Published on November 17, 2021

Similar to vitamin D, the health of your gut microbiome may be another critical determining factor in outcomes associated with COVID-19 and how your body responds to vaccination

Key Points

  •  The gut microbiome, along with vitamin D status, may determine how the body is able to respond to SARS-CoV-2 infection, and to vaccination
  • Studies have shown that abnormal gut bacteria can lead to impaired immune responses and reductions in effective antibody responses to infections and vaccines
  • There are intricate connections between the gut microbiome, vitamin D, the Renin-Angiotensin System (RAS)/ACE2 system, and the immune/inflammation response
  • Vitamin D is known to benefit the diversity of the gut microbiome and gut health, as well as immune response and overall health

In a recent post, we reviewed a paper by Lai et al. and discussed how “Micronutrients are indispensable in immune response of vaccination.” Our nutrient status can have a direct effect on our body’s first line of defense against pathogens. Nutrients have many immune-regulating roles, such as supporting the integrity of our mucous membranes and influencing the immune cells involved throughout the immune response, allowing them to be more effective in recognizing and fighting infections. Nutrient deficiencies can hinder the immune response and compromise how our immune system responds to an infection as well as to vaccination, rendering it less effective against a future exposure and attack.

By now it has been widely demonstrated that vitamin D intake and levels can heavily influence COVID-19 outcomes and survival, and that correcting a vitamin D deficiency can help improve the immune response, leading to better disease outcomes. A new paper, reviewed below, discusses how the gut microbiome, along with vitamin D, may also determine how the body is able to respond to SARS-CoV-2 infection, and to vaccination.

The Role of the Gut Microbiome in Immune Health

The gut microbiome has many influences on overall and immune health; it

  • is vital for immune cell development and function
  • maintains a balance between pro and anti-inflammatory activity, and contains immune cells that directly influence inflammation levels throughout the body; in fact, studies have shown a connection between gut health and autoimmune disease risk
  • influences the immune response within the lungs, and has been associated with the severity of lung infections, pneumonia, and sepsis

Disruption of a healthy microbiome, called dysbiosis, contributes to inflammation and the development of many diseases, including obesity, chronic diseases such as diabetes and heart disease, and even influences your mental health. Studies have also shown that abnormal gut bacteria can lead to impaired immune responses and reductions in effective antibody responses to infections and vaccines.

How is the Gut Microbiome Related to COVID-19 Disease?

Dr. Santosh Shenoy, MD, of the University of Missouri, Kansas City Medical Center, investigated the published research to learn more about the connection between the gut microbiome, ACE-2 expression (an important factor controlling inflammation during SARS-CoV-2 infection), and vitamin D, in relation to severity of COVID-19 disease, especially in the elderly whose immune function is already more likely to be impaired. His paper, “Gut microbiome, Vitamin D, ACE2 interactions are critical factors in immune‑senescence and inflammaging: key for vaccine response and severity of COVID‑19 infection” describes the research showing how the status of the gut microbiome prior to COVID infection was highly predictive of inflammatory markers and the response to infection.

The diagram below illustrates the connection between the gut microbiome, vitamin D, the Renin-Angiotensin System (RAS)/ACE2 system, and the immune/inflammation response.

Click to Enlarge & Print

Because of these connections, the gut microbiome may be another likely critical determining factor in outcomes associated with COVID-19, and in how the body responds to vaccination. Taking care of your gut health and taking steps to ensure a diverse microbiome (such as eating prebiotic and probiotic foods, including fruits, vegetables, nuts, seeds and grains that are high in fiber, foods high in omega-3 fatty acids, and fermented foods) may also help improve the immune response through improving gut health.

Could Probiotics Help Increase Vaccine Effectiveness?

According to Dr. Shenoy, probiotics may positively influence how the body responds to COVID vaccination. Previous research on the influenza vaccines has shown that those who took probiotics or prebiotics had a significantly better response in protection from vaccination to several strains of the flu virus, including H1N1, H3N2, and Influenza B strains.

Vitamin D Influences Both the Microbiome and the Immune Response

Vitamin D is a known regulator of immune system function, including within the gastrointestinal tract. Vitamin D helps protect the gut itself from pathogenic invaders, such as viruses and bacteria that can lead to digestive upset and other symptoms throughout the body, and it helps regulate inflammation that can be caused by pathogens, foods and toxins.

Vitamin D also

  • has anti-inflammatory functions; helps regulate inflammation caused by gut pathogens
  • stimulates the production of agiogenenin-4, an antimicrobial protein (similar to cathelicidin) and influences macrophage activity
  • regulates the gut microbiome, promotes the growth of healthy gut bacteria, and maintains microbial diversity
  • reduces the expression of renin (therefore reducing inflammation) and interacts directly with ACE-2 to decrease inflammation; regulation of this axis is critical to COVID outcomes

A recent study found that vitamin D supplementation over 12 weeks resulted in changes in the gut microbiome in healthy women. Vitamin D supplementation was found to beneficially increase the overall diversity of the gut microbiota, and in particular increased the relative abundance of Bacteroidetes while decreasing the relative abundance of Firmicutes. A high ratio of Firmicutes to Bacteroidetes has been correlated with obesity and other diseases whereas a decreased ratio has resulted in improvements to gut permeability and inflammation. In other words, vitamin D supplementation altered the relative levels of the healthy type bacteria (Bacteriodetes) that are especially associated with improved gut health.

