacteria and re-establishing healthy bacterial balance in your gut with prebiotic fibres/foods and probiotic supplements/foods.
  • Reducing inflammation and repairing the lining of your gastrointestinal tract.

What next?

To learn more about the testing and treatment options available it is recommended you take a free 15 minute phone consultation. During this call you can learn more about the programme and have all your questions 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 the online calendar. Just click the button below, choose a date and time convenient for you, enter your details, and Matt will call you at your chosen time.

Book Free Phone Consult


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  2. Zhuang, Xiaojun & Tian, Zhenyi & Li, Li & Zeng, Zhirong & Chen, Minhu & Xiong, Lishou. (2018). Fecal Microbiota Alterations Associated With Diarrhea-Predominant Irritable Bowel Syndrome. Frontiers in Microbiology. 9. 10.3389/fmicb.2018.01600
  3. Bajor A, Gillberg PG, Abrahamsson H. Bile acids: Short and long term effects in the intestine. Scand. J. Gastroenterol 2010; 45: 645-664.
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  9. Fan X, Sellin JH. Small intestinal bacterial overgrowth, bile acid malabsorption and gluten intolerance as possible causes of chronic watery diarrhoea.Aliment Pharmacol Ther. 2009 May 15; 29(10):1069-77
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  17. Qi Zhou, Buyi Zhang, and G. Nicholas Verne Intestinal Membrane Permeability and Hypersensitivity In theIrritable Bowel Syndrome Pain. 2009 November ; 146(1-2): 41–46
The Digestive Wellness Clinic
12 Junction St Woollahra, NSW 2025 Tel: (02) 8001 6344