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sibo fatigue and treatment

SIBO Fatigue: Signs, Causes, and Ways to Treat Naturally

By:
Claire Lockridge, ND
Last Updated: March 27, 2025
Article contents

Small intestinal bacterial overgrowth (SIBO) is commonly associated with digestive symptoms such as gas, bloating, chronic diarrhea, constipation, abdominal cramping and increased or decreased hunger. However, SIBO can also lead to many symptoms outside of the digestive tract, including joint pain, headaches, brain fog and skin changes. One of the most common symptoms of SIBO is chronic fatigue.

SIBO can contribute to lower energy levels through a number of factors. Firstly, bacterial overgrowth can interfere with absorbing many essential nutrients, such as important vitamins and minerals. Lower absorption of these nutrients can lead to fatigue and poor energy. Secondly, the overgrowth can lead to inflammation in the gastrointestinal tract. This increased level of inflammation can trigger the body’s immune response, using up resources and contributing to lower energy. Finally, SIBO is often associated with poor sleep leading to lower energy throughout the day.

What Are the Common Signs and Symptoms of SIBO?

Signs and symptoms of SIBO can vary from person to person and can be more pronounced or mild based on a person’s pre-existing health status and the severity of the infection. Symptoms that are commonly associated with SIBO include:

Digestive Upset

Symptoms such as gas, bloating, and abdominal distention are commonly seen in SIBO patients. As the pathogenic bacteria ferment carbohydrates, this leads to increased levels of gas in the abdomen.

Altered Bowel Habits

Individuals with SIBO can often experience diarrhea, constipation or a combination of both. A hydrogen prominent SIBO is often associated with symptoms of diarrhea. The excessive bacterial overgrowth produces hydrogen gas, leading to rapid movement of stool through the digestive tract. In contrast, a methane predominant overgrowth is associated with constipation. Methane contributes to the slowing of intestinal mobility and subsequent constipation.

Fatigue

Fatigue is commonly seen in those with SIBO. This can be a combination of physical and mental fatigue. Physical fatigue often manifests as muscle weakness, reduced stamina, poor endurance, slow reflexes, and decreased coordination. Mental fatigue can include symptoms such as decreased focus, poor memory, difficulty concentrating and easily feeling overwhelmed.

Nutritional Deficiencies

Unintentional weight loss and low levels of many vitamins and minerals are commonly associated with SIBO. Weight loss is often seen in those with SIBO due to the malabsorption of many macronutrients, leading to an imbalance in caloric input vs output. Common nutrient deficiencies seen in SIBO include:

  • Vitamin B 12: B 12 is generally absorbed by the terminal part of the small intestine, known as the ileum. B12 is essential for red blood cell production and nerve function. Low levels of B12 can lead to symptoms of anemia and signs of poor nervous system health, such as numbness and tingling of the extremities.
  • Iron: Low absorption of iron can commonly lead to iron deficiency anemia. This can contribute to symptoms such as fatigue, hair loss and shortness of breath,
  • Vitamin D: SIBO can decrease the absorption of Vitamin D. Vitamin D is essential for bone health and immune system function.
  • Calcium: Along with vitamin D, calcium plays a vital role in maintaining healthy bones. Low levels of both can contribute to the weakening of the bones and increased risk of osteoporosis.
  • Magnesium: Magnesium is another essential mineral that can be depleted in those with SIBO. Lower levels of magnesium are associated with cramping, weakness and cardiovascular dysfunction.
  • Zinc: Zinc plays a crucial role in skin health and proper immune system function. A zinc deficiency can lead to symptoms such as impaired immune function, poor wound healing, and dry/ irritated skin.
  • Folate: Lower levels of folate are commonly seen in those with anemia. Low folate levels can lead to anemia and impaired DNA synthesis.

Mood Changes

SIBO can have a profound impact on mental health, mood and emotional well-being. The gut and brain are connected through the gut-brain access. This means that disturbances in gut health and the gut microbiome can impact mental health. Gut dysbiosis can alter the production of serotonin, an important neurotransmitter that plays a crucial role in mood regulation. Alteration in the production of serotonin has been linked to mood disorders such as depression and anxiety.

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What’s The Connection Between SIBO and Fatigue?

Many factors are present in SIBO that contribute to the lower energy levels and fatigue commonly seen in patients. Some of the main reasons why those with SIBO experience fatigue include:

Poor Nutrient Absorption

SIBO can negatively impact nutrient absorption through factors such as competing for nutrient absorption, increased inflammation, and damage to the gastrointestinal lining. All of these contribute to the decreased absorption of many macro and micronutrients.

