Table of Contents

1. What Is SIBO?
2. Can SIBO Cause Fatigue?
3. How SIBO Affects Energy Levels
4. The Link Between SIBO and Mood Symptoms
5. The Role of Tryptophan and Serotonin
6. Other Common Symptoms of SIBO
7. Why Testing for SIBO Is Important
8. How to Test for SIBO
9. Addressing the Root Causes of SIBO
10. Tips for Supporting Recovery
11. Final Thoughts
12. References

SIBO Fatigue

Feeling constantly tired, even with a good diet and plenty of sleep?
If you also deal with bloating, gas, or irregular bowel movements, Small Intestinal Bacterial Overgrowth (SIBO) could be the hidden cause of your fatigue.

While SIBO is known for digestive symptoms, many people don’t realise it can also leave you feeling drained, foggy, and chronically low on energy. When bacteria overgrow in the small intestine, they can block nutrient absorption, trigger inflammation, and release toxins all of which can sap your energy.

In this blog, we’ll explain how SIBO contributes to fatigue, the science behind it, and what you can do to start feeling more energised and clear-headed.

What Is SIBO ?

SIBO occurs when bacteria that normally reside in the colon migrate into the small intestine, where they disrupt digestion and interfere with the absorption of essential nutrients. This overgrowth can cause classic digestive discomfort, but it also impacts the body’s energy systems resulting in tiredness that doesn’t resolve with rest.

Understanding how gut bacteria affect nutrient absorption, inflammation, and your brain chemistry can help guide more effective treatment.

Common Symptoms of SIBO

SIBO can affect many parts of the body. Some of the most common symptoms include:

• Gas and bloating: A very frequent complaint. Bacteria in the small intestine ferment food, leading to excess gas and a swollen belly.
• Abdominal pain or cramping: Discomfort often occurs after eating, especially when consuming carbohydrates.
• Diarrhea or constipation: Some people experience loose stools, while others have sluggish digestion—SIBO can cause either, or both (alternating).
• Indigestion or heartburn: Bacterial overgrowth can disrupt normal digestion, leading to a burning feeling or discomfort in the chest.
• Nutrient deficiencies: SIBO can interfere with the absorption of nutrients like vitamin B12, iron, and fat-soluble vitamins (A, D, E, K), leading to tiredness or weakness.
• Fatigue and brain fog: Many people with SIBO feel exhausted, even after a full night’s sleep, and may struggle to concentrate or think clearly.
• Unexplained weight loss or gain: In some cases, the body struggles to absorb nutrients; in others, SIBO may affect metabolism or hunger cues.
• Skin issues (like acne or rosacea): A disrupted gut microbiome can trigger inflammation that shows up on the skin.
• Food sensitivities: People with SIBO often react to a wide range of foods, especially those high in fermentable carbs (FODMAPs).

If you’re noticing a combination of these symptoms—especially alongside persistent digestive discomfort—it may be worth testing for SIBO.

Can SIBO Affect Your Mood?

New research shows that SIBO may be linked to mood problems like anxiety, depression, and feeling very tired.

A 2006 study found that people with SIBO were more likely to feel anxious or depressed. This may be because the balance of gut bacteria is disturbed, which affects how the brain and body communicate.

One important reason for this involves a substance called tryptophan, which your body uses to make serotonin the “feel-good” brain chemical. In people with SIBO, tryptophan may be used less for making serotonin and more for making other chemicals that are linked to inflammation and low mood.

Scientists have also found that the gut and brain are closely connected. Gut bacteria can affect how you feel by:

• Changing levels of brain chemicals like serotonin and GABA (which help control mood and calmness)
• Communicating through the vagus nerve, which links your gut to your brain
• Increasing inflammation and making the gut lining more “leaky,” which may affect brain health

All of this suggests that improving gut health may also help improve mood and energy.

SIBO and Fatigue and Tiredness

In clinical studies and patient case series, fatigue has emerged as a frequently reported symptom among people with SIBO. A 2018 case series published in the World Journal of Gastroenterology followed 30 patients who experienced gas, bloating, and brain fog and found that many had SIBO and elevated D-lactic acid levels, a byproduct of bacterial fermentation. These individuals commonly reported symptoms like mental cloudiness, tiredness, and lack of concentration.

Fatigue in SIBO isn’t just due to discomfort or poor sleep. It often stems from deeper physiological disruptions, which we explore below.

Why Does SIBO Cause Fatigue and low energy?

