SIBO Fatigue: How To Heal Your Gut and Regain Your Energy

SIBO fatigue: Woman with a headache sitting on a couch and holding a mug

Feeling tired all of the time? Experiencing regular aches and pains? Small intestinal bacterial overgrowth, or SIBO, could be the underlying cause of these and other symptoms, including mood disorders, brain fog, headaches, and body pain. SIBO fatigue can drain you of the energy you need for basic daily tasks and affect your mood and overall well-being.

Since SIBO fatigue and other symptoms overlap with many health conditions, it’s easy for traditional medicine practitioners to overlook SIBO as a possible root cause of non-digestive symptoms. Fortunately, the best functional medicine doctors have a keen understanding of gut health and its overall impact on the body.

In this article, we’ll explain what SIBO is, discuss five of its most commonly misunderstood symptoms, and go over the best ways to improve SIBO long-term.

What Is SIBO?

The small intestine typically has low levels of bacteria. SIBO is when bacteria that normally live elsewhere in your digestive tract overgrow in your small intestine.

The SIBOIBS Connection

Research has found a strong correlation between SIBO and irritable bowel syndrome (IBS) [1], suggesting bacterial growth in the small intestine is one of the likely reasons for IBS symptoms. Research suggests that over one-third of IBS patients have SIBO and IBS patients are five times more likely to test positive for it versus healthy controls [2].

Other research shows a correlation between SIBO, celiac disease, and inflammatory bowel disease (IBD) [3, 4].

Diagnosing SIBO

SIBO is diagnosed through a glucose or lactulose breath test, which measures hydrogen and methane gas levels in the gut. A positive SIBO test result shows the presence of hydrogen and/or methane-producing bacterial overgrowth in the small intestine.

Not everyone with a positive SIBO breath test result shows clear symptoms of SIBO. If you’re not showing SIBO symptoms but have a positive breath test, there is likely no need for treatment.

5 Commonly Misunderstood SIBO Symptoms

SIBO patients often have symptoms of gastrointestinal distress, such as stomach distension, bloating, abdominal cramping, excess gas, diarrhea, and constipation.

However, SIBO can affect more than just your gut. Some patients have a mix of digestive and non-digestive symptoms. Others have only non-digestive symptoms, which can make it difficult to connect the dots to SIBO.

The following five SIBO symptoms are often associated with other ailments. That’s why those experiencing these symptoms are advised to visit a functional medicine doctor who is well-versed in diagnosing SIBO to develop a long-term treatment plan.

1. Fatigue

There’s not much research specific to SIBO fatigue. However, one study points to imbalanced gut bacteria and SIBO in chronic fatigue syndrome patients [5].

  • Additional research shows a clear pattern of fatigue across other gut conditions. Fatigue has been identified as a symptom in more than half of IBS patients (who may also have SIBO) [6, 7]. 
  • Over 60% of individuals with non-celiac gluten-sensitivity reported tiredness as a symptom [8].
  • Nearly half of IBD patients with Crohn’s disease and ulcerative colitis claimed to suffer from fatigue and an overwhelming feeling of tiredness [9, 10]. 

Two more studies show that gut treatments are helpful for improving fatigue: 

  • In one study, treating leaky gut reduced fatigue and other symptoms in patients with chronic fatigue syndrome [11]. 
  • Another study shows low FODMAP diet improved fatigue in patients with IBS and fibromyalgia [12]. 

We often see the connection between fatigue and SIBO in the clinic. Patients generally report increased energy levels when SIBO is treated. Christine’s story is a great example of this.

2. Mood Disorders 

Once again, there’s not much research on the link between SIBO and mood disorders. However, one study of internal medicine outpatients found a correlation between mood disorders and GI conditions including SIBO [13].

Additional studies provide insights into depression, anxiety, and gut health:

  • One study surveyed patients with both IBS and a mood disorder. Two-thirds of this population experienced IBS before they had mood symptoms [14]. This implies gut disturbances may be a source of anxiety and depression.
  • Another study found that 27% of patients seeking treatment for depression also meet the criteria for IBS, and up to 90% of IBS patients seeking medical attention have major depression or other mental health issues [15]. 
  • A randomized clinical trial linked short-term feelings of depression to gluten consumption in non-celiac gluten-sensitive individuals [16].

3. Rosacea

Rosacea is an inflammatory condition of the blood vessels most often seen on the face. One study shows a much higher prevalence of rosacea in SIBO patients compared with healthy controls [17]. However, the study also yields a promising result: 93% of rosacea patients with SIBO experienced a complete elimination or significant improvement in rosacea lesions post-SIBO treatment.

4. Restless Leg Syndrome

Restless leg syndrome (RLS) is a neurological sensorimotor condition that creates an uncontrollable urge to move your legs. A couple of studies link RLS to SIBO:

  • In one study, 59% of RLS patients tested positive on a SIBO breath test [18].
  • Meanwhile, in another small study, 10 out of 13 patients with both RLS and SIBO saw at least an 80% improvement in their RLS symptoms after treatment [19].

5. Joint Pain and Headaches

In our experience, joint pain is a common complaint among gut patients. Interestingly, one small study reveals a two-week elemental diet (a gut therapy often used for SIBO patients) helped improve joint stiffness and pain in rheumatoid arthritis patients [20].

Headaches are another symptom commonly seen in gut conditions like SIBO:

  • Migraine patients may be more likely to have IBS [21].
  • In a survey of gluten-sensitive individuals, 54% of participants noted headaches as a symptom [22].
  • In a small study of non-celiac gluten-sensitive patients, dietary changes reduced the impact of migraines significantly [23].

