What Is Your Microbiome And Why Is It Important?

Written by Dr. Steve Chaney on . Posted in Microbiome

Probiotics and Hero Bacteria

Author: Dr. Stephen Chaney


what is your microbiomeSuddenly the term “microbiome” is hot. It is featured in books, internet articles, and marketing materials produced by supplement companies wanting to sell their “magic” probiotic supplements. But, you are confused. You don’t know if what you read is true or just marketing hype.  What is your microbiome anyway?

You have been asking me: “What is my microbiome? “Why is it important?” “How does it affect my health?” “Should I take a probiotic?” “What else should I do?”

I covered this topic in a section of my book, “Slaying The Food Myths” called “Our Mighty Microbiome.”  However, this is an exploding area of scientific research. Published papers on our microbiome have increased by 600% in just the past 10 years. I already need to update the information in my book.


What Is Your Microbiome?

what is your microbiome bacteriaYour microbiome is defined as the community of microorganisms (bacteria, yeast and other fungi, and viruses) that live in and on you. Most of those microorganisms are bacteria, and most of them reside in your large intestine. Thus, the term “gut bacteria” is a useful and easier to understand approximation.

We are just beginning to understand just how complex and diverse our microbiome community is. Each of us harbor about 38 trillion microorganisms (give or take a few trillion). That means we each have slightly more microorganisms than we do cells in our body. However, it is not just the sheer number of microorganisms that is impressive. It is the number of different species we harbor in our bodies that indicates the true complexity of our microbiome.

For example, we each have more than 1,000 different species of bacteria in our large intestine. Collectively, these bacteria have around 750,000 unique genes. That is 30 times more than the human genome. Even so, understanding the health implications of our microbiome would be relatively simple if we all had the same species of bacteria in our intestines, but we don’t.

We are all unique. We all have different species in our intestines. The only simplifying principle is that these bacteria seem to exist as in distinct communities that generally group together. Even so, our microbiomes are amazingly complex.


We Are What We Eat

what is your microbiome are what we eatYou have probably heard the phrase “We are what we eat” before and dismissed it. After all, we can eat carrots all day long, and we will never turn into a carrot. However, that phrase is literally true when we consider our microbiomes. For example, the microbiomes of meat-eaters have totally different families of microorganisms than microbiomes of vegetarians. We don’t yet fully understand the implications of these differences in gut bacteria. However, we think they may be responsible for some of the differences in health outcomes of meat eaters and vegetarians.

Our microbiomes are also influenced by individual foods in our diet. In part, that is because each food has a unique blend of fibers. To fully comprehend the significance of that statement, we need to understand what fibers do. Most of us think of fibers as the indigestible portion of foods. We think of it as “roughage” that helps keeps our intestines moving and binds toxins, so they can be eliminated safely. That is true, but fiber is much more.

While we can’t digest fiber, the microorganisms living in our intestine can digest much of it. That fiber becomes food for the microorganisms. We refer to food for our intestinal microorganisms as “prebiotics.”  That means you probably need to rethink what the term prebiotic really means.

In the past you have probably thought of prebiotics as supplements designed to support the growth of certain bacteria in our intestines. Now you know that prebiotic also refers to the fibers in the foods we eat. Because each food has a unique blend of fibers, each food supports the growth of slightly different populations of intestinal bacteria. This helps explain why the human microbiome is so complex.

We don’t fully understand the health consequences of these differences in our microbiome, but we think they are huge (see below). This is one reason I do not recommend any diet that eliminates whole food groups. It is easy to say we can replace the missing nutrients with a multivitamin. But, what about the missing fiber? We know that will affect our microbiome. We simply don’t know enough about the long-term health consequences of altering our microbiome to recommend eliminating high fiber foods from our diet. It’s not nice to fool with Mother Nature.

For example, in “Slaying The Food Myths” I discussed the evidence that meat-based low-carb diets are less healthy long term than primarily plant-based low-carb diets. That could be because of saturated fats and excess consumption of red meat. However, it might also be caused by the effect on the microbiome of the food groups that are eliminated in meat-based, low-carb diets.

Finally, as if all of this weren’t complex enough, there is some evidence that our microbiome is influenced by lifestyle (particularly obesity and exercise) and environment (particularly toxins in the environment). But, that’s another topic for another day.


Why Is Your Microbiome Important?


what is your microbiome hero bactriaNow you know that our microbiome is incredibly complex. You also know “We are what we eat.”  Why are those two things important? While there is a lot we don’t yet know, it appears that our microbiome has a powerful influence on our health.

