Your comprehensive guide to Chronic Diarrhea

Chronic diarrhea is no doubt the digestive symptom that’s on par with constipation in terms of frustration and disruption to normal life. Diarrhea also has the added “fun” of needing to know where the closest bathroom is at all times, lest an accident occurs.

I wanted to write this article to help you if you’re navigating chronic diarrhea because there are many possible causes and for most people, these have not been investigated. I was prompted by helping a client who had unrelenting diarrhea for many years where we worked out she likely has Bile Acid Diarrhea. I spent many hours writing this article to be as detailed - yet easy to understand - as possible. I've referenced everything where relevant. Of course, I recommend working with a qualified healthcare practitioner to confirm the correct cause/s behind the diarrhea and to assist with appropriate treatment. Medical assessment is essential to determine if there is a medical condition causing it. 

Jump to:

• Defining Diarrhea
• Stress/anxiety and high serotonin 
• Excess caffeine
• Carbohydrate malabsorption eg. lactose, fructose
• SIBO
• Post-infectious IBS (PI-IBS)
• Allergies - eg. cow’s milk protein
• Nickel Allergy
• Celiac disease
• Microscopic colitis
• Exocrine Pancreatic insufficiency (EPI)
• Bile acid diarrhea (BAD)/Bile acid Malabsorption (BAM)
• IBD
• Medications or supplements
• Hyperthyroidism (Graves disease)
• Antibiotic-associated diarrhea and Clostridioides difficile infection
• Dysbiosis and opportunistic pathogens
• Strenuous exercise 
• Increased Intestinal Permeability (“Leaky gut”)
• Mastocytosis, Mast Cell Activation Syndrome and Histamine intolerance
• Notable Mentions - Menstruation, Alcohol use
• General naturopathic recommendations
• Conclusion
• Still struggling? Work with me

This list is comprehensive, although there are also some more rare causes of diarrhea. I haven’t included IBS-D even though that is usually the most common diagnostic label - the reason is that the label IBS-D doesn’t actually explain WHY you have diarrhea. 

Being diagnosed with IBS may in fact cover up the true diagnosis - when someone is diagnosed with IBS, there may in fact be an organic identifiable condition present. There are many mechanisms that can produce the IBS-D symptoms. IBS, as a syndrome, also has no definitive pathology marker.

Currently, SIBO is a condition that is commonly investigated in the nutrition and naturopathic professions, but it’s so important to look at the bigger picture, otherwise other relevant factors will be missed.

Defining Diarrhea

Let’s start by defining diarrhea. Most of us have experienced an unfortunate explosion in the bathroom from time to time, but when it becomes chronic - longer than 4 weeks - is when the underlying cause/s really need to be identified in order to resolve it once and for all.

Diarrhea is defined as loose, unformed or watery stool, and often there may be urgency present - sometimes to the extent that fecal incontinence occurs. This is an inability to control bowel movements before getting to the bathroom. Some people also report “explosive” features. Cramps and pain may also be a common feature of the diarrhea picture. Greater than 2 bowel movements per day is common in this population. Diarrhea often occurs in the presence of fast gut motility - the contents of the bowel (ie. waste) move through so quickly that there isn’t enough time for water in the bowel to be reabsorbed. Another common feature is that more water is drawn into the bowel. Both of these factors make the bowel movement/stool more liquid than normal. Of course, there are exceptions to this - one can have slow transit time, yet a very unformed bowel movement at the other end.

Below I have outlined the various causes of chronic diarrhea and following that, naturopathic and nutritional suggestions for how you can address your diarrhea based on the cause (where appropriate). Some treatments are used to address diarrhea from a symptomatic perspective and other treatment addresses underlying cause/s so that symptomatic treatment is no longer required. Using a combined approach helps you achieve a more normal pattern of bowel movements quickly but also sustainably. 

As always, seek advice from your medical practitioner, since many of the below are medical conditions that require diagnosis and treatment. Stool testing can be done to assess electrolyte concentrations, the presence of blood or fecal leukocytes, and fat content. Depending on the results, this can help to identify what type of diarrhea is present - ie. whether it’s watery, inflammatory or fatty.