There are several mechanisms through which SIBO may lead to chronic fatigue:

Nutrient Malabsorption

One of the biggest reasons SIBO zaps your energy is because the bacteria hijack the food you eat.

When bacteria overgrow in the small intestine, they don’t just sit there they actively compete with you for key vitamins and minerals. Think of it like sharing your dinner with freeloaders who take the best bits before your body has a chance.

They consume or block the absorption of essential nutrients like:

• Vitamin B12 – Needed for red blood cells and nerve function. A lack of it can cause exhaustion and brain fog.
• Iron – Vital for oxygen delivery in the blood. Low iron equals low stamina.
• Magnesium – Involved in energy production at the cellular level. A shortage means your energy factories (mitochondria) slow down.

SIBO also disrupts digestion by damaging the small intestine lining (microvilli) and deactivating bile acids, which are necessary to break down fats. This makes it harder to absorb fat-soluble vitamins (A, D, E, K) and proteins—further depleting your body’s energy reserves.

Can SIBO Affects Fat Digestion?

Bile acids play a critical role in digesting fats and absorbing fat-soluble vitamins like A, D, E, and K. When SIBO bacteria interfere with bile acid activity, fats remain partially undigested. This can lead to:

• Loose, greasy, or pale stools (a sign of fat malabsorption)
• Dry skin and brittle nails (linked to low vitamin A and E)
• Hormonal imbalances and poor immunity (vitamin D and K deficiencies)
• Increased fatigue, since fat is a key energy source

Fat malabsorption also means your body gets fewer essential fatty acids like omega-3s that support brain function and reduce inflammation.

In short: your body’s working hard to digest food, but getting very little out of it.

No wonder you’re running on empty.

D-Lactic Acid and SIBO

D-lactic acid is a type of organic acid produced by certain strains of bacteria when they ferment carbohydrates in the gut. Unlike L-lactic acid, which is naturally produced by human cells during normal metabolism and is easily cleared from the body, D-lactic acid is metabolized much more slowly.

In people with SIBO, the overproduction of D-lactic acid can overwhelm the body’s ability to eliminate it, leading to a condition called D-lactic acidosis. This buildup can cause neurological symptoms such as fatigue, confusion, dizziness, and difficulty concentrating commonly described as “brain fog.”

It may also contribute to muscle weakness and physical exhaustion, especially after carbohydrate-rich meals. Testing for D-lactate levels inurine or blood can sometimes help identify this issue.

What causes elevated D-lactic acid levels?

Elevated D-lactic acid levels are primarily caused by an overgrowth of specific bacterial species in the small intestinesuch as Lactobacillus acidophilus and certain strains of Bifidobacterium that are capable of fermenting carbohydrates into D-lactic acid.

This is especially likely when there is excess dietary carbohydrate intake, particularly from refined sugars and starches, and impaired gut motility that allows these bacteria to thrive.

If you have a history of antibiotic use, constipation, or structural abnormalities in the gut you may be more prone to this type of bacterial overgrowth and D-lactate accumulation.

Can SIBO cause Leaky Gut and Inflammation?

When there are too many bacteria in the small intestine, they irritate and inflame the gut lining. Over time, this can wear down your intestinal barrier, creating tiny gaps in the gut wall a condition known as “leaky gut.”

When the gut barrier is compromised, substances that should stay inside your digestive tract like bacterial toxins, undigested food particles, and inflammatory compoundscan leak into the bloodstream.

One of the most concerning of these is lipopolysaccharide (LPS), a toxin found in the outer membrane of certain bacteria.

Once LPS enters your system, it triggers a powerful immune response. Your body goes into defence mode, releasing inflammatory chemicals that can make you feel drained, achy, foggy-headed, and just plain unwell.

Over time, this low-grade inflammation can exhaust your immune system and contribute to that deep, persistent fatigue that so many people with SIBO experience.

If you’ve ever felt like your brain is in a fog or your body is running on empty despite rest and good nutrition, leaky gut and inflammation could be playing a role.

Can SIBO cause Brain Fog?

Hydrogen and methane gases produced by gut bacteria can impair gut motility and alter the gut-brain axis. The result? A foggy head, slow thinking, and physical exhaustion that often accompany bloating.

When bacteria overgrow in the small intestine they ferment carbohydrates, they release hydrogen and methane gases.

These gases aren’t just uncomfortablethey can actually interfere with how your gut muscles contract, slowing down motility and leading to constipation or erratic bowel movements.

But that’s not all. These gases and other bacterial by-products can disrupt the delicate communication lines between your gut and your brain a system known as the gut–brain axis. When this axis is disturbed, it can affect everything from mental clarity to mood to energy levels.

