We cover the gut microbiome and its impact on overall health

constipated lady

The root causes of constipation

Constipation is a very common symptom that affects a wide range of people. Most people think of constipation as only having a few bowel movements a week, but constipation is more complex than that.

Constipation may involve a daily but unsatisfactory bowel movement that involves:

  • Straining during defecation
  • Lumpy or hard stools
  • Feeling like you did not pass all the stool
  • Feeling of blockage during defecation 
  • Needing to manually facilitate passage of stool

Ideally, people are having one to two bowel movements a day that are well formed, easy to pass, and complete. A bowel movement should be a quick and easy experience. 

Now, it is normal to occasionally experience constipation. Stress, travel, and changes in diet may all cause a few days of constipation. But if you have been dealing with any of the above symptoms for more than 3 months, then that may indicate a bigger problem. 

The proper formation and timely passage of stool happens in the large intestine. But the function of the entire digestive tract can affect this process. And often there is more than one factor contributing to constipation.

Potential Causes of Constipation

Nutrition: low fiber, dehydration

Lifestyle: sedentary lifestyle, high stress

Digestion: low stomach acid, low pancreatic enzymes, bile deficiency

Nervous system imbalances: dysautonomia, diabetes, traumatic brain injury, certain autoimmune diseases

Slow transit: certain medications, some chronic infections impacting the nervous system

Structural: pelvic floor dysfunction, outlet dysfunction 

Microbiome: intestinal methanogen overgrowth (IMO), Proteobacteria overgrowth, possibly hydrogen sulfide overgrowth, possibly H. pylori

Hormones: hypothyroidism, estrogen excess

Metabolic: kidney disease, electrolyte imbalances (severe), porphyria, heavy metals


Physiology of Bowel Movements


Stomach Acid

A healthy bowel movement basically requires the entire digestive tract to function properly. This starts in the stomach with proper stomach acid. Sufficient stomach acid is required to trigger the release of cholecystokinin and secretin, hormones that regulate the release of pancreatic enzymes and bile in the small intestine. Cholecystokinin is also involved in the gastrocolic reflex, which is very important for regular bowel movements. The gastrocolic reflex is the physiological process by which a meal stimulates the motility of the large intestine1. This is why most people have a bowel movement after their morning coffee or their morning meal. 

So proper stomach acid initiates a cascade of events that are important to a healthy bowel movement. This may be why many medications that reduce stomach acid, such as proton-pump inhibitors have a side effect of constipation2. This may also be why H. pylori infection in the stomach can also be associated with constipation3. H. pylori, in order to survive in the stomach, actually reduces stomach acid. 

To test your stomach acid, you can do a Heidelberg test. To test for H. pylori, you can do a urea breath test or stool antigen test. If your doctor already has an endoscopy planned, then they can test for H. pylori from a biopsy sample. The currently available stool PCR tests for H. pylori are not accurate. 

If you think your stomach acid is low, consider practicing good eating hygiene to give your body a chance to regulate stomach acid before a meal. Also, talk to your doctor about supplementing with digestive bitters or betaine HCl. 


Pancreatic Enzymes

Pancreatic enzymes are released into the small intestine in response to hormonal signals. These enzymes will help to digest food so nutrients can be absorbed in the small intestine. Insufficient pancreatic enzymes can lead to a variety of digestive symptoms, which can include constipation, though typically involves diarrhea.

Testing for pancreatic insufficiency is relatively easy. The stool can be tested for pancreatic elastase-1, a pancreatic enzyme that is not broken down in the digestive tract and is therefore, a good surrogate marker of pancreatic exocrine function. Less than 200 mcg of elastase per gram of stool is considered pancreatic insufficiency. In integrative medicine, we consider optimal to be greater than 500 mcg/g. 

Chronic pancreatitis is the most common cause of exocrine pancreatic insufficiency (EPI)4. Celiac disease, pancreatic cancer, cystic fibrosis, and diabetes are other causes of EPI4. Small intestine bacterial overgrowth (SIBO) is also linked with EPI, though the mechanism is not clear4. SIBO may cause inflammatory changes in the pancreas, but also insufficient pancreatic enzymes can cause microbiome alterations.

If you think you have low pancreatic enzymes, talk to your doctor about using supplemental or pharmaceutical digestive enzymes.



Bile is made by the liver, stored in the gallbladder, and released during meals to digest fat. Studies have shown that people with constipation have altered bile acid metabolism—they make different amounts of bile acids and not at the expected times of the day5. Essentially, slower motility may be associated with lower bile acid synthesis. Bile acids affect muscle contractions and secretions in the large intestine, all of which can impact bowel movements6. Researchers have even used synthetic bile acids to treat constipation with success7, all of which suggests that low bile acids may play a role in constipation. 

Various dysfunctions in the liver and gallbladder may result in low bile acids. However, identifying these issues can be difficult. Blood tests may include bilirubin or 7AC4. While bilirubin testing is readily available, it does not rule out all issues with bile acids. 7AC4 is a marker of bile acid synthesis but it is not available at most labs. Various imaging studies can be used to assess blockages and flow issues in the gallbladder but those can be more invasive procedures. Stool can be tested for bile acids and fecal fat, but those also have limitations. First, stool bile acid testing is not readily available and it is used to diagnose high bile acids in cases of diarrhea—it may not be helpful in identifying low bile acids in constipation. The amount of fat in the stool can indirectly indicate a problem with bile acids but it also may indicate a problem with absorption, so it is not the best test for low bile acids either.

If you think your bile is low, talk to your doctor about using digestive bitters, NAC, or phosphatidylcholine. It is very important to make sure you don’t have gallstones before using supplements.