Intestinal Inflammation

The presence of pathogenic bacteria can lead to increased inflammation of the gastro-intestinal tract. Inflammation is the body’s natural response to damage. However, chronic inflammation can lead to depletion of the body’s resources, and damage to the intestinal lining, and can often contribute to many symptoms seen in SIBO.

Increased Bacterial Metabolites

Increased bacterial metabolites are a significant feature of SIBO. The increased pathogenic bacteria ferment carbohydrates, leading to the production of metabolites, such as short-chain fatty acids and toxins. These can increase inflammation and irritation of the gut and continue to disrupt the gut barrier function. The increased production of toxins also places a further burden on the liver, which is the body’s main organ for detoxification.

Impairment of the Gut Barrier Function

The higher levels of inflammation seen in SIBO can lead to damage to the intestinal lining, leading to increased gut permeability, a condition commonly known as “leaky gut”.  This can allow toxins, bacteria, and undigested food particles into the bloodstream. This can trigger an immune response, leading to the depletion of the body’s resources, further contributing to the symptoms of low energy and fatigue.

happy full man touching tummy over kitchen

Natural Remedies for SIBO Fatigue and Other Symptoms

Dietary Changes

A Low FODMAP Diet

Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols, known as FODMAPs, are a group of short-chain carbohydrates that are often poorly absorbed in the small intestine. They are found in a number of foods, including apples, cherries, onions, garlic, wheat, and some dairy products. When these carbohydrates are consumed but not absorbed properly, they can begin to ferment, producing gas, possibly leading to increased gas, bloating and abdominal discomfort.

In regards to SIBO, a low FODMAP diet is often used as part of a management strategy to help decrease symptoms such as gas, bloating and altered bowel function. By reducing the intake of FODMAP foods, an individual can get short-term relief from some of the symptoms of SIBO. However, due to the restrictive nature of the diet, a low FODMAP diet is not recommended as a long-term treatment strategy and should be used along with other measures to eradicate bacterial overgrowth.

An Anti-Inflammatory Diet

Limiting the consumption of foods that are known to be pro-inflammatory can be helpful for those with SIBO. Because inflammation plays a significant role in the pathogenesis of SIBO, limiting foods that further promote inflammation can help to decrease symptoms and support recovery from SIBO.

Elemental Diet

The Elemental diet is a specialized and restrictive diet approach sometimes used to treat SIBO. Because this is a more restrictive diet approach, it should only be done under the supervision of a trained healthcare provider.

Elemental formulas used in this diet are composed of predigested nutrients, including amino acids, simple carbohydrates, vitamins, minerals, and some fats. Due to the predigested nature of these components, it is easier for the body to digest and absorb them.

The elemental diet can be used as a short-term therapeutic approach, usually for 2-4 weeks, for conditions including SIBO. Providing the nutrients needed for the body to function in a predigested form helps to alleviate the digestive system and allow it to recover from prolonged periods of inflammation, irritation and damage.

Natural Health Products

Antimicrobial Herbs

Antimicrobial herbs are often used to treat SIBO, either in conjunction with or as an alternative to antibiotics. These herbs contain natural properties that target and interfere with the growth of harmful bacteria in the digestive tract. Some herbs that are commonly used in the treatment of SIBO include:

  • Oregano
  • Berberine
  • Garlic
  • Neem
  • Wormwood
  • Peppermint
  • Clove
  • Thyme

It is important to remember that anti-microbial herbs should be used under the guidance of a trained professional, such as a Naturopathic Doctor (ND). They should also be used in conjunction with other treatment strategies such as dietary and lifestyle changes in the treatment of SIBO.

Digestive Support

Poor gut motility and digestion often play a key role in the development and progression of SIBO. Due to this, supplements that help stimulate digestion and aid in gut motility can be helpful in those with SIBO. Some treatments that are commonly used to support digestion in those with SIBO include:

  • Digestive Enzymes: These can help support the breakdown of carbohydrates, protein and fat, making it easier for the digestive system to use these.
  • Betaine HCL: For those with low stomach acids, supplementation with Betaine HCL can help to increase stomach acid levels, aiding in the breakdown of food in the early digestive process.
  • Glutamine: Glutamine is an amino acid that is important in the healing and maintenance of the gut lining.

Probiotic Supplements

Specific strains of probiotics have been shown to help restore a healthy balance of bacteria in the gut. It is essential to work with a health care provider, to understand what strains and doses would be most beneficial for you.

Lifestyle Changes

Stress Management

Stress levels play a significant role in the function of the digestive system. Increased stress levels can lead to decreased blood flow to digestive organs, altered gut motility, increased inflammation in the digestive tract, and changes in gut microflora. Implementing stress management techniques such as meditation, journaling, mindfulness practices, yoga, and social interaction should be part of a holistic approach to managing and treating SIBO.