That’s why many people with SIBO describe feeling “foggy,” unfocused, and mentally sluggish, especially after eating. This brain fog isn’t imagined it’s a physiological reaction to the internal turmoil happening in your gut. Add physical exhaustion from poor digestion on top of that, and it’s easy to see why SIBO can feel like a full-body drain.

SIBO Fatigue After Eating – What’s Going On?

Some people notice they feel particularly tired after meals. This can occur because meals rich in carbohydrates feed the bacterial overgrowth, causing an intense fermentation reaction that triggers gas production and toxin release.

Others may experience blood sugar crashes or histamine surges due to poor gut barrier function, further contributing to post-meal fatigue.

Can Probiotics Cause Brain Fog in SIBO?

Although probiotics are commonly used to support gut health, in some cases especially in those with SIBO they may worsen symptoms like fatigue and brain fog.

This paradoxical reaction is often due to certain probiotic strains (particularly Lactobacillus and Bifidobacterium) that produce D-lactic acid during carbohydrate fermentation.

In a compromised small intestine, where these bacteria are already overgrown, adding more of them via probiotics can exacerbate the issue.

The result is an overload of D-lactic acid, which the body struggles to clear efficiently.

This excess can cross the blood–brain barrier, contributing to neurological symptoms such as disorientation, dizziness, difficulty concentrating, and fatigue. Additionally, some probiotic blends may contain prebiotics or fermentable ingredients that feed the existing overgrowth, compounding the problem.

If you’re experiencing brain fog after starting probiotics, it’s worth consulting a practitioner and pausing use until your SIBO is properly treated.

How to Manage SIBO-Related Fatigue

If you’re feeling run down due to SIBO, these practical strategies can help support your energy while addressing the root cause of the fatigue:

• Try to leave at least 4–5 hours between meals without snacking in between.
  
  This will stiumlate something called the migrating motor complex (MMC). Think of this as a wave-like cleaning motion that sweeps leftover food, bacteria, and waste through your small intestine and into the colon. This natural cleansing process helps prevent bacterial buildupespecially important for people with SIBO.
  
  However, the MMC only works when you’re not eating. Constant snacking even small amounts can interrupt this process and allow bacteria to stay and multiply.
  
  
• Avoid high FODMAP foods: Limit refined carbohydrates and added sugars, which bacteria.
  
  Opt for low-fermentation vegetables such as courgettes and spinach and proteins such as chicken, fish, eggs. Please read our comprehensive guide on foods to avoid with SIBO.
  
  
• Consider getting tested for SIBO. A SIBO breath test measuring hydrogen and methane can identify bacterial overgrowth. If you suspect you may have SIBO, getting tested is a good first step.
  
  
  
• If your SIBO test is postive you will need to treat the overgrowth: Options include antibiotics like Rifaximin or herbal antimicrobials such as berberine and oregano oil. Please read more on our comprehensive guide for SIBO treatment .
  
  
• Address underlying causes of SIBO: SIBO can be caused by motility issues -constipation, medications, Stress, food poisoning all of these can predispose you to SIBO. If you are constipated consider taking 400 mg of Magnesium Citrate.
  
  
  
  
• Support liver detox pathways: A healthy liver is essential for clearing bacterial toxins. Nutrients like N-acetylcysteine (NAC), glycine, liver plays a key role in clearing bacterial toxins like LPS (lipopolysaccharides).
  
  
• N-acetylcysteine (NAC) –A precursor to glutathione, the liver’s master antioxidant. Typical dose: 600–1200 mg daily.
  
  
• Glycine –An amino acid that supports bile flow and detox pathways. Dose: 1–3 g daily, either in powder or capsule form.
  
  
• B-complex vitamins Particularly B2, B6, B12, and folate are involved in detoxification and energy metabolism. Choose an activated B-complex and follow label instructions (often 1 capsule daily). These nutrients help neutralise and eliminate bacterial by-products, easing fatigue and brain fog.
  
  
  
  
• Hydrate consistently: Dehydration worsens fatigue, constipation and impairs digestion. Aim for 1.5–2L of water daily.
  
  
• Replenish depleted nutrients: B12, magnesium, iron, and zinc are often low in SIBO patients. Supplement under guidance.
  
  
• Improve sleep hygiene: Aim for 7–9 hours of uninterrupted sleep, minimise blue light before bed, and create a calming evening routine.
  