For healthy bowel movements, food must flow through the gut in a timely manner. It usually takes 24-48 hours for food to complete its passage through the intestinal tract, but normal is considered anywhere from 10-73 hours8. Food may sit in the stomach for 2-5 hours, in the small intestine for 2-6 hours, and in the large intestine for 10-59 hours8. A delay in any location may result in constipation, but particularly in the large intestine. If you are experiencing abdominal distention, severe abdominal pain, nausea, vomiting or heartburn along with your constipation, that may indicate a motility disorder in the upper GI tract (stomach or small intestine). If constipation is the only significant digestive symptom, the motility disorder may just be in the large intestine. However, not all constipated patients have a motility disorder.  

Proper motility requires the right combinations of neurotransmitters, hormones, and neuropeptides at the right time in digestion. This also requires that the gut’s nervous system (enteric nervous system) properly communicates with the rest of your body’s nervous system. And it also requires that the muscles in the digestive tract are able to receive those signals from the nervous system.

So a wide variety of issues may result in motility disorders. This can include some sort of dysfunction in the nervous system, such as dysautonomia or a traumatic brain injury. This can also include damage to the nervous system from certain autoimmune diseases, high blood sugar from diabetes, chronic infections, and environmental toxins. Medications such as anticholinergics, antispasmodics, anticonvulsants, antidepressants, antihypertensives, antipsychotics, calcium channel blockers, and opiates can negatively impact motility in the gut.

Issues with connective tissue can also interfere with the nervous system properly communicating with the gut. This can include autoimmune diseases affecting connective tissue (scleroderma, lupus, etc.) or hypermobility syndromes such as Ehlers Danlos Syndrome. 

There also can be other issues with communication between the muscles in the gut and the nervous system that can be classified as outlet dysfunction. This is the inability to coordinate a bowel movement and this is present in about 50% of constipation. For many people, this is actually an acquired condition. If constipation has gone on for a long time, it may progress to outlet dysfunction. If you routinely ignore the urge to defecate, this can progress to outlet dysfunction (common in children). If you have overused stimulant laxatives, this can progress to outlet dysfunction. Also, if there is pelvic floor dysfunction (possibly secondary to childbirth), this can cause outlet dysfunction constipation.  

Hormones can also impact motility. For example, low thyroid hormones in hypothyroidism and Hashimoto’s can cause constipation. Estrogen decreases GI motility12, so this may contribute to constipation symptoms in the first half of the cycle, the follicular phase. If you experience excessive rise in estrogen before ovulation or if you have too much estrogen during the luteal phase, this may also contribute to constipation at other times of the menstrual cycle. Progesterone also slows down motility13, so constipation in the luteal phase may also be related to progesterone. This constipation will improve once progesterone and estrogen levels drop, triggering your period. 

There are a wide variety of tests for assessing motility but they are not necessarily readily available. Many patients struggle to get doctors to order these tests or insurance to cover them. Tests include manometry, dynamic scintigraphy, rectal sensitivity testing, sitz markers, barium studies, and a smart pill. The smart pill provides information about motility throughout the entire digestive tract compared to the other studies. If you suspect pelvic floor dysfunction, you may consider an assessment by a pelvic floor physical therapist. 

An at home assessment of motility, which is not without significant limitations, involves consuming 1-2 cups of beets and then timing how long it takes for your stool to turn red. 

If you have a motility disorder, it is important to identify and treat the cause of the motility disorder. In the meantime, you can ask your doctor about using prokinetics to stimulate motility. There are a wide variety of pharmaceutical and natural prokinetic agents. The best prokinetic depends on the location of the motility disorder.



The microbiome also has a very large impact on bowel movements through a variety of mechanisms. First, microbiome metabolites can impact motility in the gut. Methane gas, produced by organisms such as Methanobrevibacter, can slow down transit time and peristalsis, resulting in constipation9. Methane gas can affect the small intestine or the large intestine, depending on where the methane-producing microbes are located. They can be overgrown in the small intestine as well as the large intestine.

If you have high levels of methane producers, talk to your doctor about allicin, oregano, or partially hydrolyzed guar gum.

Sufficient levels of butyrate in the large intestine is also important for healthy motility. Butyrate may regulate serotonin in the gut, which can increase peristalsis10. So low butyrate producers may be causing or contributing to constipation. 

Low Bifidobacterium may also contribute to constipation11, though research has not been consistent or conclusive. 

If your butyrate producers or Bifidobacteria are low, talk to your doctor about using prebiotics such as inulin, resistant starch, arabinogalactan, xylooligosaccharides, and others.

High hydrogen sulfide producing bacteria may also play a role in constipation. Traditionally, diarrhea has been associated with high hydrogen sulfide producers, like Bilophila and Desulfovibrio, but clinically, many practitioners see constipation. Since hydrogen sulfide producers metabolize bile acids in the large intestine, the mechanism for causing constipation may have to do with bile acids. 

If your hydrogen sulfide producers are elevated, talk to your doctor about using bismuth subsalicylate, inulin, and other herbs and probiotics.

Also in clinical practice, we sometimes see high Proteobacteria causing constipation, but high Proteobacteria can result in a wide variety of digestive symptoms. If your Proteobacteria is elevated, you will first need to determine which specific Proteobacteria are causing the elevation to determine the best treatment options.

Constipation is a complicated, multifactorial symptom. In conventional medicine, the standard of care is to treat with laxatives and not to do any testing. So it can be very difficult for patients to get to the bottom of their constipation. So it is important to find a practitioner who will assess your full medical history to consider all of the above factors and then order the right tests to identify the right treatments. Because constipation is never caused by a laxative deficiency. 




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