Nutrients & Fat Malabsorption in SIBO/IBS Patients 2023 Guide

Nutrients & Fat Malabsorption in SIBO/IBS Patients

Have you ever felt like your stomach is bloated within a few hours after eating? Even if you have not experienced a high degree of abdominal swelling, any amount of bloating could be a visible sign of irritable bowel syndrome (IBS).

If you frequently experience bloating or gas, or have to deal with IBS, then there is a possibility that you have excessive gut bacteria in your small intestine. It is a condition called small intestinal bacterial overgrowth (SIBO), which we will discuss in detail so that you know how to distinguish and eliminate it.

What is Small Intestinal Bacterial Overgrowth (SIBO)?

As you have rightly guessed, SIBO occurs when an abnormally large population of gut bacteria colonize and proliferate in the small intestine. The bacteria found in your gastrointestinal tract constitute your gut microbiome.

Therefore, they play an important role in your bone health, thyroid function, immune system, and overall health. As a matter of fact, scientists have found that your gut microbiome consists of billions of microorganisms, with about 1,000 species of bacteria.

Most of the bacteria are typically located in your colon and large intestine, where they assist in breaking down food, synthesizing vitamins, and eliminating waste. When the bacteria found in your colon and large intestine start colonizing and thriving in your small intestine, the disorder called SIBO occurs 1.


It can also happen when the population of otherwise healthy bacteria increases in your small bowel itself. These bacteria prevent your body from digesting the nutrients from the food you take, including carbohydrates, fat, starches, sugar, protein, and vitamins.

Since these excess bacteria feed on all the nutrients, fermentation of carbohydrates takes place, producing hydrogen. The hydrogen produced by the bacteria can feed microorganisms in your small intestine called archaea, which in turn produces methane.

Therefore, with the occurrence of SIBO, an excessive amount of methane, hydrogen, or both are produced in the digestive system. This excess gas can lead to flatulence, belching, and severe bloating.

How can You Know that You Have SIBO?

When you been affected by SIBO, you may experience non-specific, unexplained symptoms, which can be quite difficult to differentiate from those that are associated with other GI problems. As a matter of fact, SIBO can make other GI problems worse, while other GI issues can worsen the symptoms of SIBO, creating a cycle of illness.

The common signs and symptoms of SIBO include:

  • Abdominal pain, cramping
  • Gas, bloating, belching, and diarrhea
  • Constipation (not as common as diarrhea)
  • Inflammatory bowel disease (IBD) or irritable bowel syndrome (IBS)
  • Food intolerances like casein, fructose, lactose, gluten, and specifically histamine intolerance
  • Deficiencies of vitamin and minerals, including vitamins B12, A, D, and E
  • Chronic illnesses like diabetes, chronic fatigue syndrome, neuromuscular disorders, autoimmune diseases, and fibromyalgia
  • Pale, bulky, odorous stools
  • Leaky gut
  • Skin rashes, including redness of the face

The abovementioned symptoms can manifest in people in different ways, often showing no signs whatsoever, which is the reason why SIBO goes undetected.

Malabsorption of Fat and Other Nutrients in SIBO/IBS Patients


SIBO and IBS typically interfere with the absorption of nutrients, causing malnutrition. Its health effects typically cause subtle, vague symptoms, including weight loss, fatigue, and depression.

People with SIBO and IBS, because of malnutrition, can develop critical health problems, such as low red blood cell count and fragile bones. Nutritional deficiencies associated with small intestinal bacterial overgrowth include:

1. Fat Malabsorption

When you have SIBO, bile acids that are produced by the liver and responsible for breaking down and absorbing fat are deficient. Malabsorption of fat is characterized by greasy, odorous, and floating stools with possible health effects, including fatigue, weight loss, bloating, and occasionally diarrhea 2.

2. Carbohydrate Malabsorption

Bacterial overgrowth in the small bowel also interferes with the absorption of carbs. For this reason, people with SIBO sometimes avoid taking carbs to prevent diarrhea, gas and bloating. Overall, malabsorption of carbohydrates can cause low energy and weight loss.

3. Protein Malabsorption

Changes caused by SIBO in the small intestine interfere with the absorption of protein, resulting in decreased immune functions and weight loss. Malabsorption syndrome can also lead to malnutrition and diarrhea.

4. Vitamin Malabsorption

If you have SIBO, fat-soluble vitamins are not properly absorbed, which may lead to the following problems:

  • Vitamin A deficiency: May cause immune deficiency and vision problems
  • Vitamin D deficiency: May cause depression and fragile bones
  • Vitamin E deficiency: May interfere with healing wounds
  • Vitamin K deficiency: May cause easy bruising or bleeding
  • Vitamin B12 deficiency: May cause peripheral neuropathy, which results in the pain of your toes and fingers. The deficiency may also lead to enlarged, dysfunctional RBCs (megaloblastic anemia), which cause fatigue and irritability

5. Iron Malabsorption

People with SIBO may have a deficiency of iron, which causes small, dysfunctional RBCs (microcytic anemia) and numerous other health effects, including loss of energy and fatigue.

What are the Treatment Options?


If you are affected by SIBO, you need to treat the condition so that you can eliminate the bacterial overgrowth and restore the small intestine’s natural balance.

The different treatment options include management of underlying medical conditions (like scleroderma or pancreatitis), administration of antibiotics to lessen bacterial overgrowth, and nutritional supplementation. Not all these treatment methods are needed, as your treatment will be based on the symptoms and effects of the condition that you are experiencing.

Remember that the symptoms of SIBO fluctuate over time, which means you can take a break or stop treatment for some months, or years. Make sure to consult with your doctor about recurring symptoms so that you can reduce flare-ups.

1. Antibiotics

Although there are many antibiotics that can be used for reducing bacterial overgrowth in your small intestine, rifaximin is the most common antibiotic used for SIBO.

2. Management of Underlying Conditions

If you have been diagnosed with an underlying medical condition that makes you susceptible to SIBO, managing that medical problem can help reduce the excess bacteria in your small intestine. The treatment plan is based on various factors. Some medical conditions, including Crohn’s disease, act up periodically, but others that occur due to intestinal surgery can be permanent.

3. Nutritional Supplementation

When a GI condition like SIBO or IBS causes fat malabsorption or other nutritional deficiencies, your healthcare professional will likely advise a blood test to look for vitamin levels and then prescribe supplementation accordingly.

Since nutritional deficiencies related to SIBO arise from malabsorption of nutrients, your doctor may prescribe intravenous supplementation instead of oral medications.

4. Dietary Modifications

Modifying your diet may be useful as adjunctive therapy for treating SIBO. FODMAP diet, for example, can be undertaken after consulting your nutritionist and doctor.

People with SIBO often suffer from flare-ups after consuming certain foods that contain fructose or lactose 3. If you have an intolerance towards any specific food, then avoiding it can help in keeping SIBO from acting up.


Small intestinal bacterial overgrowth (SIBO) is a digestive condition that has now become recognized as the cause of nutrient malabsorption, malnutrition, and intestinal disturbance. Getting the right diagnosis and then formulating a proper treatment plan for bacterial overgrowth may take time. However, you will surely feel more energetic and comfortable once the condition is managed.

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