How To Improve SIBO Fatigue and Other Symptoms

SIBO fatigue: Variety of ingredients on a black surface

SIBO is not always resolved quickly; however, it’s usually possible to significantly reduce symptoms in a matter of weeks. A comprehensive treatment approach that includes diet and other supports like antimicrobials, enzymes, and probiotics is usually the most successful for SIBO patients [24, 25].

1. SIBO Diets 

Below, we’ll discuss the three diets that can help improve SIBO fatigue and other symptoms: low-FODMAP diet, specific carbohydrate diet (SCD), and elemental diet.


A low-FODMAP diet eliminates certain carbohydrates — fermentable oligosaccharides, disaccharides, monosaccharides, and polyols — that may lead to an overgrowth of bad bacteria and a general feeling of malaise. Consuming high-FODMAP foods can trigger bloating, cramping, diarrhea, and constipation, along with non-digestive symptoms like fatigue and brain fog [26]. 

While there is no direct evidence showing the low-FODMAP diet is helpful for SIBO, several meta-analyses and clinical trials suggest a low-FODMAP diet is beneficial for IBS and IBD patients [27, 28, 29, 30]. Since those conditions are closely linked with SIBO, we can infer that a low-FODMAP diet can help with SIBO symptoms, too.

Specific Carbohydrate Diet

The specific carbohydrate diet, or SCD, was developed about 100 years ago to manage celiac disease in children. Today, the diet is a protocol for many patients with IBD and other autoimmune disorders to help manage symptoms [31, 32, 33, 34].

SCD eliminates complex carbohydrates (disaccharides, oligosaccharides, and polysaccharides) that may be difficult for your body to break down, leading to an overgrowth of bad bacteria in your gut and eventually SIBO.

SIBO patients who still experience symptoms with a low-FODMAP diet may find relief with the SCD. However, the SCD is much more restrictive and therefore not recommended unless there have been no signs of improvement with a low-FODMAP diet. Only simple sugars, fruits, and vegetables with simple sugars are allowed on the SCD.

Elemental Diet

When other dietary changes don’t improve SIBO symptoms, the elemental diet may be a viable approach. 

The elemental diet eliminates solid foods and replaces them with nutrient-rich liquid meals to give your digestive system a break and reduce exposure to irritants. Doing this can calm gut inflammation by starving bad gut bacteria that contribute to SIBO.

There isn’t much research regarding the elemental diet and SIBO, but one study shows a 14-day elemental diet normalized lactulose breath tests and improved IBS symptoms in 80% of patients with SIBO [35].

Since this is the most challenging of SIBO diet approaches, we usually try other treatment options first.

A Note About SIBO Diets

Therapeutic diets are not meant to be followed closely over the long term. Elimination diets like the low FODMAP diet or SCD diet help you identify trigger foods that cause your worst symptoms. The long-term goal is to broaden your diet as much as possible while gaining knowledge about what specific foods you need to avoid to manage your symptoms.

After the initial elimination phase (normally two weeks), you can gradually reintroduce foods and monitor any symptoms. Foods that don’t trigger a reaction can be safely added back to your diet. On the other hand, foods that trigger symptoms should be avoided.

2. SIBO Supports

In addition to improving your diet, you can incorporate some digestive support during SIBO treatment: probiotics, digestive enzymes, antimicrobials, and stomach acid support.


Probiotics are good bacteria that keep your gut healthy. Contrary to a commonly held opinion that probiotics should not be used for SIBO treatment, a meta-analysis of multiple studies shows probiotics actually improve outcomes for SIBO patients [36]. Specifically, probiotics reduce bacterial overgrowth and hydrogen concentrations, leading to a reduction in abdominal pain and other symptoms.

Digestive Enzymes

Many SIBO symptoms are the result of the body’s inability to digest certain carbohydrates and sugar. Digestive enzymes may help limit SIBO symptoms and encourage total digestion of these foods, as this randomized control trial shows [37].

Stomach Acid Support

Low stomach acid is a common condition that increases the risk of developing SIBO [38, 39, 40]. That’s because stomach acid plays an important role in neutralizing the bacterial content of food before it’s digested. 

For those with low stomach acid, supplementing with Betaine HCl can help to restore acid levels in the stomach and can help to inhibit the growth of bacteria.

3. Antimicrobial Treatment

Antimicrobials are strong herbal medicines intended to kill or limit the growth of microorganisms in the small and large intestine. Plant-based antimicrobials can correct your intestinal ecology without creating any further imbalances in your gut microbiome. 

One study shows herbal antimicrobial therapy works as well as the prescription antimicrobial Rifaximin in treating SIBO symptoms [41].

Not all SIBO patients require treatment with herbal microbials. It’s best to first try diet and digestive supports before taking a course of herbal microbials.

Find Relief From SIBO Fatigue Today

Doctor giving a health plan to her patient

If you regularly struggle with fatigue, brain fog, and other unexplained symptoms, SIBO may be the root cause. That’s why it’s important to pay attention to improving your gut health.

SIBO has a reputation for being difficult to treat and relapses can happen. However, treatment success is possible when treatments are tailored to individual patients. A trusted functional medicine practitioner can be very helpful in confirming a SIBO diagnosis and personalized a long-term treatment plan to prevent bacterial overgrowth, and SIBO fatigue, from recurring.

Dr. Ruscio, DC and his qualified staff at Austin Functional Medicine have years of experience helping patients with gastrointestinal health, nutrition, and health coaching. If you’re regularly struggling with unexplained symptoms, make an appointment with us and start your journey toward a healthier life. New patients are currently accepted in-person and via telemedicine.


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