Intestinal Dysfunction: Symptoms, Tests, and Treatments

Your source for quality supplements

Shop Now

Intestinal Dysfunction Symptoms, Tests, Treatments in Lyme Disease Image

About Intestinal Dysfunction
Symptoms, Testing, and Treatments

Many with Lyme disease and tick-borne infections have intestinal dysfunction caused by the illness or treatment. Symptoms and signs of intestinal dysfunction include:

  • intestinal and abdominal bloating and gassiness,
  • constipation,
  • loose stools,
  • diarrhea,
  • undigested food, and
  • abdominal cramping.

In this article I lay out a screening and testing approach I use with my patients at Marty Ross MD Healing Arts. While the focus of this article is about tests and a screening questionaire, I also provide treatment ideas through links to other articles on this site or limited recommendations here.

Note, this article does not address constipation. Some people that have methane producing small intestinal bacteria overgrowth (SIBO), which I describe below, can have constipation as a key part of that diagnosis. For those people treating SIBO can improve the constipation. In the future, I plan to write an article about constipation.  

First - Intestinal Yeast Overgrowth

Too many yeast in the intestines can occur before treating Lyme. But treating Lyme with herbal and prescription antibiotics can kill good intestinal bacteria, leading to intestinal yeast overgrowth and intestinal dysfunction.

Don’t Trust The Tests - A Yeast Questionnaire is Best

Testing for yeast has many problems and is often not correct. These tests include

  • stool studies to see if there are large quantities of yeast,
  • blood tests to see if someone has antibodies against yeast, and
  • urine tests to see there are excessive organic acids, like arabinose, produced by yeast.

Because these tests are not reliable, I use a yeast screening tool. This tool looks at risk factors for yeast and intensity of yeast symptoms. In my experience, I find improvements in intestinal dysfunction when I treat intestinal yeast overgrowth with antimicrobials when a score is over 140.

Yeast Treatment Steps

See Kills Yeast: A Brief Guide for treatment ideas.

Why Yeast Testing Is Not Accurate

Stool studies often do not show excessive yeast when someone has a screening score of 140 or higher. Yet, I usually find great benefit in treating yeast in these situations. That is why I say stool studies are not accurate.

Yeast normally live in healthy amounts in our intestines. Usually intestinal yeast do not lead to intestinal dysfunction because other germs and bacteria in the gut keep the yeast under control. Because yeast live in the gut normally, they can trigger the immune system to make antibodies. Detecting yeast antibodies in the blood does not mean yeast are growing too much. It just means the immune system has seen the yeast even at healthy levels.

Yeast do make organic acids, like arabinose and tartaric acid that get absorbed into the blood. These are then cleaned out by the urine where they can be detected. However, there are no studies that validate whether elevated organic acid tests in the stool truly mean that someone has increased intestinal yeast. In addition, there are no studies that show if too many yeast always produce excessive organic acids like arabinose or tartaric acid. So - these tests are not reliable.

Next Up - SIBO

Too many bacteria living in the small intestines can trigger gassiness and bloating. This condition is called Small Intestine Bacterial Overgrowth (SIBO). It can sometimes lead to poor food digestion too. If a person has a normal yeast screening score and is gassy or bloated - or is treated for intestinal yeast, but does not improve - then it is time to test for SIBO.

The SIBO Tests

There are two ways to test for SIBO. One is to have a culture of your small intestines. If too many bacteria grow, then a person has SIBO. An intestine specialist has to perform this test using a scope which is passed through the mouth into the intestines. Because of cost and comfort issues, this test is often not done.

The easiest way to test is called a SIBO Breath Test. It is not as exact as the test above. In the breath test a person swallows lactulose or glucose sugar water. Then, over a two or three hour time period you collect breath samples. If a person’s breath contains high amounts of hydrogen or methane, the test is positive. This test can be performed at home. In my practice, I use the test kit from Genova Diagnostics.

The downside to the SIBO Breath Test is it only finds up to 70 percent of people that have the illness. So you could have a negative test, but still have the condition. For this reason, the small intestine culture is much more accurate.

SIBO Treatment Steps

Read Small Intestinal Bacterial Overgrowth (SIBO) in Lyme Disease for treatment steps.

When All Else Fails - Comprehensive Stool Analysis

Think of getting a comprehensive stool analysis if the yeast questionnaire is negative or if treating yeast does not correct cramping, loose stools and/or constipation. Get a SIBO test done too while doing a comprehensive stool analysis if you have lots of gassiness and bloating in addition to cramping, loose stools and/or constipation after treating for intestinal yeast overgrowth.

Genova Diagnostics, Doctor’s Data, GI Map, and Great Plains Lab all offer a comprehensive stool analysis. For this test, you collect a sample of stool and then send it to the lab for evaluation. The lab will look for

  • parasite and bacterial infections that should not be there,
  • amounts of common bacteria and parasites that should be there,
  • calprotectin,
  • pancreatic elastase,
  • beta-glucuronidase, and
  • zonulin.

If testing shows you have a parasite or a bacterial infection, treat these with the appropriate herbal or prescription antimicrobial based on the infection.

About Calprotectin

Calprotectin is an inflammatory chemical that is present in Crohn's Disease and/or Ulcerative Colitis.

