Vitamin B12 Deficiency in GI Conditions: Exploring the Causes

Vitamin B12 Deficiency in GI Conditions: Exploring the Causes

Published on Thursday, July 20, 2023 by Elyse Krawtz

While increasingly plant-based diets are trending, vitamin B12 is too important to ignore. 

Vitamin B12 is a water-soluble vitamin found in fish, seafood, meat, poultry, dairy, and eggs, and I see its deficiency more often than you might expect in the gastrointestinal nutrition space.

It is easy to miss or mistake vitamin B12 deficiency for other problems. But if it is severe and missed for too long, its effects can become irreversible. B12 deficiency causes anemia with abnormally large red blood cells and also can cause both gastrointestinal and neurological symptoms. 

Signs of a B12 deficiency can include: 

  • Fatigue and pallor (signs of anemia)
  • Jaundice
  • Peripheral neuropathy (numbness, weakness, or tingling in extremities)
  • Glossitis (a swollen tongue) 
  • Diarrhea
  • Headaches
  • Neuropsychiatric disturbances
  • Ataxia
  • Loss of proprioception
  • Dementia

There are several ways to become vitamin B12 deficient. 

Not eating enough vitamin B12 is the most obvious way to become deficient. Anyone consuming little-to-no animal products in their regular diet should supplement with vitamin B12 through fortified foods and/or dietary supplements. This certainly includes vegans, but one who rarely includes animal products or undereats, in general, could have insufficient B12 intake. 

Interestingly, a study of 130 individuals with IBS from the Journal of the Academy of Nutrition and Dietetics found that the most restrictive phase of the Low FODMAP diet tended to increase vitamin B12 intake compared to control and sham diets. 

So, eating enough B12 can keep deficiency at bay…right? Not always. Here is where it gets interesting. 

Vitamin B12 absorption is complex--literally. It requires a complex with intrinsic factor, a chemical produced by special cells in the stomach, before absorbing in the ileum (the last part of the small intestine). As the NIH describes, part of the process involves stomach acid and pancreatic enzymes freeing B12 to form the right complex. Therefore, deficiency can occur when there is damage to or removal of parts of the gastrointestinal tract involved in the B12 absorption process. 

Many gastrointestinal surgeries carry a risk of B12 deficiency. Examples of surgeries that can cause vitamin B12 malabsorption are:

  • Bariatric surgery like gastric bypass, sleeve gastrectomy, biliopancreatic diversion/duodenal switch
  • Gastrectomy for gastric cancer
  • Small intestine resections for Crohn’s disease or cancer 
  • Gastrointestinal surgeries for other reasons not listed here that alter the stomach or the small intestine, especially the ileum

Someone without part of their stomach or ileum could technically consume enough B12 and still deal with deficiency due to malabsorption. But diet and surgery are not the only causes of B12 deficiency. 

Gut dysbiosis can directly or indirectly lead to B12 deficiency. Small intestinal bacterial overgrowth (SIBO) may lead to malabsorption and vitamin B12 deficiency, according to a 2020 American Gastroenterological Association practice update. Certain infections, like tapeworms, can steal vitamin B12. Others, like H. pylori, could harm the vitamin B12 absorption process by impairing the stomach and causing atrophic gastritis, according to a 2020 Journal of Clinical Medicine review and a 2022 Gastroenterology practice update

Autoimmune and inflammatory disorders can cause vitamin B12 deficiency. Pernicious anemia involves an inappropriate immune attack on intrinsic factor, compromising its function in B12 absorption. People with celiac disease or Crohn's disease could experience damage to the ileum, leading to vitamin B12 malabsorption and deficiency. Finally, atrophic gastritis has autoimmune causes, which can harm stomach function in the B12 absorption process. 

Older adults are more likely to experience B12 deficiency. This may be related to atrophic gastritis, pernicious anemia, or infections, but decreasing appetite and intake of food or medications could also contribute. 

Certain medications can increase B12 deficiency risk. Acid-reducing medications and metformin are two common medications that can change the B12 absorption process, but others also could. 

Here are 6 B12 Tips for People with IBS: 

  1. Ask your doctor about monitoring B12 if you have a history of deficiency or are at risk. Typical tests that help evaluate your B12 status include a complete blood count, serum B12, methyl-malonic acid, and homocysteine. Individuals who are at high risk of deficiency or actively repleting may require more frequent testing. 
  2. Talk to your RD if you plan to substantially reduce or eliminate animal products. B12 deficiency due to dietary inadequacy is avoidable. An RD can set you up for success with supplementation, fortified foods, and monitoring recommendations. Some (but not all!) plant-based processed foods may be fortified with supplemental B12, such as nut milk, protein bars, tofu, nutritional yeast, and cereals. And though B12 is the focus of this article, it isn’t the only vitamin or mineral that you need to plan for if you give up animal products. 
  3. Talk to your RD about the correct form of B12 for you. Your RD can recommend the B12 type and form appropriate for you, such as sublingual liquid drops, oral tablets, nasal spray,  intramuscular injections, or a combination plan for repletion and maintenance.  
  4. Don’t lose touch with your bariatric or GI RD if you’ve had surgery. A good bariatric RD is trained and focused not just on your weight loss but on your specific surgically-induced nutritional risks and can help you ensure you’re preventing, catching, and repleting deficiencies. The same goes for experienced GI RDs who serve post-surgical patients over the long term.
  5. Older adults should ask their doctor about monitoring and supplementing B12 as they age. B12 deficiency symptoms can be mistaken for part of the aging process, but it doesn’t have to be. Don't be afraid to advocate for B12 monitoring for yourself or, if you're a caretaker, for loved ones. 
  6. Mind medication-B12 interactions. Talk to your pharmacist about deficiency risks and nutrient interactions if you take medications.  

  1. Ankar, A., & Kumar, A. (2022, October 22). Vitamin B12 Deficiency. National Institutes of Health, National Library of Medicine, National Center for Biotechnology Information.
  2. Staudacher, H. M., Ralph, F. S. E., Irving, P. M., Whelan, K., & Lomer, M. C. E. (2020). Nutrient Intake, Diet Quality, and Diet Diversity in Irritable Bowel Syndrome and the Impact of the Low FODMAP Diet. Journal of the Academy of Nutrition and Dietetics, 120(4), 535–547.
  3. Vaqar, S., & Shackelford, K. (2023, May 8). Pernicious Anemia. National Institutes for Health, National Library of Medicine, National Center for Biotechnology Information.
  4. Quigley, E. M. M., Murray, J. A., & Pimentel, M. (2020). AGA Clinical Practice Update on Small Intestinal Bacterial Overgrowth: Expert Review. Gastroenterology, 159(4), 1526–1532.
  5. Gravina, A. G., Priadko, K., Ciamarra, P., Granata, L., Facchiano, A., Miranda, A., Dallio, M., Federico, A., & Romano, M. (2020). Extra-Gastric Manifestations of Helicobacter pylori Infection. Journal of clinical medicine, 9(12), 3887.
  6. Shah, S. C., Piazuelo, M. B., Kuipers, E. J., & Li, D. (2021). AGA Clinical Practice Update on the Diagnosis and Management of Atrophic Gastritis: Expert Review. Gastroenterology, 161(4), 1325–1332.e7. 

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