Sleep Optimization

Prioritizing and optimizing sleep can not only help improve energy in the short term, but is also important for the longer-term treatment of SIBO. Sleep is crucial for recovery and repair, including the repair of the gut lining in those with SIBO.

Regular Exercise

Participating in regular physical activity can help improve energy levels, aid in digestion, and improve overall health. However, it is important to remember to exercise at a frequency and intensity that your body can handle. Extreme exercise or overexertion can lead to a worsening of symptoms due to increased stress on the body.

Identifying Concerns and When to Consult a Medical Professional

When dealing with SIBO fatigue, it’s essential to recognize when symptoms might point to more concerning health issues. If fatigue persists despite efforts to manage it, or if you notice additional symptoms like drastic weight loss, severe abdominal pain, or blood in your stool, it is time to consult a medical professional. These could be signs of more serious conditions requiring immediate medical attention.

In these situations, a naturopathic doctor can play a critical role. Naturopathic doctors are trained in both conventional and natural medicine, allowing them to provide a holistic approach to diagnosing and treating health concerns. They look beyond the symptoms to identify underlying imbalances in the body that might contribute to your health issues. By working with a naturopathic doctor, you can develop a comprehensive treatment plan that focuses on alleviating symptoms and promoting long-term health and well-being.

How Can a Naturopathic Doctor Help with the Treatment of SIBO Fatigue?

Naturopathic Doctors (NDs) play an important role in the treatment and management of SIBO. By creating a personalized approach, a ND can help determine what is the best course of treatment for each case of SIBO. NDs take a holistic approach to health, meaning they focus on addressing the root cause and taking into account all aspects of a person’s mental and physical well-being.

Some benefits of working with a naturopathic doctor include:

A Comprehensive Assessment

An ND can conduct a thorough history and assessment in order to determine the next best steps in cases of digestive concern. In Ontario, NDs can also order tests, such as SIBO breath tests, to help confirm the presence of SIBO.

An Individualized Treatment Plan

All cases of SIBO are different. Due to this, it is vital to work with a trained healthcare professional to determine what treatments and modalities are best for you.

Dietary Guidance

NDs are trained in different dietary approaches to supporting those with SIBO. Working with an ND can help determine which dietary changes are best for you. Working closely with an ND regarding your diet also helps to optimize nutrient intake.

Natural Therapies

NDs can utilize a range of natural therapies, including herbal medicine and targeted supplementation to help address SIBO overgrowth and alleviate fatigue.

Gut Health Optimization

NDs can help to support overall gut health and work to rebalance and optimize the gut microbiome. SIBO relapse is common, especially in the first few months after treatment. Therefore, gut health support and optimization is an integral part of SIBO treatment and remission maintenance.

Lifestyle Modifications

NDs know that gastrointestinal health is also dependent on lifestyle habits. NDs can offer comprehensive guidance and treatment recommendations with regard to stress management, environmental exposure, sleep habits and exercise to help promote and maintain overall health.

Get a Tailored SIBO Treatment from an experienced Naturopathic Doctor

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Additional Reading


What Is Small Intestinal Bacterial Overgrowth (SIBO)?

SIBO is characterized by an abnormal and excessive overgrowth of pathogenic bacteria in the small intestine. The small intestine is mainly responsible for absorbing nutrients from our food, including macronutrients such as carbohydrates, fats and proteins, and micronutrients such as vitamins and minerals. During a SIBO infection, the overgrowth of bacteria begins to ferment undigested carbohydrates, leading to increased gas production, contributing to common symptoms such as gas and bloating. The increased gas in the digestive tract can also contribute to changes in bowel habits, such as constipation, diarrhea, or even alternating bowl patterns.

The overgrowth of bacteria can also impact nutrient absorption, through increased competition for both macro and micronutrients. This can commonly lead to a deficiency or lower levels of vitamins such as vitamin B 12 and vitamins A, D, E and K. It can also lead to lower levels of minerals, particularly calcium and iron.

What causes Small Intestinal Bacterial Overgrowth (SIBO)?

Although the exact cause of SIBO is not known, SIBO is associated with several risk factors. Poor dietary habits, certain medications and conditions that alter intestinal mobility have all been associated with an increased risk of developing SIBO.

claire lockridge headshot 2
Written By:
Claire Lockridge

Dr. Claire Lockridge ND, has a degree in Naturopathic Medicine from the Canadian College of Naturopathic Medicine and a Bachelor of Science undergraduate degree with a minor in Nutrition from the University of Arizona. She integrates her extensive knowledge of nutrition and psychology to provide optimal care to her patient base.

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