Let's take a look at potential causes of your diarrhea.

Stress/anxiety and high serotonin 

This is one of the most common causes of diarrhea. Our autonomic nervous system broadly has two parts - the parasympathetic and the sympathetic, which are both important and need to be well balanced. Digestion is mostly governed by the parasympathetic nervous system, colloquially known as the “rest and digest” system. When someone is more sympathetic dominant, digestion is one of the first body functions to be negatively affected. Think of those stressful feelings you get in your gut and it makes sense. There is a neural connection between the brain and what’s known as the enteric nervous system in the gut, which is considered the second brain. 

Enterochromaffin cells (EC) in the gut produce serotonin, which is essential for proper gut motility. At times, the ECs produce excess serotonin based on the recognition of stress hormones. The excess serotonin results in diarrhea because serotonin speeds motility - sometimes excessively so. Dietary irritants - eg. spicy foods -  and bacterial byproducts can also result in excess serotonin production.

Additionally, if an individuals’ SERT (serotonin transporter) isn’t functioning correctly, too much serotonin stays within the gut environment, also contributing to diarrhea along with pain and cramping.

Excess serotonin may also be present in carcinoid syndrome - a reminder to always consult your medical practitioner if you are dealing with any chronic gut issues.

There are likely other factors aside from serotonin in the stress = diarrhea scenario, but it was worth highlighting for this article, especially because there is an assumption that more serotonin is always a good thing.

Recommendation: Work on managing stress levels - I know it’s a cliche and easier said than done, but it’s still important. Depending on your situation, this will look different for two people. One person may thrive with regular yoga, another may benefit from daily walks in nature. Other naturopathic and nutritional treatments can help, such as adaptogenic herbs, B vitamins, magnesium and zinc where appropriate. Other approaches can be helpful such as re-framing stress or difficulty - I’m currently reading a book about stoicism called Reasons not to worry by Brigid Delaney.

Excess caffeine

Caffeine is a stimulant that increases gut motility by promoting colonic motor activity with contractions. Excess caffeine can stimulate the stress response - which, as detailed above - can result in excess serotonin that results in diarrhea. Caffeine can also relax the rectal muscles quite effectively, leading to a bowel movement soon after consumption. In some cases, this relaxing effect may be too much, resulting in sudden diarrhea. For someone that has consumed caffeine for a long time, they may be unaware of the effect and not make the connection.

Recommendation: if you consume caffeine-containing food or drinks, spend some time observing your bowel movements in relation to caffeine consumption. If you have chronic diarrhea, consider cutting back on caffeine or putting stress management techniques in place. One trick is to mix decaf coffee 50:50 with regular coffee. So you're still getting your caffeine buzz, but it's a little easier on the nervous system. Low caffeine matcha tea is also now available (mostly in the US), so that can also be mixed with regular matcha.

Carbohydrate malabsorption eg. lactose, fructose

Lactose intolerance is probably the most well known - and most medically well accepted - food intolerance. Infants have a greater capacity to tolerate lactose because they are mostly consuming breast milk. As we age, the production of lactase - the enzyme that digests lactose - reduces, and this is typically when people notice issues. Some ethnic groups also tend to make less lactase than others such as people from East Asia but also Italian, West African, Arabic, Jewish and Greek. Lactose intolerance typically causes gas, bloating and diarrhea - the latter due to excess water being drawn into the colon, which then makes stool more liquid. It can be managed quite well on a low-lactose diet - an entirely lactose-free diet is often unnecessary because there is always an amount that individuals can tolerate. Some types of dairy are quite low in lactose, so most people can keep in many types of dairy in their diet. The prebiotic GOS (Galacto-oligosaccharides) can improve lactose intolerance. 

Recommendation: A low lactose diet and GOS is my recommendation here. For most people, they can tolerate a certain amount of lactose, so it's usually not necessary to cut out lactose-containing foods altogether. Lactase enzymes can also be helpful for some occasions where you may have less control of what you're eating.

