IBS Not Getting Better?

IBS Not Going Away? Here are 5 Reasons You Can’t Heal 

If you have Irritable Bowel Syndrome (IBS) you may have been told that your condition is permanent and something “you’ll just have to live with”.

However, after years of practicing functional medicine and battling my own digestive issues, I can tell you with confidence that IBS can be resolved (or at the very least, improved).

IBS is not your problem, it’s just a diagnosis. 

The first step to healing IBS is not to just treat the symptoms but to identify the underlying cause of your irritated bowels. Historically, we’ve thought IBS was rooted in stress and anxiety (hence, using antidepressants as treatment). But more recently we’ve discovered that the gut microbiome plays a huge role. Specifically, a gut infection called small intestinal bacterial overgrowth (SIBO).1

In either case, IBS is usually complex and multi-factorial, and treatment must address both underlying gut infections and upstream digestive issues. These upstream issues include low stomach acid, motility disorders, gallbladder disease, pancreatic enzyme deficiency, hypothyroidism and others.

If you’ve had trouble fully healing your gut or have experienced recurrent SIBO—even after changing your diet, taking medications, supplements etc.—addressing these upstream issues could be the key to solving your digestive issues for good.

Ready for your ah-ha moment? Then let’s look at each of these a little more in-depth including their symptoms and solutions.

1: Low stomach acid (hypochlorhydria)

I realize you’ve probably heard the exact opposite, but I’ve observed many patients with digestive complaints struggle with having low stomach acid vs. too much.

This is called hypochlorhydria, or deficiency of hydrochloric acid.

The symptoms of low stomach acid can include bloating, belching, feeling tired after meals, trouble digesting foods (especially meat), and even heartburn (I’ve experienced this one myself).

As we know, many patients with digestive complaints are often treated for excess stomach acid with acid blocking medications like Proton Pump Inhibitors (PPIs). There’s a time and a place for these medications (so talk to your doctor!), but they can deplete certain nutrients, do not address the underlying cause, and can even exacerbate digestive issues like IBS,2 and SIBO.3

Low stomach acid is a significant risk factor for bacterial overgrowth since it is the first barrier that helps us break down bacteria from foods and oral secretions4 (one day I’ll write more about the importance of good oral hygiene for gut health!)

At least two studies show that acid blocking medications cause bacterial overgrowth in the small intestine in 50% of patients.5,6

Hypochlorhydria is also a set up for gut infection with H. Pylori7, food sensitivities/allergies,8 and malabsorption of protein, iron, B12 and minerals like calcium and magnesium.

Conventional medical literature acknowledges low stomach acid as an issue associated with things like:

  • Aging
  • Chronic stress
  • Thyroid disease
  • Autoimmune conditions
  • Chronic H pylori infection
  • Nutritional deficiencies (especially zinc and vitamin B1)
  • Gastric bypass surgery
  • And of course, acid blocking medications like PPIs

It has long been known as a problem among naturopathic and integrative doctors, and I believe that hypochlorhydria is more common than most conventional doctors might think.

I tell my patients that God gave us an acidic stomach for a reason: to help digest food and keep pathogens out. 

Thus, if you have low stomach acid, this is an issue that must be addressed if the gut is ever to fully heal.

How do you find out if you have low stomach acid?

A gastroenterologist can measure intragastric pH, but this is not done very often in the clinical setting.

A simple and cost effective way to do this at home is to self-test using a high quality Betaine Hcl supplement. Ideally this should be done under the supervision of a functional medicine physician.

I have my patients start with 1 capsule with a meal containing protein, then increase by 1 capsule at each consecutive meal until they feel warmness, burning or GI discomfort. If they’re able to take a high dose (6 capsules) without ever feeling a thing, my suspicion is that they have hypochlorhydria.

Note: I do NOT attempt a HCL test if patients have peptic ulcer disease (PUD); take NSAIDs, steroids, or other medications that can cause an ulcer. Also people on acid blocking medications (PPI or H2 blockers) cannot use Hcl.