Strengthen Your Immune Response by Improving Your Gut Health and Getting Enough Essential Nutrients

Your immune system relies on certain nutrients in order to mount an effective immune response, regardless of whether it is responding to a vaccine or a live pathogen. Deficiency of any of these nutrients could hinder that response.

Could getting more of certain nutrients help to decrease your levels of inflammation and improve your immune response? Find out by testing your vitamin D, omega-3s, magnesium and other essential elements (including copper and zinc), as well as your inflammation levels, with the Immune Boost home test kit offered by GrassrootsHealth. Measuring levels is the only way to know if you are supporting your immune system and whether additional changes should be made, with supplementation, dietary changes, or both.

Test Your Vitamin D Levels At Home

Having and maintaining healthy vitamin D levels and other nutrient levels can help improve your health now and for your future. Choose which to measure, such as your vitamin D, omega-3s, and essential minerals including magnesium and zinc, by creating your custom home test kit today. Take steps to improve the status of each of these measurements to benefit your overall health. You can also track your own intakes, symptoms and results to see what works best for YOU.

Enroll and test your levels today, learn what steps to take to improve your status of vitamin D (see below) and other nutrients and blood markers, and take action! By enrolling in the GrassrootsHealth projects, you are not only contributing valuable information to everyone, you are also gaining knowledge about how you could improve your own health through measuring and tracking your nutrient status, and educating yourself on how to improve it.

What Does it Take YOU to Get Your D to 40 ng/ml (100 nmol/L)?

Did you know your health could be greatly affected by making sure you have a vitamin D level of at least 40 ng/ml (100 nmol/L)? Help us help you.

STEP 1 - Do you know what your vitamin D level is? If not, be sure to test today to find out.

STEP 2 – Determine your target level. Are you at your target level? Experts recommend a level of at least 40-60 ng/ml (100-150 nmol/L).

STEP 3 – Need to boost your level? Use the D*calculator to see how much vitamin D it may take to reach your target. Opt for the Loading Dose for a quicker boost.

STEP 4 – Optimize how your body absorbs and utilizes vitamin D with co-nutrients and these simple steps.

STEP 5 – Re-Test! This is an important step to make sure you have reached your target level, and to ensure you are not taking too much! Re-testing after 3-4 months is recommended.

STEP 6 – Adjust, Repeat…

Give your immune system the nutrients it needs to support a healthy you and protect yourself from unnecessary diseases, especially COVID-19.


The first Randomized Controlled Trial on vitamin D and COVID-19 has shown a 96% lower risk of ICU admission for those receiving vitamin D (as 25(OH)D to quickly boost vitamin D blood levels) along with the standard treatment, compared to those receiving standard treatment alone.

These results support many previous observational studies showing a relationship between vitamin D levels and intake and COVID-19 severity.

Review the Latest Nutrient Research for COVID-19

GrassrootsHealth Nutrient Research Institute has launched the new Immune Boost project with the use of our myData-myAnswers nutrient health system that nearly 15,000 people are already using for their health. Specific markers that influence immune health are suggested for testing as part of this project including:

  • Vitamin D
  • Omega-3 Index
  • Essential elements magnesium, selenium, and zinc
  • hsCRP

Our goal is to demonstrate how one can use the Nutrient Research Model established by Dr. Robert Heaney to show the effect of vitamin D serum levels of at least 40 ng/ml (100 nmol/L) on risk reduction for all ethnicities in the population. Status and intake of other nutrients will also be analyzed for any type of relationship to immune status and symptom severity. Join the project today!

Please let us know if you're interested in helping sponsor this project.

CLICK HERE for updates and new information about the project.

Through GrassrootsHealth Nutrient Research Institute, you can also test your essential elements magnesium, copper, zinc and selenium, toxins such as lead, mercury and cadmium, as well as your omega-3 levels, inflammation levels and thyroid stimulating hormone (TSH) level. Find out your levels today! Log on to the test selection page (click the link below) to get your tests and see for yourself if your levels can be improved.

Make sure you track your results before and after, about every 6 months!

Click Here to Access the Test Page

How can I track my nutrient intake and levels over time?

To help you track your supplement use and nutrient levels, GrassrootsHealth has created the Personal Health Nutrient Decision System called

For each specific supplement, you can track what days you take it, how much, and many other details.  This will help you know your true supplemental intake and what patterns of use work for you to reach and maintain optimum nutrient levels. Check it out today!