Fructose malabsorption, which may also be known as fructose intolerance, can cause similar symptoms to lactose intolerance. Malabsorbed or unabsorbed fructose has an osmotic effect, drawing water into the colon and often resulting in diarrhea. There is currently ongoing debate as to whether fructose malabsorption is caused by SIBO or not - Jason Hawrelak PhD, believes that it is in some cases, so he recommends fructose testing as a reliable test for SIBO (ideally lactulose testing would also be conducted for an individual alongside fructose testing). Classic fructose intolerance can also be present - this is where a high hydrogen level is detected in the large intestine (colon) rather than the small intestine - this can also cause diarrhea.

Recommendation: A low fructose diet* - either standalone or as part of a low FODMAP or SIBO diet - is recommended here along with consuming any fructose with some protein which helps with fructose digestion. SIBO treatment is also essential.

*Typically this means consuming foods low in fructose or with an ideal fructose:glucose ratio (as glucose helps with fructose digestion)

SIBO

Hydrogen SIBO (Small Intestinal Bacterial Overgrowth) is associated mostly with IBS-D more so than IBS-C. There are a few proposed ways this type of SIBO can cause chronic diarrhea.

• Increased products of carbohydrate malabsorption - due to the effect of the SIBO bacteria on brush border enzyme production - and the resultant fermentation may draw excess water into the bowel which then results in watery stool
• Damage to the gut mucosa from certain microbes - including those found in SIBO - may cause irritation or a lactase deficiency which means a certain amount of lactose will cause diarrhea
• Deconjugation of bile salts - caused by SIBO bacteria - can lead to fat malabsorption. A high enough level of malabsorbed fat will often present as diarrhea

Hydrogen sulfide SIBO or LIBO (H2S) - H2S is a gas that is beneficial and essential to our health in reasonable amounts. When this gas is produced excessively in the gut - whether in the small intestine, large intestine - or both -  it can cause digestive symptoms including diarrhea. Hydrogen sulfide SIBO occurs due to excess production of hydrogen - which is a fuel source for hydrogen sulfide and also methane - in combination with an overgrowth of the bacteria that can produce H2S. This latter factor may be due to diet or other factors - you can read my in-depth article about hydrogen sulfide here.

Recommendation: Assess the microbiome and treat appropriately - this will be different for everyone. Trio Smart breath testing can be helpful although it may not detect all cases of hydrogen sulfide SIBO and it doesn’t indicate what is going on in the large intestine - which is where a stool test is required.

Post-infectious IBS (PI-IBS)

Post-infectious IBS is a condition triggered by a gastrointestinal infection or food poisoning and is usually caused by either bacteria (eg. Campylobacter), parasites (eg. Giardia) or viruses (eg. Norovirus). PI-IBS may be implicated in up to 30% of cases of IBS.

Intestinal enteritis (IE) is the medical term for the inciting infection - for some people, the symptoms they experience continue for some time afterwards. This is when PI-IBS is the diagnosis. It mostly presents with diarrhea but can also present with mixed constipation and diarrhea.

One of the ways the original infection can cause the PI-IBS is via damage to the nerves controlling the migrating motor complex (MMC) which can then trigger SIBO. The MMC is a major protection against SIBO as it’s a cleansing wave that sweeps out excess bacteria from the small intestine. The dysfunctional MMS and resulting SIBO usually results in high levels of hydrogen gas production, which we know often causes diarrhea. For most people, this damage actually resolves itself within a few months, but for those still experiencing symptoms after this, then it’s a good idea to get an IBS Smart test which measures the relevant antibodies. These people are often found to have a higher rate of SIBO relapse than other people with SIBO and they may actually require yearly SIBO treatment.

Recommendation: if possible, take the IBS Smart test and consider that the SIBO may need to be treated yearly

Allergies - eg. cow’s milk protein

An IgE-mediated allergy to cow milk protein can either cause moderate or severe/life-threatening symptoms. Diarrhea fits into the category of a moderate symptom. Sometimes the reaction may be delayed by more than two hours and the allergy test might be negative. Strict avoidance of cow’s dairy is very important in both instances.