• Incorporate gentle movement: Yoga, walking, or stretching can enhance circulation, reduce stress, and improve lymphatic flow without taxing your system.
  
  
• Reduce stress: Chronic stress impairs gut motility and immune resilience. Practices like breathwork, meditation, or journaling can help.
  
• Track symptoms: Use a journal or app to monitor fatigue triggers and improvements, helping tailor your treatment.
  
• Work with a practitioner: If you’re feeling run down due to SIBO, book a consultation so we can help you address the root cause and find a solution.
  

Frequently Asked Questions

Can SIBO make you tired all the time? Yes. Chronic fatigue is a common but under-recognised symptom of SIBO. It results from nutrient deficiencies, inflammation, and bacterial toxin exposure.

How long does fatigue last after SIBO treatment? Some people feel more energetic within weeks, while others may need additional support for nutrient repletion and gut healing.

Does treating SIBO help with chronic fatigue syndrome (CFS)? In some cases, yes. While not all CFS is caused by SIBO, treating SIBO may reduce symptoms for people with overlapping diagnoses.

Ready to Take the First Step?

If you’re dealing with persistent fatigue, gas, or bloating, SIBO could be the missing link.

Order your SIBO breath test here to start your journey toward better gut health and restored energy.

Book a consultation with a SIBO specialist

References

1. Pimental, M., et al. (2006). “Small intestinal bacterial overgrowth: a comprehensive review.” Gastroenterology. https://
2. Quigley, E.M.M. (2011). “Small intestinal bacterial overgrowth: roles of antibiotics, prebiotics, and probiotics.” Gastroenterology Clinics of North America, 40(4), 829–847.
   
   
3. Zhao, Y., et al. (2018). “Gut microbiota and depression: mechanistic insights and therapeutic implications.” Brain, Behavior, and Immunity, 69, 632–641.
   
4. Kelly, J.R., et al. (2015). “Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders.” Frontiers in Cellular Neuroscience, 9, 392.
   
5. Galland, L. (2014). “The gut microbiome and the brain.” The Journal of Medicinal Food, 17(12), 1261–1272.
   
6. Furness, J.B., et al. (2013). “The enteric nervous system and gastrointestinal innervation: integrated local and central control.” Advances in Experimental Medicine and Biology, 817, 39–71.
   
7. Camilleri, M., et al. (2012). “Motor functions of the gastrointestinal tract and functional gastrointestinal disorders.” GI Motility online.
   
8. Bhattarai, Y., et al. (2017). “Role of gut microbiota in regulating the function of the enteric nervous system.” The Journal of Neurogastroenterology and Motility, 23(4), 567–580.
   
9. Chojnacki, C., et al. (2017). “The role of low-grade inflammation in the pathogenesis of depression and anxiety in patients with small intestinal bacterial overgrowth (SIBO).” Psychiatry Research, 259, 173–178.
   
10. Bures, J., et al. (2010). “Small intestinal bacterial overgrowth syndrome.” World Journal of Gastroenterology, 16(24), 2978–2990.
    
    

Author – Victoria Tyler BSc Hons MBANT

Victoria Tyler owns and runs two busy clinics : Nutrition and Vitality and the IBS and Gut Disorder Clinic.

Nutrition and Vitality, along with the IBS and Gut Disorder Clinic, were founded with the goal of helping patients alleviate IBS symptoms by uncovering and addressing the root causes of their digestive issues.

As a Registered Nutritional Therapist, Victoria holds a BSc (Hons) in Nutritional Therapy and has trained with the Institute of Functional Medicine. She is also accredited by BANT and CNHC.

Before transitioning into health, Victoria earned a degree in Economics and an MBA, working with corporations including Canon and Vodafone. However, her own health challenges led her to pursue a career in Nutritional Therapy.

With a passion for learning, Victoria is committed to staying at the forefront of Functional Medicine. She helps patients manage IBS and other digestive disorders, including SIBO, Candida, and IBD, by identifying and addressing their root causes.

Victoria strongly believes that every symptom has an underlying cause, and there is always a solution to every health condition. To learn more, or to see patient reviews, visit Victoria’s profile on Google.

DISCLAIMER: The information provided in this article is intended for general informational purposes only and should not be construed as medical advice, diagnosis, or treatment. The products and methods mentioned are not a substitute for professional medical advice from a trained healthcare specialist. Always seek the guidance of your doctor or other qualified health professional with any questions you may have regarding your health or a medical condition. Never disregard professional medical advice or delay in seeking it because of something you have read on this website. Use of the information and products discussed is at your own risk.