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The Hormone Clarity Guide
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.
Some of the most striking SIBO cases I see in practice don’t present with digestive symptoms at all.
Joint pain. Skin flares. Bladder urgency. Brain fog. These patients have often been worked up extensively — rheumatology, dermatology, neurology — without a clear answer. When we test for SIBO, it comes back positive. When we address it, the systemic symptoms improve.
This is the part of SIBO that most people — and many clinicians — miss. Digestive complaints like bloating, gas, constipation, and diarrhea are common, but they’re not required. SIBO can drive significant inflammation in the skin, joints, bladder, muscles, and brain without obvious gut involvement. Here’s the mechanism.
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:
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.
LPS endotoxemia doesn’t develop in isolation. The microbiome is the terrain that determines how much LPS gets produced, how well the intestinal barrier holds, and how effectively your immune system moderates the response.
When keystone gut bacteria are depleted — which is increasingly common — gram-negative populations can expand unchecked, LPS production increases, and barrier integrity declines. This is something I assess routinely using Tiny Health shotgun sequencing, which gives a much more complete picture of the microbial ecosystem than standard stool panels.
My Gut Microbiome Guide covers the terrain-level picture in more depth — why microbial diversity is declining in Western guts, what that loss means for immunity and inflammation, and what evidence-based rebuilding actually involves.
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.
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.
Chronic pain, systemic inflammation, nutrient deficiencies that don’t respond to supplementation, and a long list of food sensitivities: these are patterns I investigate as a connected picture, not isolated complaints.
SIBO testing is a reasonable starting point if you have any combination of digestive symptoms alongside inflammatory, autoimmune, or unexplained systemic symptoms. A breath test can confirm bacterial overgrowth; from there, investigation into the microbiome and gut barrier gives the full picture.
If you’re ready to investigate what’s driving your symptoms, my Monthly Care program is where that work happens — testing, interpretation, and a protocol built around your specific findings.
Stay tuned for our next post, where we’ll discuss how to identify SIBO and outline effective treatment options.
Do you have any questions about this article or about root cause functional medicine?
Dr. Laura Paris is a women’s health specialist who provides integrative, holistic Functional Medicine care and Acupuncture at her two clinics in Capitola and Monterey, California. She also works with women remotely in the United States through telehealth appointments.
Her unique approach to root-cause medicine includes a whole-body view including hormones, digestion, microbiome and gut health, nutrition, autoimmunity and inflammation, blood sugar regulation, and energy metabolism. Learn more about Dr Laura Paris here, and message her directly here.
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I have sibo and it’s bad on me
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.
Apparently the auto correct. Changed some of my words. Enteropathic. Coli, iliocecal valve.
Ilene I am sorry but I am not able to give personal medical advice here, I hope you understand.
i really enjoyed reading this article, it has a lot of valuable info it’s the first time to know it, thanks for sharing
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).
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.
What types of fecal tests do you order for people with colitis. Specifically do you use VIOME or one of the other companies that test good and bad gut bacteria?
I use shotgun sequencing technology which maps out the entire microbiome and the percentage that each microbe takes up. Currently Tiny Health lab is the best option in the United States for shotgun sequencing because they provide all the data (Viome does not). They also have a good price point and a user-friendly online interactive platform.