Nickel Allergy

A nickel allergy as it relates to diarrhea and other gastrointestinal issues is unfortunately not very well known to either the general public or the medical profession, but is highly relevant to those with diarrhea, reflux, eczema and endometriosis. Nickel is ubiquitous - in food, water, medical implants, jewelry etc - but our body has no need for it and can become hypersensitive. The highly regarded MELISA test can be used to determine if this is a factor for you, unfortunately it's not available in Australia.

Recommendation: It's impossible to avoid all nickel, but minimising exposure via food and water sources can be very helpful.

Celiac disease

Celiac disease is an autoimmune condition where gluten consumption damages various structures in the digestive tract and causes inflammation. When a person with celiac disease consumes gluten or still has a lot of damage in the small intestine, diarrhea can occur due to malabsorption of nutrients. This symptom may take time to improve after starting a gluten-free diet and in some cases, a person with celiac may also have microscopic colitis. Many people with celiac disease need to remove other types of food from their diet aside from gluten-containing foods due to cross-reactivity.

Recommendation: strict, life-long avoidance of gluten is essential for those with celiac disease. Other foods may mimic gluten and also need to be avoided in some cases.

Microscopic colitis

Microscopic colitis is a form of inflammation in the large intestine that’s often not visible to the human eye - including during colonoscopy - or sometimes presents as slightly red tissue. It is diagnosed by biopsy where a tissue sample is taken during a colonoscopy and examined under a microscope. Due to inflammation, the colon cannot reabsorb water appropriately, so the water remains in the colon and is then expelled with waste, resulting in loose stool/diarrhea which is often watery. Microscopic colitis often co-occurs with bile acid malabsorption.

Recommendation: Reduce gut inflammation and assess/improve the microbiome

Exocrine Pancreatic insufficiency (EPI)

The pancreas secretes hormones that help manage blood sugar balance, but it also secretes enzymes that help to digest our food. In some people, when the latter function is impaired, the lack of enzymes leads to malabsorption. In turn, this malabsorption means fat is excreted in high amounts in bowel movements - this can be very soft, smelly and/or explosive. 

There is a two-way relationship between SIBO and EPI - firstly, a low level of pancreatic enzymes can be a causative factor for SIBO. Pancreatic enzymes are released not just at mealtimes, but also as part of the Migrating Motor Complex (or MMC) - a protective mechanism helping to sweep out bacteria from the small intestine to prevent overgrowth.

The bacteria found in SIBO may also cause inflammation of the pancreas, making EPI worse.

Recommendation: Pancreatic enzymes (eg. Creon) may be required and B vitamins are believed to help stimulate enzyme release. Additionally, adequate stomach acid is important in the digestive cascade.

Bile acid diarrhea (BAD)/Bile acid Malabsorption (BAM)

The terms Bile Acid Diarrhea (BAD) and Bile Acid Malabsorption (BAM) are often used interchangeably, but essentially they refer to the same thing. Bile Acid Diarrhea is the symptom and Bile Acid Malabsorption is the cause.

In most cases, one or both of the following underlying drivers is present in an individual dealing with this:

• Impaired feedback loop in the liver and gallbladder causing excess bile acid production
• Inability to appropriately re-absorb bile acids in the terminal ileum, the last portion of the small intestine

Dysbiosis appears to be both cause and effect in both scenarios.

Risk factors include celiac disease, Crohn’s disease, SIBO or EPI, microscopic colitis. It’s commonly triggered by gallbladder removal and is believed to be one of the more common causes of what is labeled as IBS-D.

Recommendations: A low fat diet and a gradual increase in soluble fibre, including psyllium. Addressing gut dysbiosis is also important along with inflammation. In terms of diagnosis, tests for BAD such as SeHCAT are not available worldwide but alternatives include plasma C4 testing and possibly faecal bile acid measurement.

