Stomach and Intestine Problems: Natural Medicines

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Stomach and Intestines Problems in a Lyme disease treatment Image from Marty Ross MD

About Stomach and Intestine Issues in Lyme Disease

As a result of Lyme disease, side effects of medications or supplements, and disruption of the normal healthy bacterial/yeast balance in the intestines you may have problems with your stomach or intestines. These issues include:

  • nausea,
  • pain or burning in the chest, area below the chest bone, or the abdomen,
  • loose stools or diarrhea,
  • intestinal gassiness and bloating, and/or
  • abdominal cramping.

Because there are a variety of causes to these symptoms, it is helpful to have a physician or other licensed health care practitioner evaluate any of these issues.

In this article I review the helpful and effective natural medicine approaches to correct stomach, food pipe and intestine issues. I include the name of the herbs and the effective dosing. 

Nausea in Lyme Disease

Nausea can be an effect of the illness or a side-effect of medications, especially tetracyclines like doxycycline and minocycline. It may often be alleviated with gingerpeppermint, or spearmint tea or with chewed deghlyzerated licorice (DGL). It is not clear how ginger, peppermint, or spearmint work. DGL works best when chewed. Saliva and licorice work together to form a gelatinous mucus layer that protects the stomach lining from irritating medicines, and this allows inflamed tissue to heal.

Esophagitis or Gastritis in Lyme Disease

Esophagitis and Gastritis are due to inflammation of the lining of the food pipe and the lining of the stomach respectively. Symptoms of these include a burning or gnawing pain under the chest bone for esophagitis and in the area below the chest bone for gastritis. Both of these conditions are also helped with chewed DGL.

Diarrhea/Abdominal Pain or Cramps in Lyme Disease

Diarrhea with or without abdominal pain or cramps can be due to leaky gut syndrome from yeast overgrowth, C. difficile infection, or a direct side effect of antibiotics. Healthy functioning intestines are populated with a balance of good bacteria and yeast. The yeast and bacteria compete with each other for intestinal territory.

Good bacteria decline due to the use of

  • antibiotics,
  • environmental stresses,
  • immune suppression from chronic illness,
  • the use of steroids, and/or
  • other factors.

When this happens, yeast can grow to take over the territory vacated by the good bacteria. The imbalance of yeast and bacteria is called dysbiosis.

Dysbiosis from too few healthy bacteria and/or too many yeast leads to leaky gut syndrome and poor digestion. In this situation there is a breakdown of the protective gelatinous covering of the intestinal lining and damage to the cells that line the intestines. In leaky gut syndrome toxins and allergic agents are absorbed into the bloodstream creating toxin excess, inflammation, and allergic reactions. Indigestion can also occur because there is poor breakdown and absorption of nutrients in the intestines.

Overgrowth of C. difficile bacteria in the intestines can be a cause of ongoing watery diarrhea with or without crampy abdominal pain. It is caused by being on antibiotics. C. difficile normally lives in the intestines in balance with the other intestinal organisms. However some antibiotics result in the germ becoming excessive. In excess it releases a toxin that leads to severe diarrhea and abdominal cramping. There is a stool test that physicians and healthcare practitioners use to determine if a person has this infection. When it is present, antibiotics must be stopped and an effective one for C. difficile started. Saccharomyces Boulardi is a beneficial yeast that lives in the intestines that can help in C. difficile problems.

To treat crampy abdominal pain and diarrhea that is not a direct side effect of a medication or the result of C. difficile, there are a number of things to do. Replenishing the healthy bacteria of the intestines with a good probiotic is helpful. At times adding Saccharomyces Boulardi, a healthy yeast that lives in the intestines, is helpful too. Carob powderfound at grocery stores helps to constipate. See if there is yeast overgrowth of the intestines and treat it. See Kills Yeast: A Brief Guide for more information about this. If yeast are not the problem then L-glutamine can help. It helps rebuild the gelatinous intestinal mucous lining and is a cell fuel for intestinal cells that helps them heal. The gelatinous layer can also be helped with an herbal combination product that supports the mucous layer. Such products can include DGL, plantains, slippery elm, and marshmallow. Digestive enzymes can help break food down when healthy bacteria are not able to do so.


