Vitamin D And Your Gut Microbiome

There’s a lot we don’t know about the human gut microbiome. We know this collection of bacteria, viruses and other critters residing in our digestive tract have crucial roles in many areas of our health. For many of these, we’ve barely scratched the surface of research.

It seems that every week, we learn something new about our gut microbiomes. Of course, the same can be said about vitamin D and other nutrients. Now, we’ve learned something new that connects vitamin D and the human gut microbiome that could be very important to multiple areas of health.

It seems that researchers working out of the University of California San Diego (UCSD) and their collaborators have shown that the makeup of your gut microbiome is influenced by your levels of active vitamin D, according to research published in the journal Nature Communications. Their work also uncovered a new understanding of vitamin D and how we measure it.


Vitamin D is important for bone health and other important aspects of health, including immunity. Recent research has repeatedly shown that people with low vitamin D levels are at greater risk of acquiring COVID-19, as well as at greater risk for severe symptoms. Low vitamin D is also linked to greater risk of heart disease, cancer and other diseases.

If you read my recent article about vitamin D (3 Key Ways To Get Enough Vitamin D,) you already know that vitamin D has two basic forms, D2 and D3. The latter seems to be more effective for overall health. But even as a vitamin in the bloodstream, it has several forms. One is a precursor that must be metabolized into the active form to be used.

“We were surprised to find that microbiome diversity — the variety of bacteria types in a person’s gut — was closely associated with active vitamin D, but not the precursor form,” said senior author Deborah Kado, MD, director of the Osteoporosis Clinic at UC San Diego Health. “Greater gut microbiome diversity is thought to be associated with better health in general.”


The study was associated with the National Institute on Aging (NIA.) NIA funded the Osteoporotic Fractures in Men (MrOS) study, on whose behalf the study was led. Kado worked with a team including other researchers from UC San Diego.

In spite of the importance of vitamin D to overall health, studies have shown that supplemental vitamin D has little to no positive impact on health outcomes. This was also the conclusion of the largest randomized clinical study to date, which included 25,000 adults. Kado, however, thinks there may be a a flaw in the conclusions

“Our study suggests that might be because these studies measured only the precursor form of vitamin D, rather than active hormone,” said Kado, who is also professor at UC San Diego School of Medicine and Herbert Wertheim School of Public Health. “Measures of vitamin D formation and breakdown may be better indicators of underlying health issues, and who might best respond to vitamin D supplementation.”


Using a technique known as 16s rRNA sequencing, the team analyzed blood and stool samples from 567 men participating in the MrOS study. This technique identifies and quantifies the types of bacteria in each stool sample, based on unique genetic markers. In the blood serum, a technique called LC-MSMS was used to quantify vitamin D metabolites in the blood samples. This allowed them to identify vitamin D precursors, active hormones and the breakdown product.

All the men in the sample were in good health. Their mean age was 84, and they lived in six different cities around the US.

The research team found several very interesting things. First, they found a positive link between active vitamin D and overall diversity in the gut microbiomes of the men. They also found that 12 specific kinds of bacteria showed up more frequently in the microbiomes of men with high levels of active vitamin D. Most of these were the type of bacteria that produce butyrate.


You may remember from my article, Does Dietary Fiber Improve Brain Function As We Age?, that butyrate helps preserve brain function as we age. This beneficial fatty acid also helps keep your gut lining healthy.

“Gut microbiomes are really complex and vary a lot from person to person,” Jiang said. “When we do find associations, they aren’t usually as distinct as we found here.”

One aspect of vitamin D production that could not be controlled across the sample group was production from exposure to sunlight. As you might have guessed, the men who lived in San Diego got the most sun. As a result, they had the highest levels of precursor vitamin D.


The real surprise was the lack of a connection between where the men lived and their serum levels of active vitamin D hormone.

“It seems like it doesn’t matter how much vitamin D you get through sunlight or supplementation, nor how much your body can store,” Kado said. “It matters how well your body is able to metabolize that into active vitamin D, and maybe that’s what clinical trials need to measure in order to get a more accurate picture of the vitamin’s role in health.”

“We often find in medicine that more is not necessarily better,” Thomas added. “So in this case, maybe it’s not how much vitamin D you supplement with, but how you encourage your body to use it.”


This study is a static look at the microbes and vitamin D levels for these men. Many things can effect the levels of vitamin D, including diet, sleep habits, medications, geography and more. The team feels that more research is needed to understand the relationship between gut bacteria and vitamin D metabolism.

They’d also like to know if, based on further research, interventions could be used at the microbiome level to improve bone health and other health outcomes.

Certainly, we’re not done with research in this important area. But one thing is for sure. This is one more reason for all of us to make sure we’re getting our vitamin D!

Keep the faith and keep after it!

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Journal Reference – Robert L. Thomas, Lingjing Jiang, John S. Adams, Zhenjiang Zech Xu, Jian Shen, Stefan Janssen, Gail Ackermann, Dirk Vanderschueren, Steven Pauwels, Rob Knight, Eric S. Orwoll, Deborah M. Kado. Vitamin D metabolites and the gut microbiome in older men. Nature Communications, 2020; 11 (1) DOI: 10.1038/s41467-020-19793-8

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