IBD

Recurrent and bloody diarrhea is the most common and debilitating symptom of Inflammatory Bowel Disease - of which Crohn’s and Ulcerative Colitis are the two main types. The diarrhea of IBD is caused by inflammation and mucosal damage which interferes with electrolyte balance, leading to water accumulation and eventually diarrhea. A secondary factor called “leak flux” also contributes to diarrhea - this involves the epithelial layer - including tight junctions - not functioning correctly.

Recommendation: Reduce inflammation, support butyrate levels, avoid food triggers, address SIBO if present, address large intestine dysbiosis if present, support immune function 

Medications or supplements

Medications such as Metformin can cause diarrhea as can some SSRIs. Metformin may result in bile acid malabsorption (BAM) as detailed above. SSRIs influence serotonin activity not just in the brain but also in the gut - serotonin plays an important role in gut peristalsis - a type of propulsive movement that helps waste move through. Diarrhea can also result from chemotherapy treatment. In some cases, diarrhea can be a sign of toxicity caused by a medicine. Supplements including herbal medicines may also cause diarrhea - if you suspect this is the case - speak to your prescribing practitioner.

Recommendation: Always consult a medical professional to discuss your use of medication, especially if you develop new symptoms.

Hyperthyroidism (Graves disease)

Autoimmune Graves disease is the main cause of hyperthyroidism, where the thyroid produces an excessive level of hormones. Every body system is affected, including the digestive system. Movement of waste products through the digestive tract speeds up, resulting in less water being absorbed back into the body in the colon - this results in looser stool. The number of bowel movements also tends to increase in the hyperthyroid state. It’s important to keep in mind that autoimmune conditions such as Graves increase the likelihood of another autoimmune conditions being present - the relevant ones to diarrhea being Celiac disease and IBD.

Recommendations: work with your healthcare professional to address the overactive thyroid function and balance immune system activity

Antibiotic-associated diarrhea and Clostridioides difficile infection

Antibiotic-associated diarrhea (AAD) occurs when someone experiences 3 or more episodes of loose stool that can start either during or after a course of antibiotics. It’s caused by the dysbiosis that often results from the antibiotics indiscriminately killing off “good” bacteria while they target the “bad” bacteria. The likelihood of AAD occurring is increased depending on the length of treatment, the type of antibiotics used and whether more than one antibiotic has been used. In some cases, the opportunistic pathogen C. difficile can lead to an infection - this prolongs the AAD and may be accompanied by other symptoms such as nausea, weight loss, decreased appetite, abdominal cramping and low grade fever. C. difficile infection can be deadly, so it’s important that it’s investigated promptly.

Recommendations: investigate C. difficile, address the dysbiosis by restoring the microbiome with prebiotics and a microbiome-friendly diet. FMT (Fecal Microbiota transplant) may be necessary if C. difficile is unresponsive to first line interventions.

Dysbiosis and opportunistic pathogens

Opportunistic pathogens or “pathobionts” are microbes that can cause health issues as a result of gut dysbiosis. This is because the friendly bacteria - and the immune system within the gut - are control mechanisms that keep these microbes under control. These microbes are a normal part of the microbiome - it’s just that when the opportunity arises, they can become pathogenic and cause issues for the human that hosts them.

Some examples of opportunistic pathogens include Clostridioides difficile, Klebsiella pneumoniae, Enterotoxigenic Bacteroides fragilis, Proteus mirabilis and Enterococcus faecalis.

Many of these microbes are associated with inflamed mucosa in the gut and can contribute to the development of colitis.

Recommendations: address dysbiosis, including reducing the typically high proteobacteria found in dysbiosis; support immunity including secretory IgA levels, support growth of butyrate-producing bacteria. Take any medical treatment as recommended.

Strenuous exercise 

Diarrhea and urgency often occur in long-distance runners, especially those running marathons.

This is believed to be due to a dramatic drop in blood flow to both the small and large intestine during strenuous exercise. Impaired blood flow may lead to decreased intestinal absorption of nutrients and impaired water reabsorption in the colon resulting in diarrhea.

Intestinal transit time may also speed up. This leads to a more rapid passage of bowel contents - and less water reabsorption - causing looser stools.

