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SIBO: Addressing and Managing Nutritional Deficiencies

by Michael Stanclift, ND

Patients with digestive problems aren’t always taken seriously by primary care providers. Often cases are dismissed with the nebulous diagnosis of irritable bowel syndrome (IBS), when the problem hasn’t been adequately worked up and given the proper attention. A recent study in Scientific Reports found that up to half of patients diagnosed with IBS also have a treatable and consequential condition called small intestinal bacterial overgrowth (SIBO). SIBO in and of itself has many underlying causes, and can cause deficiencies in both macro and micronutrients.2 These deficiencies can slowly sap a patient’s health. We’re going to uncover what to look for, so that you can discover these deficiencies and correct them.

Clinical Presentation

Patients with SIBO can present with a varied constellation of GI-related problems, such as diarrhea (which can present as steatorrhea), constipation, bloating, vitamin and macronutrient deficiencies, which we’ll outline below.2-4 Symptoms can vary from mild to severe, based on the species present, the duration of their illness, concurrent ailments, and individual factors including diet.2,3 Let’s look at some of the nutritional deficiencies that can develop from SIBO.

Common Nutrient Deficiencies

As the name implies, with SIBO we see an overgrowth of bacteria in the digestive tract which throws off the delicately balanced orchestra of breaking down and absorbing food leading to nutritional deficiencies. The overgrowing bacterial populations can consume more than their fair share of vitamins such as B1, B3 and B12.3 Other nutrients like fats and the fat-soluble vitamins A,D and E can become deficient from poor breakdown of foods, or damage to the intestinal cells from overgrown bacteria.2 Through similar mechanisms, sugars, proteins, iron, and B12 (which have complex absorption processes) can also become deficient.2-4

Interestingly, some nutrients can actually be elevated above normal levels with SIBO. Bacteria are responsible for making some of our vitamins, like folate and vitamin K, and when bacteria is overgrown they can produce more than we need.2 This can potentially become a problem with vitamin K, because too much of it can interfere with proper blood-thinning treatment.2

Here are the nutrient deficiencies to watch for with SIBO:


      • Vitamin A2
      • Vitamin B1 (thiamine)3
      • Vitamin B3 (nicotinamide)3
      • Vitamin B12 (cobalamin)2-4
      • Vitamin D2
      • Vitamin E2
      • Iron2


      • Fats2-4
      • Carbohydrates4
      • Protein4

Nutrients that may be elevated in SIBO:

      • Vitamin B9 (folate)3
      • Vitamin K2,3

Symptom Management

Because SIBO is an issue with overgrown bacteria, my experience has proved that reducing those bacteria with antimicrobial herbs or drugs is often needed to get a patient’s symptoms under control. When those therapies are unable to get symptoms under control, or if patients are especially motivated, then trying a low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) diet may help.5,6 This involves eliminating or drastically restricting foods that contain FODMAPs, for a period of weeks, and then slowly reintroducing them to see if they reproduce symptoms.5,6 Elimination diets like the low FODMAP, that impact consumption of fruits, vegetables, and whole grains also come with the risk of exacerbating nutrient deficiencies and must be used judiciously.5 In cases where steatorrhea is a particular problem, using medium chain triglycerides (often referred to as MCTs) might be helpful.6,7 Often with SIBO treatment, a combination of therapies are needed to help patients navigate their condition.

Final Thoughts

SIBO has multiple mechanisms that cause nutritional deficiencies, in carbohydrates, proteins, fats, and micronutrients, like vitamins and iron. Some experts suggest testing for the nutritional deficiencies listed above, even before establishing a diagnosis of SIBO (since there could be other digestive causes for them).2 Once we’ve identified a deficiency we can correct it by supplementing nutrients, while concurrently addressing the causative bacteria, as the loss of these nutrients often creates a vicious circle wherein the bacteria worsen the deficiencies and the lack of nutrients make it more challenging to return to the gut microbiota to normal. To learn more about the workup and treatment of SIBO, see this article by Vincent Pedre, MD next.



  1. Poon D et al. A systematic review and meta-analysis on the prevalence of non-malignant, organic gastrointestinal disorders misdiagnosed as irritable bowel syndrome. Sci Rep. 2022;12(1):1949.
  2. Bushyhead D et al. Small intestinal bacterial overgrowth. Gastroenterol Clin North Am. 2021;50(2):463-474.
  3. Quigley EMM et al. AGA clinical practice update on small intestinal bacterial overgrowth: expert review. 2020;159(4):1526-1532.
  4. Bures J et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol. 2010;16(24):2978-2990.
  5. O’Brien L et al. What Are the Pearls and Pitfalls of the Dietary Management for Chronic Diarrhoea?. Nutrients. 2021;13(5):1393.
  6. Jacob A. Treatment and Management of SIBO ­– Taking a dietary approach can control intestinal fermentation and inflammation. Today’s Dietitian Website. Updated 12/2012. Accessed 5/31/2022.
  7. Fitzgerald K et al. Managing SIBO through dietary interventions. Institute for Functional Medicine Website. Accessed 5/31/2022.


Michael Stanclift, ND graduated from Bastyr University’s school of naturopathic medicine and practiced in Edinburgh, Scotland, and Southern California. He enjoys educating other healthcare providers and impacting the lives of their many patients. When he’s not working, he spends his hours with his wife and two children.

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