Some people with Lyme also develop constipation with infrequent bowel movements and cramping. One cause of this is a palsy of the nerves that make the intestines work due to nerve injury from the Lyme infection. Constipation is also a side effect of medications such as narcotics for pain or anti-depression medications. Constipation is alleviated when water is held within the intestines. This is accomplished by increasing fluid intake and taking foods or nutrients that attract water. Foods rich in fiber attract water. In addition high dose Vitamin C and magnesium salts attract water too. Foods rich in fiber also stimulate the lining of the intestines which cause the muscles within the intestinal lining to squeeze the intestinal contents forward.

Options in Lyme Disease Treatment


Try ginger, spearmint, and peppermint alone or in combination first. If these do not work then try the deghlyzerated licorice first alone then in combination with the teas.

  • Ginger. Drink or sip as often as needed throughout the day. Create a tea using tea in bags from the grocery store (use organic when possible to avoid toxins). You can also make ginger tea from scratch by slicing or grating peeled or unpeeled ginger into small pieces and placing a handful into boiling water for 10 minutes. Note: unpeeled ginger can have mold on its covering. Strain the liquid before drinking.
  • Spearmintand/or Peppermint. Drink or sip as often as needed throughout the day. Create a tea using tea in bags from the grocery store (use organic when possible to avoid toxins.)
  • Deghlyzerated Licorice 75 mg. Chew 2 pills of each 20 minutes before eating 3 times a day.  (Chewing is required for saliva to mix with the licorice to fully activate its beneficial effects.)

Esophagitis or Gastritis

  • Deghlyzerated Licorice 75 mg. Chew 2 pills 20 minutes before eating 3 times a day. (Chewing is required for saliva to mix with the licorice to activate its effects.)

Diarrhea with/without Abdominal Pain or Cramps

When diarrhea comes on with the addition of a new herbal or prescriptive anti-microbial it is often due to a side effect of the medicine. Increasing your probiotic as a first step is often helpful or adding Saccharomyces Boulardi. Sometimes it is necessary to use both a probiotic and Saccharomyces Boulardi. Add Carob powder if necessary too.

  • Probiotic 5-10 billion cultures. Start at 2 pills 1 time a day. For diarrhea double the dose to 2 pills 2 times a day. Be sure to take it as far away from antibiotics as possible. (Use a high quality strain that uses strains that are proven to re-populate the intestines. The product should make such claims on the label.)
  • Saccharomyces Boulardi 250 mg. Start at 2 pills 1 time a day. For diarrhea double the dose to 2 pills 2 times a day. Be sure to take it as far away from anti-yeast medications as possible.
  • Carob powder. Find it at your grocery store as an organic source. Take 1 tablespoon 1 to 3 times a day added to food.

See the background section above for recommendations regarding yeast. Treat yeast if present first as recommended in Kills Yeast: A Brief Guide Also if having severe diarrhea, your physician should test for C. difficile. If you have C. difficile, in addition to the antibiotic prescribed for this take Saccharomyces Boulardi during the treatment and in an ongoing basis to prevent return of C. difficile. When probiotics, Saccharomyces Boulardi, or treating yeast (if present) do not entirely work, then add L-Glutamine or digestive enzymes or do both. For ongoing burning abdominal pain around the belly button or below the belly button, sometimes working with an herbal combination product to rebuild the gelatinous coating of the small intestines can be helpful too.

  • L-Glutamine. Take 3-12 grams a day in 3 divided doses throughout the day.
  • Digestive Enzymes.  1 to 3 pills 20 minutes before meals 3 times a day. Adjust based on beneficial effect.
  • Herbal Combination Product.  1 pill 3 times a day. This could include a combination of DGL, plantains, slippery elm, and marshmallow.


Increase fluid intake to 48 to 64 oz of water daily. Have a diet rich in fiber by increasing the intake of fruits, vegetables, whole grains, and legumes or beans. If this does not work then add Vitamin C or magnesium or a combination of both.

  • Vitamin C.  Start at 2000mg a day and increase up to 10,000mg a day by adding 1,000mg a day. Adjust until you have desired stool frequency and consistency.
  • Magnesium Malate or Citrate 150 to 200mg.  Take 1 pill in the am and 2- 3 pills a night times a day. Adjust to desired stool frequency and consistency. Magnesium at night can also help with sleep.


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.

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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).

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