Recommendations: preventative measures may be needed such as using tannin-rich herbs and foods to reduce fluid in the colon or eating unripe bananas and white rice in the week leading up to a race

Increased Intestinal Permeability (“Leaky gut”)

Many people with IBS have increased intestinal permeability that can lead to diarrhea due to activation of the mucosal immune system following entry of antigens and bacteria. Increased intestinal permeability is likely present even in those without IBS, for example those with autoimmune conditions.

Recommendations: Glutamine, S. boulardii (Biocodex strain eg Florastor), LGG probiotic, supporting Akkermansia muciniphilia levels, minimising gluten and alcohol intake, addressing dysbiosis and managing stress are all helpful for leaky gut. For some people, the casein protein in dairy may need to be avoided.

Mastocytosis, Mast Cell Activation Syndrome and Histamine intolerance

Conditions that involve mast cells and histamine are varied in terms of etiology and severity of symptoms, although most of them do share a wide crossover of signs and symptoms. Gastrointestinal symptoms such as diarrhea are very common in these conditions due to the high level of mast cells in the GI tract and also because histamine is commonly found and metabolised in the gut - either due to bacterial production, immune activity or in the food we eat. High levels of histamine or impaired ability to metabolise it are common factors in histamine-related digestive symptoms.

Recommendations: Try to find a mast-cell literate medical professional and also utilise the services of a naturopath or nutritionist who can also support you in dietary changes and ways to support the body’s production and handling of histamine. Many natural substances are mast cell stabilisers for example and there are also histamine binders that can ease symptoms. Stress is a big driver of histamine production, please see the section on stress for suggestions.

Notable Mentions - Menstruation, Alcohol use

As I was finishing this article, I remembered two other common causes of diarrhea that are worth noting - one is comedically referred to as "period poos" or "period poops" for the Americans, and the other is alcohol use.

Around menstruation, you may notice loose stool or diarrhea and the reason for this is that the prostaglandins produced to trigger the shedding of the uterine lining also have an effect on bowel function - especially because of the proximity of the uterus to the bowels. If you want to mitigate this, I suggest eating a bit differently in the lead up to your period - include some white rice 1-2 times a day for a few days beforehand and add an unripe banana or two. Other things such as tannin-rich herbs can help - black tea for example has lots of tannins. Some women experience the opposite - constipation - and you can read my top tips for constipation for help if that's you.

Regular alcohol use is so common and normalised these days that it's easy to forget that it can have a negative effect on digestion - it's not just the liver and brain that are affected. I'm not opposed to occasional drinking, but drinking culture especially here in Australia is definitely concerning. If you or someone you know is drinking most days, you may not make the connection between alcohol and your diarrhea. The main reasons alcohol can cause diarrhea are due to the increase in intestinal permeability it causes (see above); increased motility, irritation of the gut lining and the effect on the microbiome - alcohol itself is antimicrobial so it can kill off beneficial bacteria. The best treatment here is obviously to minimise alcohol intake as much as possible - perhaps re-framing your relationship with it so that it's an occasional indulgence rather than an every day thing.

General naturopathic recommendations

While you're working with a healthcare professional to determine the cause of your chronic diarrhea, here are suggestions for symptomatic relief:

• Eat some white rice every day - ½ to 1 cup of cooked white rice each day (not all in one sitting) - jasmine rice, sushi rice or sticky rice are the best choices (Basmati ferments too much)
• Green bananas - one per day
• Drink some black tea for the tannins
• Activated charcoal between meals (and 2 hours away from supplements and medications)
• The Biocodex strain of S. Boulardii can provide symptomatic relief - either Florastor or Perenterol Forte are ideal
• Support your nervous system - either with behavioural change, breathwork, rest, lifestyle changes, supplements

Conclusion

As you can see, there are quite a few potential causes of your chronic diarrhea and identifying the correct one is essential - not only for symptom relief, but also to ensure your digestion and general health are the best they can be. If you have any questions, feel free to leave me a comment below!

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