Vitamin D Metabolites and the Gut Microbiome

Vitamin D metabolites and health: delving deep into the gut microbiome may offer an explanation to why randomized controlled trials of vitamin D supplements do not provide a benefit
Vitamin D Metabolites and the Gut Microbiome

The composition and functionality of the human gut microbiome are important in determining health and disease.  Each of us harbor an estimated 10-100 times more bacteria in our gut than our own gastrointestinal tract cells. These gut microbes are involved in regulating metabolism, physiology, and immune function. Since vitamin D plays an integral role in regulating calcium absorption from the gut and has also been implicated in affecting immunity, we hypothesized that the gut microbiome may be an important regulator of vitamin D metabolism.

 To test this hypothesis, we studied 567 older community-dwelling men representing six clinical sites across the United States who were mean age of 84 (SD = 4.1) and who provided stool samples and blood between 2015-16. We performed 16S ribosomal rRNA sequencing to define sub-Operational Taxonomic Units using Deblur and Greengenes 13.8 and used LC-MSMS to quantify serum vitamin D metabolites that included 25(OH)D, 1,25(OH)2D, and 24,25(OH)2D.  The men’s average BMI was 27 kg/m2, with 89% reporting their self-rated health as good/excellent. Men who resided in San Diego had on average more days of sunshine than the other 5 sites with corresponding higher levels of 25(OH)D as expected since sun exposure is known to affect 25(OH)D. However, we found no significant differences between sites with regards to the active vitamin D hormone (1,25(OH)2D), likely reflecting appropriate physiologic regulation according to the individual’s biological needs (Figure 1).

Figure 1: 25(OH)D levels vary with site and sun exposure, but 1,25(OH)2D levels do not

In our paper recently published in Nature Communications, we demonstrate strong correlations between the active vitamin D hormone and microbial a-diversity, b-diversity as well as 12 specific taxonomies, most of which are known butyrate producers. Furthermore, investigating measures of vitamin D flux, the 1,25(OH)2D/25(OH)D hydroxylation or “activation ratio” and the 24,25(OH)2D/25(OH)D vitamin D metabolic ratio (VMR) or “catabolism ratio”, we reported significant associations with increased microbial a-diversity in these men. Strikingly, we found no significant associations between 25(OH)D and measures of gut microbial a-diversity or specific taxonomies.

 To assess vitamin D sufficiency in humans, physicians order 25(OH)D levels in the blood because it is a stable measure that reflects bodily stores of vitamin D. However, the active vitamin D hormone is 1,25 dihydroxy vitamin D (1,25(OH)2D) that binds the vitamin D receptor. The vitamin D receptor is highly expressed in the human gut. Many large observational studies conducted across the world suggest that persons with vitamin D deficiency may suffer from a multitude of adverse health outcomes such as increased cancer, cardiovascular disease, SARS-CoV-2 infection, and earlier mortality (1-4). However, many other studies, including a recent large well-conducted randomized controlled clinical trial of vitamin D supplementation in over 25,000 persons did not demonstrate any health benefit (5). Based upon the most recent randomized controlled trial results, perhaps the focus on vitamin D supplementation as opposed to better understanding the underlying pathophysiologic mechanisms should be reevaluated.

 The consistency of the findings across different measures of active vitamin D and measures of vitamin D flux but not 25(OH)D in relation to measures of gut microbial diversity and butyrate producing bacteria is remarkable. The National Academy of Medicine (previously known as the IOM) concluded that the evidence for a threshold of optimal 25(OH)D levels should be 50 nmol/L (20 ng/mL), as this level allows for adequate intestinal calcium absorption with no increased benefit demonstrated with higher vitamin D levels (6). The existing evidence to date supports the concept that a physiologic range of effectiveness exists, that more is not necessarily better, and now our study results question the utility of measuring a marker of bodily storage without considering the underlying physiology.

 Our study design was cross-sectional in nature so we were unable to comment upon directionality of the strong and significant association between active vitamin D, its related metabolic ratios and gut microbial diversity or specific butyrate producing bacteria.  Regardless of directionality, we demonstrate in 567 older men assessments of vitamin D flux are more accurate measures of biological relevance than 25(OH)D in that they correlate with both vitamin D status (Figure 2) as well as with measures of gut microbial a-diversity. Apart from the study of the gut microbiome, future investigations should consider measures of vitamin D flux in relation to relevant clinical outcomes. With regards to the gut microbiome, additional investigation is warranted to understand the cellular interactions between commensal bacteria, their metabolic products, their hosts, and vitamin D substrates in regulating vitamin D metabolism to optimize calcium absorption, immune function, and perhaps even additional important cellular processes that remain to be discovered.

Figure 2. Vitamin D metabolic ratios vary with vitamin D status


  1. Yin L, Ordóñez-Mena JM, Chen T, Schöttker B, Arndt V, Brenner H. Circulating 25-hydroxyvitamin D serum concentration and total cancer incidence and mortality: a systematic review and meta-analysis. Prev Med. 2013 Dec;57(6):753-64. doi: 10.1016/j.ypmed.2013.08.026. Epub 2013 Sep 10. PMID: 24036014.
  2. Wang TJ, Pencina MJ, Booth SL, Jacques PF, Ingelsson E, Lanier K, Benjamin EJ, D'Agostino RB, Wolf M, Vasan RS. Vitamin D deficiency and risk of cardiovascular disease. Circulation. 2008 Jan 29;117(4):503-11. doi: 10.1161/CIRCULATIONAHA.107.706127. Epub 2008 Jan 7. PMID: 18180395; PMCID: PMC2726624.
  3. Meltzer DO, Best TJ, Zhang H, Vokes T, Arora V, Solway J. Association of Vitamin D Status and Other Clinical Characteristics With COVID-19 Test Results. JAMA Netw Open. 2020 Sep 1;3(9):e2019722. doi: 10.1001/jamanetworkopen.2020.19722. PMID: 32880651; PMCID: PMC7489852.
  4. Fan X, Wang J, Song M, Giovannucci EL, Ma H, Jin G, Hu Z, Shen H, Hang D. Vitamin D Status and Risk of All-Cause and Cause-Specific Mortality in a Large Cohort: Results From the UK Biobank. J Clin Endocrinol Metab. 2020 Oct 1;105(10):dgaa432. doi: 10.1210/clinem/dgaa432. PMID: 32620963.
  5. Manson JE, Cook NR, Lee IM, Christen W, Bassuk SS, Mora S, Gibson H, Gordon D, Copeland T, D'Agostino D, Friedenberg G, Ridge C, Bubes V, Giovannucci EL, Willett WC, Buring JE; VITAL Research Group. Vitamin D Supplements and Prevention of Cancer and Cardiovascular Disease. N Engl J Med. 2019 Jan 3;380(1):33-44. doi: 10.1056/NEJMoa1809944. Epub 2018 Nov 10. PMID: 30415629; PMCID: PMC6425757.Bottom of Form
  6. Institute of Medicine. Dietary reference intakes for calcium and vitamin D. Washington, DC: National Academies Press, 2011.

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