I might also recommend a thiamine (Vitamin B1) supplement, as thiamine deficiency has been shown to inhibit gastric acid secretion in at least one animal study,9 and is thought to play a role in gut motility by way of the autonomic nervous system.

2: Motility disorders

The first barrier function against bacterial overgrowth in the small intestine is adequate stomach acid, and the second is gut peristalsis—the involuntary movement of the intestinal muscles that transports the contents of your gut.10

Between meals and when sleeping, the migrating motor complex (MMC) directs a cyclic, recurring pattern in the stomach and small bowel.

After eating, stronger and more irregular waves of peristalsis help empty your stomach and move food through your GI tract.

Issues with motility can lead to SIBO due to stasis of food and bacteria in the stomach and small intestine.11

Risk factors for poor motility and slow peristalsis include:

  • Celiac disease
  • Adhesions from endometriosis and abdominal surgeries (including c-sections)
  • Surgery that alters the structure and function of the digestive tract
  • Small intestine strictures caused by radiation, medications, and/or Crohn’s disease
  • Long-standing diabetes
  • Connective tissue disorders

Clinically I find that motility issues are often rooted in the gut-brain and thyroid-gut connections.

For example, when the nervous system is in a state of chronic stress, our fight-or-flight response (the sympathetic nervous system) takes over. Thus, we need to activate our rest-and-digest response (the parasympathetic nervous system) for better gut motility.

Same if your thyroid is underactive, so it pays to have that properly checked. A 2007 study found among people with a history of autoimmune hypothyroidism, 54 percent had a positive breath test for SIBO (small intestinal bacterial overgrowth) compared to 5 percent of controls.12.Since thyroid hormones are also essential to peristalsis/gut motility,13 hypothyroidism can create a “perfect storm” for unhealthy bacteria to thrive in the small or large intestine. The thyroid-gut connection is so important (and interesting) that I wrote an entire article about just that…so be sure to check it out.

Solutions for motility really depend on the underlying cause—some tools include stress reduction, meditation, deep breathing, yoga, intermittent fasting, and visceral massage for those with adhesions from endometriosis and abdominal surgeries. I might also recommend supplements/ medications like bitters, 5-HTP (a serotonin precursor),14 Low-dose Naltrexone (LDN),15,16, 17 or thyroid medication (if indicated).

3: Gallbladder disease and insufficient bile flow

Gallbladder disease is very common, and I’d bet you know at least one person who has had their gallbladder removed because of acute cholecystitis (aka: inflammation of the gallbladder) likely due to gallstones.

There are a lot of different risk factors for gallbladder disease, and there are a few ways we might be able to help prevent gallstones and stimulate bile flow naturally.

First, here’s a brief overview of how our gallbladder works: Cholecystokinin (CCK) is a hormone that acts on two types of receptors found in the gut and central nervous system. CCK is released after meals and stimulates the production of bile in the liver as well as its release from the gallbladder. CCK also stimulates release of pancreatic enzymes.18

The main symptom of gallbladder disease is right upper quadrant and epigastric pain (pain felt below your ribs in your upper abdomen), especially after meals.

It’s also common to see problems with fat malabsorption and deficiency of fat-soluble vitamins A, D, E, and K since bile is important for breakdown and absorption of fats.

But what’s under-appreciated is bile’s role as an antimicrobial.

“Bile salts are potent antimicrobial agents and are an important component of innate defenses in the intestine, giving protection against invasive organisms. They play an important role in determining microbial ecology of the intestine and alterations in their levels can lead to increased colonization by pathogens.”19

Bile even plays a role in gut motility by way of the migrating motor complex (MMC)—read above!20

This would suggest that the healthy bile flow is intimately involved with the gut microbiome, and that gallbladder disease is a set up for imbalances in gut bacteria, such as dysbiosis and SIBO (both causes of IBS)—which is what I see clinically.

My favorite way to support bile flow is to take bitters before meals. Bitter herbs like dandelion and gentian have been used for centuries to help prime the digestive processes.

