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Symptoms of SIBO You May Not Expect

Written by Dr. Michael Ruscio, DC on January 27, 2025

Written by Dr. Michael Ruscio, DC on January 27, 2025 — Reviewed by Heidi Turner

• Symptoms of SIBO|
• What Causes SIBO|
• SIBO Treatment|

The beneficial bacteria you’ve come to know as probiotics are most beneficial when they stay where they belong—in the large intestine. When excess bacteria grow in the small intestine, your healthcare professional may provide a SIBO diagnosis. 

Small intestinal bacterial overgrowth (SIBO) is known to cause many digestive symptoms like gas, bloating, constipation, and diarrhea. But did you know that SIBO may also cause non-digestive symptoms like fatigue, brain fog, poor mood, headache, joint pain, and much more?

If you struggle with symptoms like these, which may seem unrelated to gut health, it’s worth investigating whether or not they’re symptoms of SIBO.

Let’s take a closer look at the array of symptoms you may encounter that could point to SIBO as the underlying cause.

Symptoms of SIBO

SIBO symptoms can vary from person to person. While some may have digestive symptoms, others have no symptoms at all. 

More frustrating for SIBO patients is the long list of non-digestive symptoms they may experience. Some symptoms of SIBO (fatigue, poor mood, brain fog, and “lack of well-being” for example) can seem vague with no evident cause. It can be surprising to learn that they often originate in the gut.

Here’s an overview of the broad range of possible SIBO symptoms.

Digestive Symptoms

More often than not, patients with SIBO have symptoms similar to irritable bowel syndrome (IBS). These include 1:

• Bloating
• Distension
• Indigestion
• Cramping
• Reflux
• Flatulence
• Motility issues like diarrhea and/or constipation.

Research suggests that SIBO is the cause of many cases of IBS (though not all) and may also be associated with inflammatory bowel disease (IBD)—including colitis and Crohn’s disease 2. Associations between SIBO and celiac disease and non-celiac gluten sensitivity have also been found 3.

Fatigue

Of all the symptoms of SIBO, fatigue is often the most debilitating and frustrating.

There’s plenty of anecdotal evidence to suggest that fatigue is common for SIBO patients—I observe this in the clinic all the time. But, it’s important to always check clinical observations against science. Unfortunately, I haven’t found any studies that investigate whether SIBO causes fatigue, so there is simply a lack of research information in this area.

However, if we look at studies into other gastrointestinal conditions, some associated with SIBO 1 2, we see a clear pattern of fatigue across gut conditions.

• IBS: One study found fatigue was very common in patients with irritable bowel syndrome (IBS), and it was associated with poor quality of life 4. A meta-analysis of 17 studies found more than 50% of IBS patients have fatigue symptoms 5. 
• Non-Celiac Gluten Sensitivity: A very large study of non-celiac gluten sensitivity found a lack of well-being and tiredness were reported as the most common symptoms after bloating and abdominal pain 6. Sixty-eight percent of gluten-sensitive individuals reported a lack of well-being, and 64% reported tiredness.
• IBD: Fatigue is also a symptom in nearly 50% of patients with inflammatory bowel disease (IBD), according to another review 7. This includes patients with Crohn’s disease and ulcerative colitis. One survey of IBD patients found lack of energy was more burdensome than digestive symptoms 8.

SIBO can cause inflammation in the gut. Since much of the nutrition you get from food is absorbed in the small bowel, inflammation in the gut can lead to malabsorption. That can then lead to nutrient deficiencies or malnutrition, and in turn—fatigue. Also pain, in general, can lead to mental and physical fatigue.

Gut treatments have also been shown to help with fatigue: 

• Treating leaky gut reduced fatigue and other symptoms in patients with chronic fatigue syndrome 9. 
• A low FODMAP diet improved fatigue in patients with IBS and fibromyalgia 10. 

We often see this pattern in the clinic—clients often tell me they got their energy back after improving their gut health.

So, while we wait for more research specific to SIBO, it’s safe to connect fatigue with gut conditions in general.

Mood Disorders

There’s quite a bit of research connecting general gut health to mood disorders, and a couple of new studies look at SIBO specifically. 

One study found that patients with SIBO experienced anxiety and depression as well as reduced tryptophan metabolism in the gut. Tryptophan is a precursor to serotonin, a hormone that’s important for mood stability and a sense of well-being. Being able to metabolize tryptophan properly can directly affect mood.

