Top 10 Nutrients Malabsorbed in SIBO and Their Impact on Health

Small Intestinal Bacterial Overgrowth (SIBO) is a condition where an excessive number of bacteria colonize the small intestine, leading to improper digestion and malabsorption of essential nutrients. These bacteria interfere with nutrient absorption by fermenting carbohydrates prematurely, competing for nutrients, and damaging the intestinal lining. Over time, this leads to deficiencies that contribute to a range of systemic symptoms and chronic health conditions.

SIBO can be diagnosed using a non-invasive breath test which measures levels of hydrogen and methane gases produced by bacteria in the small intestine. If you suspect SIBO is affecting your health, contact our clinic to order a breath test. Testing is available for both new and existing patients or as a referral from a healthcare provider.

Nutrients Malabsorbed in SIBO

1. Vitamin B12

• Symptoms of Deficiency: Fatigue, weakness, brain fog, tingling or numbness in hands and feet, mood disorders

• Associated Conditions: Pernicious anemia, nerve damage, cognitive decline, depression

• Why It’s Deficient in SIBO: Bacteria in the small intestine consume B12 before it can be absorbed, leading to low levels. Inflammation of intestinal tissues also decreases B12 absorption.

2. Iron

• Symptoms of Deficiency: Fatigue, dizziness, pale skin, shortness of breath, hair loss

• Associated Conditions: Iron-deficient anemia, restless leg syndrome, impaired immune function

• Why It’s Deficient in SIBO: Inflammation in the gut and bacterial interference reduce iron absorption.

3. Magnesium

• Symptoms of Deficiency: Muscle cramps, irregular heartbeat, constipation, anxiety, poor sleep

• Associated Conditions: Migraines, osteoporosis, hypertension, neurological dysfunction

• Why It’s Deficient in SIBO: Poor absorption due to gut inflammation and excessive loss through diarrhea and yes, modern foods contain less magnesium due to soil depletion.

4. Vitamin D

• Symptoms of Deficiency: Bone pain, muscle weakness, frequent infections, mood disorders

• Associated Conditions: Osteoporosis, immune dysfunction, seasonal affective disorder

• Why It’s Deficient in SIBO: Fat malabsorption due to bacterial overgrowth impairs vitamin D absorption.

5. Vitamin A

• Symptoms of Deficiency: Night blindness, dry skin, immune dysfunction, slow wound healing

• Associated Conditions: Increased infection risk, vision problems, skin disorders

• Why It’s Deficient in SIBO: Damage to the small intestine lining reduces fat-soluble vitamin absorption.

6. Zinc

• Symptoms of Deficiency: Poor wound healing, hair loss, weakened immune function, taste and smell disturbances

• Associated Conditions: Increased susceptibility to infections, delayed healing, hormonal imbalances

• Why It’s Deficient in SIBO: Bacteria interfere with zinc absorption, and chronic gut inflammation further reduces uptake.

7. Calcium

• Symptoms of Deficiency: Muscle cramps, brittle nails, dental problems, osteoporosis risk

• Associated Conditions: Bone loss, increased fracture risk, muscle spasms

• Why It’s Deficient in SIBO: Fat malabsorption impairs calcium absorption, and inflammation reduces uptake.

8. Vitamin K

• Symptoms of Deficiency: Easy bruising, excessive bleeding, poor bone health

• Associated Conditions: Increased risk of osteoporosis, blood clotting disorders

• Why It’s Deficient in SIBO: Bacteria in the small intestine interfere with vitamin K synthesis and absorption.

9. Folate (Vitamin B9)

• Symptoms of Deficiency: Fatigue, irritability, anemia, digestive issues

• Associated Conditions: Neural tube defects in pregnancy, depression, cognitive decline

• Why It’s Deficient in SIBO: Bacterial overgrowth consumes folate before it can be absorbed.

10. Essential Fatty Acids (Omega-3 and Omega-6)

• Symptoms of Deficiency: Dry skin, brain fog, joint pain, chronic inflammation

• Associated Conditions: Cardiovascular disease, cognitive dysfunction, inflammatory conditions

• Why It’s Deficient in SIBO: Fat malabsorption prevents adequate intake of these essential fats.

How to Address Nutrient Deficiencies in SIBO

If you suffer from persistent digestive issues, fatigue, or unexplained symptoms, it’s essential to assess whether SIBO is impacting your nutrient absorption. Testing is available to diagnose SIBO and guide a treatment plan tailored to your needs.

✅ Step 1: Get Tested for SIBO – Order a non-invasive breath test through our clinic to determine whether SIBO is contributing to your symptoms.

✅ Step 2: Treat the Root Cause – If SIBO is present, treatment options include dietary changes, herbal antimicrobials, antibiotics, prokinetics or peptides to restore gut health.

✅ Step 3: Nutrient Replenishment – Depending on deficiencies, targeted supplementation with high-quality vitamins, minerals, and digestive support can help restore balance.

Schedule your SIBO breath test today to take the first step toward optimizing digestion, nutrient absorption, and overall wellness.