Also, certain foods called cholagogues—radishes, arugula, endive, watercress, and other spicy bitter vegetables—may help stimulate bile flow (plus, they taste good!).

Finally, I often recommend a supplement called phosphatidylcholine which is a component of healthy bile.21

For people who have had their gallbladder removed, I usually recommend taking supplemental ox bile and digestive enzymes with meals.

4. Pancreatic enzyme deficiency

The pancreas is both an endocrine and exocrine organ—which means it produces both hormones (insulin) and also pancreatic enzymes.

Pancreatic enzymes are critical to healthy digestion and gut function, as they help break down protein into amino acids, carbohydrates into simple sugars, and fats into fatty acids and cholesterol.

Risk factors for pancreatic enzyme deficiency (also known as pancreatic exocrine insufficiency or PEI) include cystic fibrosis, pancreatic cancer, chronic pancreatitis, Celiac disease, and Crohn’s.22

Clinically I see this (and most things) on a spectrum. Meaning, early stages are more mild and not as obvious, but can worsen over time if not addressed. This is the beauty of working with a functional medicine doctor, we specialize in recognizing issues early on before they become a full-blown, painful problem.

Symptoms of pancreatic enzyme deficiency can include mild abdominal discomfort, bloating, cramping, and gas. If these symptoms sound similar to SIBO that’s because there is a proven connection between PEI and SIBO.23 Literature also describes “loose, greasy, foul-smelling, voluminous stools that are difficult to flush, float, or stick to the bowl.”24

We can test for pancreatic insufficiency by measuring a fecal elastase level.

Pancreatic enzymes are available as a prescription medication. I also recommend them as a supplement for some people and generally prefer the animal based pancreatic enzymes because plant-based enzymes are grown on a mold medium, which makes them unsuitable for people with mold sensitivity (like me).

5. Treating infections

Addressing the previous four upstream issues is key. However, if you want to overcome chronic digestive issues for good we need to look beyond things like “inflammation” and “food sensitivities” and address the underlying infection(s).

This is best accomplished by working with an integrative functional medicine doctor who can recommend the appropriate diagnostics and a combination of natural remedies and medication to completely address the infection.

I can’t stress how important lab work is here! Because if you don’t know what type of infection you’re dealing with (bacterial overgrowth, candida/fungal overgrowth, parasites, etc.) you cannot get the treatment you need to heal.

For example, just a few decades ago in most integrative health circles Candida Albicans overgrowth was considered the “cause” of every type of digestive complaint. Likewise, many doctors got on the parasite-train and believed everyone with chronic digestive complaints had parasites. However, though it’s true that Candida and parasites can contribute to digestive issues, the only way to know for sure is to test not guess!

Need some help swimming upstream?

Click here to learn more about me and my functional medicine approach to individualized healthcare.

Ready to get started now? I’m currently accepting a limited number of new patients based in Colorado, Texas, and Michigan. Click here to apply and we’ll be in touch soon!


  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366247/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991651/
  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609274/
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609274/
  5. https://pubmed.ncbi.nlm.nih.gov/8881809/
  6. https://pubmed.ncbi.nlm.nih.gov/8307444/
  7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991651/
  8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528619/
  9. https://pubmed.ncbi.nlm.nih.gov/716330/
  10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609274/
  11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099351/
  12. https://academic.oup.com/jcem/article/92/11/4180/2598186
  13. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4056127/
  14. https://www.gastrojournal.org/article/S0016-5085(19)36715-0/abstract
  15. https://accpjournals.onlinelibrary.wiley.com/doi/10.1002/phar.2086
  16. https://journals.sagepub.com/doi/full/10.1258/ebm.2011.011f08
  17. https://sa1s3.patientpop.com/assets/docs/255330.pdf
  18. https://www.yourhormones.info/hormones/cholecystokinin/
  19. https://www.frontiersin.org/articles/10.3389/fmicb.2017.01581/full#h1
  20. https://pubmed.ncbi.nlm.nih.gov/7714463/
  21. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113756/
  22. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858980/
  23. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858980/
  24. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858980/

About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas.  She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP)

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