 After they took rifaximin (an antibiotic to treat SIBO), their anxiety and depression improved, and their tryptophan levels improved 11. 

Another study found that SIBO was more common in patients with severe IBS, anxiety, and depression 12.

We can also look to studies on other digestive issues for insights into the gut’s connection to depression and anxiety.

Multiple survey studies show that a majority of IBS patients report experiencing depression and anxiety 4 13. Some study subjects with non-celiac gluten sensitivity also reported anxiety (39%) and depression (18%) 6.

Can gut treatments help with mood disorders?

• A meta-analysis of 10 clinical trials showed probiotics are effective for treating mild to moderate depression 14.
• Probiotics and a healthy diet were shown to reduce anxiety symptoms in more than half of the subjects in a systematic review of 21 anxiety studies 15.
• Finally, additional research suggests that a gluten-free diet may improve the mood of those with celiac disease, IBS, and non-celiac gluten sensitivity 16.

Rosacea

One compelling study links SIBO and rosacea 17, an inflammatory condition of the blood vessels most often seen on the face—red, flushed cheeks, sometimes bumpy and blotchy, sometimes with visible capillaries.

Researchers in this study found a much higher prevalence of rosacea in SIBO patients when compared to healthy controls. What’s very exciting is that 93% of rosacea patients with SIBO saw complete elimination or significant improvement in rosacea lesions after SIBO treatment 17. In this study, the treatment was a targeted antibiotic called rifaximin. However, neomycin is also used to treat SIBO in a clinical setting.

In a 2024 trial looking at rosacea and SIBO, supplementation with oral and topical herbal antimicrobials reduced SIBO and led to a 20% improvement in rosacea. It also boosted short-chain fatty acid production in the gut 18.

Restless Leg Syndrome

Restless leg syndrome (RLS) has also been connected to both SIBO and IBS. 

One study found SIBO and IBS are common in patients with RLS 19, with 59% of RLS patients testing positive on a SIBO breath test. Another small study treated 13 patients with both RLS and SIBO using a combination of an IBS medicine (tegaserod), zinc, a daily probiotic, and rifaxamin 20. Ten of the 13 patients achieved at least 80% improvement in their RLS symptoms.

Joint Pain and Arthritis

Another common complaint I see in my clients with gut problems is sore joints and arthritis. One small study used a two-week elemental diet (a gut therapy often used for SIBO patients) to improve joint stiffness and pain in subjects with rheumatoid arthritis 21. 

Headache

SIBO patients may also suffer from headaches. Once again, this symptom is commonly seen in other gut conditions.

Research suggests migraine patients may be more likely to have IBS 22. In a survey of gluten-sensitive individuals, 54% identified headaches as a symptom 6.

In one small study of patients with non-celiac gluten sensitivity, dietary changes significantly reduced the impact of migraine on patients’ daily activities 23.

What Causes SIBO?

SIBO, like many other gut conditions, falls under the broad term of digestive tract dysbiosis. Dysbiosis simply means an imbalance of intestinal bacteria, fungi, and other microorganisms.

There should be a balance of beneficial, neutral, and even a few potentially harmful microbes in the large intestine (like E. coli). In a healthy person, those microbes are diverse and abundant, with the healthy bugs keeping the potentially harmful ones in check.

The majority of gut microbes live in the large intestine, while the small intestine is home to a much smaller number of bacteria in a healthy person.

In a person with SIBO, there are too many microbes in the small intestine, hence “bacterial overgrowth”. With too many microbes in the wrong place, they are more harmful than helpful.

This overgrowth could be a result of underlying conditions or risk factors like 24: 

• Poor diet (high in sugar and processed foods)
• Low stomach acid (because it fails to kill harmful bacteria before it enters the small intestine)
• Prolonged use of proton pump inhibitors
• Motility disorders like gastroparesis (when your food doesn’t move through your intestines at a quick enough pace)

• Anatomical abnormalities like small bowel diverticulosis
• A surgical procedure like a gastric bypass that left a blind loop in the small bowel unintentionally where unwanted bacteria may collect
• Other medical conditions like diabetes, obesity and hypothyroidism 25 26 27

Why SIBO Leads to Non-Gut Symptoms

When you understand the connections between a balanced gut microbiome, your immune system, inflammation, and nutrient absorption, it’s easier to understand how a condition like SIBO can lead to a wide array of health problems.

