The Short Answer

SIBO (small intestinal bacterial overgrowth) occurs when bacteria from the large intestine move into the small intestine, where they ferment food and produce gas, causing bloating, constipation, or diarrhea. While testing can help confirm SIBO, addressing the root cause — whether poor digestion, low stomach acid, chronic stress, or impaired brain-gut communication — is essential to prevent relapse and restore digestive health.

What is SIBO, and why does it cause digestive symptoms?

If you have gas, bloating, diarrhea, or constipation, or all of the above, you may have SIBO.

SIBO stands for small intestinal bacterial overgrowth, a condition in which bacteria from the large intestine move into the small intestine where they do not belong.

These bacteria feed off the sugars and carbohydrates you consume, causing them to produce large amounts of gas. This leads to bloating, belching, and flatulence, but also constipation or diarrhea, depending on the type of gas produced.

Too many of these bacteria in the small intestine also inflame the intestinal lining, damaging it and causing leaky gut (intestinal permeability). Intestinal permeability allows undigested foods, bacteria, yeast, and other foreign invaders into the bloodstream. This eventually sets the stage for inflammation, autoimmunity, and chronic disease to develop.

Testing and managing SIBO

There are many tests and protocols available for SIBO. Lab tests have many false negatives, so listening to your symptoms is equally important as test results.

Managing SIBO often requires a diet that restricts most foods except meats and a limited variety of vegetables. Treatment protocols involving supplements and/or medications exist to address SIBO, and sometimes it’s a matter of trial and error to find an approach that works for your system.

However, treating the bacterial overgrowth alone isn’t enough; if you want to prevent relapse, you need to understand why you developed SIBO in the first place.

Common causes of SIBO in autoimmune patients

Autoimmune patients and those with chronic illness are particularly vulnerable to digestive dysfunction. Common causes of SIBO include:

• Food poisoning
• Poor diet and excess sugar
• Low stomach acid
• Repeated antibiotic use
• Chronic stress
• Problems with brain function or vagal health

The brain-gut connection and SIBO

Poor brain function is a very common but often overlooked cause of SIBO. The gut and the brain maintain close communication with one another through the vagus nerve, which means impaired brain function causes gut problems such as SIBO.

When brain function is poor, the digestive tract cannot produce sufficient digestive juices and hormones. Motility, the movement of food through the intestines, slows down so that food sits longer in the gut. This leads to bacterial overgrowth. The valve between the small and large intestines does not stay shut properly, allowing bacteria from the colon to enter the small intestine. These are examples of how poor brain function and vagal dysfunction lead to SIBO.

This is why we often see SIBO alongside brain injuries, brain inflammation, brain degeneration, and brain aging, conditions that affect people across many autoimmune conditions and chronic illnesses.

The elderly are particularly vulnerable to malnutrition as a result of SIBO. So are individuals born with autism and other neurodevelopmental disorders. Fortunately, simple exercises for the vagus nerve, which connects the brain to the gut, help improve digestion and prevent relapses of SIBO.

Why addressing root causes matters for autoimmune health

For autoimmune patients, including those managing Hashimoto’s low thyroid or other chronic conditions, SIBO often signals a deeper digestive or neurological issue. Treating only the bacterial overgrowth without addressing what caused it leaves the door open for relapse.

At RedRiver, we work with patients to determine whether their SIBO stems from stress, poor stomach acid, brain-gut dysfunction, or dietary factors. Once the root cause is identified, sustainable dietary and therapeutic changes can be made to restore digestive health and reduce the autoimmune trigger that SIBO represents.

Contact RedRiver Health and Wellness to work with a functional medicine doctor who understands how SIBO connects to autoimmunity and chronic illness.