Vitamin D

Vitamin D, Gut Bacteria & Your Immune System

by Mike Mutzel




Vitamin D Favorably Changes Gut Bacteria Linked with Health and Disease


Vitamin D is much more than a vitamin relegated to bone development and calcium absorption. Vitamin D receptors are found on various non-musculoskeletal tissues, including various immune cells (macrophages, B and T lymphocytes), prostate, breast, colon, and various neurological tissues (microglia, astrocytes, glial cells, neurons, oligodendrocytes).

Directly or indirectly, vitamin D controls more than 200 genes, including genes responsible for the regulation of cellular proliferation, differentiation, apoptosis and angiogenesis, decreasing cellular proliferation of both normal and cancer cells. (1).

When serum levels fall below 20 ng/mL, monocytes and macrophages cannot initiate an innate immune response (1).

Studies dating back to as early as 2002 reveal that people living at higher latitudes, and thus having more prevalent vitamin D deficiency, are at increased risk for Hodgkin’s lymphoma and colon, breast, prostate, ovarian, pancreatic, and other cancers. They are also more likely to die from these cancers compared to people at lower latitudes (2).

A few years later, scientists found that low vitamin D levels are linked with reduced insulin sensitivity, insulin resistance and obesity (3).

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Fast forward to 2020 and multiple authors have published articles about the relationship between vitamin D deficiency and COVID-19 (4). Vitamin D sufficiency is independently associated with decreased disease severity (5). A meta-analysis of 27 articles found that severe cases of COVID-19 infection are 64% more likely to have vitamin D deficiency compared to mild cases.

Part of this protective effect may be due to how vitamin D impacts the composition of the gut microbiota. A recent study, co-authored by long-time vitamin D enthusiast Michael Holick, found that vitamin D levels are positively correlated with Akkermansia species, a healthy genera of intestinal bacteria (6). They also observed favorable changes in the abundance of Bacteroides spp. and Parabacteroides spp. after eight weeks of vitamin D supplementation. These bacteria are found to be suppressed in patients with active inflammatory bowel disease.


Mechanistically, it appears that vitamin D offers some level of inside-out control, impacting both host immune response and composition of the gut microbiome. As we approach the shortest day of the year, it makes sense to supplement with 4,000 IU per day of vitamin D3.


It’s been long known that between November to March at latitudes above 35 N (San Francisco, CA), very little, if any, vitamin D is produced in human skin during exposure to sunlight due to the zenith angle of the sun. Moreover, if you live in the city, chances are your blood levels of vitamin D are quite low. One study reported that 84 percent of urban residents were vitamin D deficient compared to only 38 percent of rural residents. (7).


Related Video:Vitamin D, Deep sleep & Gut Bacteria w/ Dr. Stasha Gominak




  1. May E, Asadullah K, Zügel U. Immunoregulation through 1,25-dihydroxyvitamin D3 and its analogs. Curr Drug Targets Inflamm Allergy. 2004;3(4):377-393. doi:10.2174/1568010042634596.
  2. Holick M. (2002). Vitamin D: The underappreciated D-lightful hormone that is important for skeletal and cellular health. Curr Opin Endocrinol Diabetes Obes. 2002(9):87-98. doi:10.1097/00060793-200202000-00011.
  3. Botella-Carretero JI, Alvarez-Blasco F, Villafruela JJ, Balsa JA, Vázquez C, Escobar-Morreale HF. Vitamin D deficiency is associated with the metabolic syndrome in morbid obesity. Clin Nutr. 2007;26(5):573-580. doi:10.1016/j.clnu.2007.05.009.
  4. Idelson PI, Rendina D, Strazzullo P. Nutrition and the covid-19 pandemic: three factors with high impact on community health. Nutr Metab Cardiovasc Dis. 2020.
  5. Maghbooli Z, Sahraian MA, Ebrahimi M, et al. Vitamin D sufficiency, a serum 25-hydroxyvitamin D at least 30 ng/mL reduced risk for adverse clinical outcomes in patients with COVID-19 infection. PLoS One. 2020;15(9):e0239799. Published 2020 Sep 25. doi:10.1371/journal.pone.0239799.
  6. Charoenngam N, Shirvani A, Kalajian TA, Song A, Holick MF. The effect of various doses of oral vitamin D3 supplementation on gut microbiota in healthy adults: a randomized, double-blinded, dose-response study. Anticancer Res. 2020 Jan;40(1):551-556. doi:10.21873/anticanres.13984.
  7. Manicourt DH, Devogelaer JP. Urban tropospheric ozone increases the prevalence of vitamin D deficiency among Belgian postmenopausal women with outdoor activities during summer. J Clin Endocrinol Metab. 2008;93(10):3893-3899. doi:10.1210/jc.2007-2663.


  1. What is the recommended dosage? My one son is an autistic (all kinds of gut/brain issues) and other has Chronic Lyme+ (same situation) and I tested with “lowest D level” my Dr had seen…. but I’m concerned about taking too much? Thanks so for the needed and informative piece.

    • Hi Sara!

      Most doctors and studies start people at 4,000 to 6,000 IU per day for vitamin D. That’s a safe starting zone and you can re-test from there.

      Hope that helps!


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