SIBO Causes Whole-Body Pain and Inflammation

This is the second post in our series about Small Intestine Bacterial Overgrowth (SIBO). If you missed the first post, you can read it here.

You might believe that SIBO only affects those with digestive issues, but this is not always the case. SIBO symptoms typically include digestive discomfort like bloating, constipation, gas, or diarrhea. However, it’s possible to have SIBO without any noticeable digestive complaints. What many don’t realize is that SIBO can cause inflammation in other parts of the body, from the skin to the bladder, muscles, joints, and brain.

Woman with muscle pain from small intestine bacterial overgrowth

How SIBO Triggers Systemic Inflammation

Here’s a simple explanation of how SIBO causes inflammation and pain in other areas of your body:

In a healthy gut, the small intestine should have low bacterial populations, primarily aerobic, gram-positive bacteria like Lactobacillus. However, SIBO involves an overgrowth of anaerobic, gram-negative bacteria. These bacteria produce lipopolysaccharides (LPS)—a toxic endotoxin that can cause major problems.

Excessive LPS damages the lining of the small intestine, leading to leaky gut. This allows LPS to enter your bloodstream, triggering immune responses and inflammation throughout your body. This is called “LPS endotoxemia,” which is linked to many inflammatory and pain conditions, including:

  • High LDL cholesterol
  • Parkinson’s and Autism Spectrum Disorder
  • Interstitial cystitis
  • Autoimmune diseases like Hashimoto’s Thyroiditis and Rheumatoid Arthritis
  • Inflammatory pain syndromes such as fibromyalgia and osteoarthritis
  • Skin conditions like acne and rosacea

If you have an autoimmune disease or chronic inflammatory condition, it’s worth exploring whether SIBO could be contributing. If you also experience digestive issues like bloating, constipation, diarrhea, or gas, it’s a strong sign to test for SIBO.

SIBO and Nutrient Deficiencies

SIBO often results in malabsorption, leading to nutrient deficiencies. When the small intestine is inflamed, as it is with SIBO, your ability to properly digest food is compromised. It also affects your ability to absorb key nutrients. Studies show that SIBO is linked to deficiencies in vitamins A, D, and B12.

Bacteria in the gut need iron to create biofilms—sticky layers that shield them from the immune system. In cases of SIBO, bacteria use up your iron, leaving you deficient. If you have low iron levels despite taking supplements or eating iron-rich foods, SIBO may be the culprit. Additionally, SIBO is often linked to poor thyroid function, possibly due to the thyroid’s high need for iron.

You can test these vitamins and iron levels through a blood test. If you’re low in any of these, consider that SIBO might be a factor. To optimize your nutrient levels, you may need to address the underlying bacterial overgrowth and heal the small intestine lining.

SIBO and Increased Food Intolerance

We discussed how SIBO can lead to leaky gut. When this is present, undigested food particles can pass through your gut lining and enter your bloodstream. This can cause your immune system to react to these food particles, resulting in food intolerances and inflammation. If you have multiple food sensitivities, you likely have some level of leaky gut—which can be caused by SIBO.

Once SIBO is treated and the gut lining is healed, many people find they can tolerate foods they previously couldn’t. Leaky gut and food intolerances are often part of the broader picture of SIBO.

Ready to Heal from SIBO?

If you’re struggling with chronic pain, inflammation, or unresolved health conditions, SIBO could be the missing link. Addressing bacterial overgrowth in the small intestine can reduce systemic inflammation, restore nutrient absorption, and transform your health.

Take the first step today by scheduling a SIBO breath test. After your test, book a consultation with us to review your results and develop a customized treatment plan to target the root cause of your symptoms and help you feel your best.

Stay tuned for our next post, where we’ll discuss how to identify SIBO and outline effective treatment options.

Dr. Laura Paris is a women’s health specialist who provides Acupuncture and Functional Medicine care at her two clinics in Capitola and Monterey, California. She also works with women remotely in the United States through telehealth appointments. Learn more about Laura here, and message her directly here.

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7 Comments

  1. I just finished treatment of SIBO with Xifaxin and m feeling better. I also had empathic E. Coli and was treated with another antibiotic as well. My Calprotectin level was 1190 and normal should be under 50. I had a colonoscopy last week and have no Crohns or UC. I am feeling better,, but still have terrible bloating and cramps. I had a resection of my cecum, ascending colon and first part of my small intestine including my illegal valve which is no doubt the cause of my SIBO. I am wondering why my Calprotectin was so high. My gastro says it wasn’t because of the SIBO. What’s your opinion? I am waiting for results from biopsies for microscopic colitis, but do not think I have that.

    1. Apparently the auto correct. Changed some of my words. Enteropathic. Coli, iliocecal valve.

    2. Ilene I am sorry but I am not able to give personal medical advice here, I hope you understand.

  2. Great article! I have all the classic symptoms of SIBO, including food intolerances. Trio smart breath test confirmed it (methane). Three rounds of Xifaxan and metronidazole and I still have symptoms. It’s tough to get rid of, but especially with methane type (IMO).

    1. Agree! I had stubborn methane SIBO myself. Treatment should be for a full 28 days from my understanding, with the medications. And then it’s really important to address motility.

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