Steps to Adress Elevated Calprotectin

If Calprotectin is elevated, you should see a GI specialist to have a colonoscopy evaluation of your intestines to see if you actually have one of these conditions.

About Elastase

Elastase is an enzyme made by the pancreas. If it is low, it means your pancreas is not making enough digestive enzymes. Lack of digestive enzymes leads to poor digestion and loose stools with cramping. A cause of this can be dysfunction of the intestinal skin (epithelium) caused by imbalance of good intestinal bacteria. Healthy intestinal epithelium signals the pancreas to make pancreatic digestive enzymes. This imbalance in healthy bacteria is called intestinal dysbiosis.

Steps to Address Elevated Elastase

The treatment for pancreatic insufficiency includes probiotics and pancreatic enzymes.

About Beta-glucuronidase

Beta-glucuronidase is an enzyme made by unhealthy bacteria. It breaks off water soluble chemicals that liver detoxification places on fat-based toxins. These now water soluble toxins mix with stool and then get pooped out. But excessive beta-glucuronidase breaks the water soluble group off these toxins. These fat-based toxins then get reabsorbed back into the bloodstream. So elevated Beta-glucuronidase means you have intestinal dysbiosis.

Steps to Address Elevated Beta-glucoronidase

The treatment for this is probiotics and killing any bacteria pathogens or infections that show up in the stool studies with an appropriate antimicrobial targeting those germs. For information about how to use probiotics see Probiotic Strategies in Lyme Disease Treatment.

About Zonulin

Zonulin is a chemical made by intestinal epithelium when there is dysbiosis or in reaction to gliadin found in wheat. Zonulin causes gaps to develop between intestinal cells - leading to leaky gut syndrome. In leaky gut syndrome gaps in the intestinal barrier allow partly digested food, toxins, and allergens to reach immune cells that line the intestines triggering allergy and inflammatory chemical production - including cytokines. So increased Zonulin can indicate leaky gut syndrome. However, there is a question about the accuracy of this test. It is possible to have leaky gut syndrome while having normal zonulin. And the test at times may falsely determine zonulin even when it is not present.

Steps to Treat Leaky Gut Syndrome

See Leaky Gut Syndrome: A Treatment Guide for more information.

Watery Stools Only

If your main problem is watery stools with cramping, get a stool test for Clostridium difficile (C. diff) toxin. This test is run by a regular lab. C. diff is a bacteria that lives in healthy amounts in the intestines. At times when a person is on antibiotics or has been on antibiotics, this germ can grow too much releasing a toxin that causes cramping and watery diarrhea. 

Steps to Treat C. Difficile

For more information see C. Difficile Diarrhea: Prevention Treatment.


The ideas and recommendations on this website and in this article are for informational purposes only. For more information about this, see the sitewide Terms & Conditions.


View Citations

  1. Sturgeon C, Fasano A. Zonulin, a regulator of epithelial and endothelial barrier functions, and its involvement in chronic inflammatory diseases. Tissue Barriers. 2016;4(4):e1251384. Published 2016 Oct 21. doi:10.1080/21688370.2016.1251384 (View
  2. Serek P, Oleksy-Wawrzyniak M. The Effect of Bacterial Infections, Probiotics and Zonulin on Intestinal Barrier Integrity. Int J Mol Sci. 2021;22(21):11359. Published 2021 Oct 21. doi:10.3390/ijms222111359 (View)  
  3. Vanuytsel T, Tack J, Farre R. The Role of Intestinal Permeability in Gastrointestinal Disorders and Current Methods of Evaluation. Front Nutr. 2021;8:717925. Published 2021 Aug 26. doi:10.3389/fnut.2021.717925 (View
  4. Siddiqui I, Majid H, Abid S. Update on clinical and research application of fecal biomarkers for gastrointestinal diseases. World J Gastrointest Pharmacol Ther. 2017;8(1):39-46. doi:10.4292/wjgpt.v8.i1.39 (View
  5. Herman A, Herman AP. Could Candida Overgrowth Be Involved in the Pathophysiology of Autism? Journal of Clinical Medicine. 2022; 11(2):442. (View)
  6. Rezaie A, Buresi M, Lembo A, et al. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. Am J Gastroenterol. 2017;112(5):775-784. doi:10.1038/ajg.2017.46 (View)
Marty Ross MD Image

Follow Marty Ross MD

See full profile: on LinkedIn.
See the latest: on Twitter, YouTube, and Instagram.

About The Author

Marty Ross, MD is a passionate Lyme disease educator and clinical expert. He helps Lyme sufferers and their physicians see what really works based on his review of the science and extensive real-world experience. Dr. Ross is licensed to practice medicine in Washington State (License: MD00033296) where he has treated thousands of Lyme disease patients in his Seattle practice.

Marty Ross, MD is a graduate of Indiana University School of Medicine and Georgetown University Family Medicine Residency. He is a member of the International Lyme and Associated Disease Society (ILADS), The Institute for Functional Medicine, and The American Academy of Anti-Aging Medicine (A4M).

keep up with our LATEST!

Subscribe to receive our FREE pdf download book: How to Successfully Treat Lyme: Key Info before You Treat or Treat Again & The Ross Lyme Support Protocol; health tips; updates; special offers; and more.