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Alyssa Simpson RD, CDE, CLT
Alyssa Simpson

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Sibo Doctor Approved
certified gastrointestinal nutritionist
Sibo Doctor Approved
certified gastrointestinal nutritionist

What Are SIBO Complications and Side Effects? Answers to Your SIBO FAQs

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Woman sitting on the arm of a couch looking concerned about the complications of SIBO.

Table of Contents

Got questions about SIBO complications and side effects? Well, I’ve got answers! In this installment of our SIBO FAQ series, we’re diving into the nitty-gritty details about what can happen when you’re dealing with small intestinal bacterial overgrowth. From preventing SIBO recurrence to understanding its potential connections with other health issues, I’ve got you covered.

How can I prevent SIBO from recurring?

Unfortunately, SIBO has a high recurrence rate, especially if it was only treated with antibiotics. Antibiotic treatment may be able to deal with a single occurrence of SIBO. But unless you address the underlying health or dietary issues that allowed SIBO to develop in the first place, it’s likely to come back. I highly recommend you work with a qualified healthcare practitioner who can do the following:

✔ Help identify the underlying causes of your SIBO

✔ Develop a tailored treatment plan

✔ Recommend long-term preventative measures to keep your SIBO from coming back

Obviously this is an article, so I can’t diagnose you or recommend a personalized treatment plan here. But there are some general things that I can recommend that help many people with SIBO (and a variety of other digestive conditions):

? Keep your intake of sugar and processed food low.

? Focus on stress management techniques.

? Exercise regularly.

? Improve your sleep.

What are the complications of SIBO?

Like most health concerns, ignoring SIBO won’t help. SIBO isn’t going to go away on its own. And when it’s left untreated, SIBO can lead to complications. Because the bacteria are competing for a share of the food you eat, many of these complications come in the form of nutrient deficiencies.

Fat, Protein, and Carbohydrates

When you have an overgrowth of bacteria in your small intestine, your body can have trouble breaking down both macronutrients (fat, protein, and carbs) and certain micronutrients (vitamins and minerals). When you aren’t able to absorb the nutrients from the food you eat, you can end up with unintended weight loss and even malnutrition.

The bile salts produced by your liver digest fats. But the bacteria that are growing out of control when you have SIBO break down the bile salts before they can do their job. And when you aren’t breaking down your dietary fats, you can end up with diarrhea. And if the bacteria (and the undigested fats) harm the lining of your small intestine, you won’t absorb the carbohydrates and protein as well either.


When you can’t properly absorb the fats you eat, you also miss out on absorbing the fat-soluble vitamins (A, D, E, and K).

Bacteria in the small intestine also interfere with vitamin B12 — the vitamin that assists in the normal functioning of your nervous system. Vitamin B12 deficiency can lead to weakness, fatigue, tingling, numbness in your hands and feet, and eventually to mental confusion. And it’s possible that the damage to your central nervous system from B-12 deficiency may not be reversible.


Over time, SIBO-related damage can keep your body from properly absorbing the calcium you eat. That affects your bones — and can result in complications like osteoporosis. Poor calcium absorption can also eventually cause kidney stones.

Can SIBO cause weight gain?

SIBO is not typically associated with weight gain. It’s more likely to cause unintentional weight loss. But I definitely don’t recommend it as a diet plan! If that crossed your mind, you might want to go back and re-read the previous section on the damage SIBO can do.

Because SIBO interferes with your body’s ability to absorb nutrients from the foods you eat, it can cause unintentional or unexplained weight loss. But it doesn’t always. So if your weight has remained fairly constant, but you have other symptoms of SIBO, I recommend you see a qualified practitioner for testing.

Can SIBO cause anxiety and depression?

While SIBO itself is not a direct cause of anxiety and depression, it can certainly affect your gut health. And what happens in your gut can impact mental health issues including anxiety and depression. The gut-brain axis — the communication network between the gut and the brain — is deeply involved in regulating emotions and mental health.

Research suggests that imbalances in gut bacteria — like those seen in SIBO — can influence this axis and potentially contribute to mood disorders. And honestly, anything that negatively impacts your physical health is going to affect all areas of your life, including your mental well-being.

Is there a connection between SIBO and autoimmune diseases?

While research is ongoing, SIBO is a likely contributor to autoimmune disease — like inflammatory bowel disease (IBD), scleroderma, celiac disease, and Hashimoto’s hypothyroidism. One of the underlying causes of autoimmune disease is “leaky gut”.

Leaky gut occurs when the lining of the small intestine develops perforations — holes and becomes permeable. When this happens, partially digested particles of food escape the small intestine and enter the bloodstream where they trigger an immune system response. This immune response, especially when it happens over and over again, could contribute to the development or exacerbation of certain autoimmune conditions.

And yes, SIBO is likely to cause leaky gut.

How do I avoid SIBO complications?

Collaboration with a qualified healthcare practitioner is key in managing SIBO and its associated complications. A good practitioner can provide personalized guidance, develop a tailored treatment plan, and monitor your progress to ensure the best possible outcomes. Someone with lots of experience helping SIBO patients can guide you to the diet and lifestyle changes that will make the biggest difference in addressing your unique symptoms.

There is hope. I’ve helped dozens of people overcome their challenges with SIBO so they can stop worrying about their digestive symptoms and get back to living their lives. With a little help, you can take control of your digestive health and work towards alleviating SIBO-related complications.

Next week we’ll wrap up our final installment in the SIBO FAQ series, where I’ll address more burning questions and provide further insights into managing this complex condition. Remember, knowledge is power, and together we can tackle SIBO head-on.

If you’re ready for a personalized plan to address your digestive symptoms, I’m here for you. I’ve helped hundreds of people overcome digestive issues like SIBO, IBS, and more. You can schedule a consultation here.

In the meantime, there are things you can do today that can get you on the road to feeling better. Click the link below to download your free copy of the IBS Resource Guide. I wrote this guide specifically for people with IBS and SIBO. The resources in this guide are the ones I use every day with my patients.


Free IBS Resource Guide
The Top 5 IBS Resources I Use Every Day
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