Gut dysbiosis, inflammation, immune reactions (and overreactions), as well as nutrient malabsorption can lead to a wide array of symptoms and chronic health conditions, including malnutrition.

Immune System

The health of your digestive tract and the health of your immune system are closely linked. Unbalanced gut bacteria activate your immune system. In fact, your small intestine contains the greatest density of immune cells in your body 28. A chronically over-activated immune system leads to inflammation and immune reactions 29 30.

Inflammation

As a result of gut dysbiosis, your over-reactive immune system produces inflammation. Chronic inflammation is now understood as the root cause of many health conditions 31, both minor and life-threatening. The long list includes rosacea 32, cardiovascular disease 33 34, and Parkinson’s disease 35—conditions that have been associated with SIBO in research 17 36 37.

Nutrient Absorption

Chronic inflammation leads to digestive tract lining damage 38. This can impair nutrient absorption. Severe cases of SIBO can lead to nutritional deficiencies. Malabsorption of fats and carbohydrates, vitamin deficiencies (especially vitamin B12, A, D, E, K, and iron), and, for some, weight loss and anemia also result from SIBO 39.

Testing for SIBO

It’s possible to confirm SIBO with diagnostic testing—a glucose or lactulose breath test, which measures the methane and hydrogen content of your breath—but I find that my clients can get relief from certain gut health protocols, even without the test.

In many cases, it makes sense to save money on testing and go straight to a gut health protocol that will likely provide health benefits either way. Most natural therapies treat many causes at once. Interventions like probiotic supplements and a low FODMAP diet will likely help get your health and wellness back on track.

SIBO Treatment

SIBO treatment is best done through a combination of research-backed tactics that address intestinal dysbiosis and improve overall digestive health. Depending on the patient, this may include:

• Probiotics 40 –  In the clinic, we see the best results with the triple therapy approach
• Diet 41 –  I always advocate starting with the least restrictive low-FODMAP diet first, then graduating to the Specific Carbohydrate Diet (SCD) if needed, and then to the Elemental Diet if the first two aren’t providing relief.
• Fasting 42
• Digestive supports 43
• Herbal antimicrobials like oil of oregano 44
• Antibiotic drugs such as Rifaximin or neomycin

Why Try the Low FOMAP Diet, and What To Do if It Doesn’t Work?

A low FODMAP diet reduces or eliminates specific foods that fall within the category of FODMAP. FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. That might not mean much, but those words all describe specific constituents in carbohydrates, including otherwise healthy fruits and vegetables.

High-FODMAP foods include things like cruciferous veggies (broccoli, cauliflower), legumes (lentils and beans), and certain fruits, especially dried. Foods like these can be irritating and further exacerbate symptoms of SIBO because they are harder to digest. Because they are poorly absorbed in the small intestine, they provide a food source for the bacteria living there. This creates gas, which leads to symptoms like bloating and stomach pain. 

For a complete FODMAP food list you can download this free low FODMAP guide.

By reducing FODMAPs, you can:

• Reduce inflammation and leaky gut
• Starve SIBO 
• Reduce symptoms of SIBO
• Improve motility

I ask my clients to follow this diet for four to six weeks. If they don’t experience relief from this diet, then they may need to further restrict to the Specific Carbohydrate Diet (SCD). 

The Specific Carbohydrate Diet removes more carbohydrates than the low FODMAP diet. Starchy vegetables, grains, and all processed sugars are excluded. Only simple sugars, fruits, and vegetables with simple sugars are allowed 45. 

The Elemental Diet would be the next step if the carb-restricted options don’t provide relief. It’s a predigested shake, meant to give your digestive tract a temporary break to heal and repair.

Poor Gut Health May Be the Root Cause of Your Fatigue

If you struggle with symptoms like fatigue, brain fog, poor mood, headaches, and other unexplained symptoms, I encourage you to pay attention to improving your gut health. Don’t let inflammation and immune dysregulation wreak havoc on your health.

You don’t need a gastroenterologist to provide a SIBO diagnosis and treatment plan for you to begin to take action on your health.

By introducing probiotics and removing the foods that could be causing the biggest issues, you’re most of the way there. In some cases, you may need a doctor to prescribe a targeted antibiotic, but many of our clients are able to clear SIBO without a prescription.

My book, Healthy Gut, Healthy You, provides a step-by-step process for better gut health and fewer burdensome symptoms. Or head over to our clinic and set up a time to talk with a trained practitioner. We’d love to help you get started.

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