For example, we know that our gut bacteria can convert components of the foods we eat into compounds that are absorbed into our bloodstream and either have a positive or negative effect on our health. Let me give you some specific examples:

  • “Good” intestinal bacteria produce butyrate in the process of digesting fiber. Butyrate, in turn, is thought to support intestinal health and activate genes that lower blood cholesterol levels.
  • “Bad” intestinal bacteria convert carnitine (a normal human metabolite found in meat, particularly red meat) into trimethylamine-N-oxide or TMAO, which is thought to increase the risk of heart disease. In a cruel twist of fate, these particular “bad” bacteria seem to be prevalent in the microbiome of meat-eaters, but absent from the microbiome of vegetarians.
  • We have been told that polyphenols are good for us. However, polyphenols are poorly absorbed. Fortunately, polyphenols are rapidly metabolized by our microbiome into metabolites that are more easily absorbed. Many experts think it is those microbiome-produced metabolites that are responsible for the health benefits of polyphenols. If everyone’s microbiome is different, how does that affect the health benefits of polyphenols. A recent study  puts this into perspective. The authors fed an apple extract to 12 individuals and measured 110 polyphenol metabolites in their blood over the next 5 hours. The pattern of blood metabolites was different for every individual in the study. Furthermore, the pattern of blood metabolites correlated with differences in the species of bacteria in their intestine.

I have given examples of 3 different kinds of food-microbiome interactions here. There are more examples of each type of food-microbiome interaction in the literature. This just adds another layer of complexity. Not only does the food we eat affect our microbiome, but our microbiome influences how we metabolize the foods we eat. We are just beginning to understand how these differences influence our health. However, based on what we currently know, here are some of the ways our microbiome can influence our health:

Current evidence suggests that “bad” bacteria and yeast in our intestines may:

  • Compromise our immune system.
  • Create a “leaky gut”, which allows partially digested foods to get into the bloodstream where they can trigger inflammation and auto-immune responses.
  • Adversely affect brain function and moods.
  • Convert components of the foods we eat into compounds which increase the risk of cancer and heart disease.
  • Perhaps, even make us fat.

In contrast, “good” bacteria:

  • Crowd out the bad bacteria and prevent the health problems they cause.
  • Break down undigested fiber into compounds that are beneficial to our health.


What About Probiotics?

what is your microbiome probioticsNow you know how important our microbiome is to our health, you are probably wondering whether you should add one or more probiotic supplements to your health regimen. Let me give you a brief primer on probiotic supplements.

“Hero Bacteria”: We have over 1,000 species of bacteria in our microbiome, and they work together in families. With that complexity, you may be wondering how someone could hope to create a probiotic supplement that worked. Fecal transplants (all the intestinal bacteria from a healthy individual) have been used for some life-threatening conditions, but I don’t think that is an approach most of us want to consider.

For better or worse, modern science uses a reductionist approach. We focus on a single component of a system and test its effectiveness in clinical studies. In the probiotic world, we focus on an individual strain of bacteria. If it proves effective in clinical studies, it is given a name and is used in probiotic supplements. It becomes what I call a “hero bacteria.”

For example, if scientists were looking for a probiotic supplement to aid with digestion or immunity, they would test dozens of strains initially. They would then select the one strain for further study. It may have been selected because it performed best in the preliminary studies. However, it may have been selected based on other characteristics, such as how easy it was for the scientist to grow in a culture dish. That strain is then put through rigorous clinical trials. If it performs well there, it becomes a “hero bacteria” suitable for a probiotic supplement. It has been “proven” to provide a specific benefit to our health.

However, it is not the only bacteria to provide that benefit. It might not have even been the “best” bacteria. It may have simply been the one that grew best in the lab.

Rule #1: Look for one or more named “hero bacteria” in your probiotic supplement. They have been proven to provide a specific health benefit.

Not All “Hero Bacteria” Are Created Equal: In some cases, companies that have developed a particular strain of “hero bacteria” have published the clinical studies supporting their claims in peer-reviewed journals. In other cases, they make the study claims, but say their data is “proprietary.” I am a skeptic. If they haven’t published their data, I assume it wasn’t good enough to be published.

Rule #2: Avoid any probiotic supplements that do not provide you with studies published in peer-reviewed scientific journals showing that studies with their “hero bacteria” support their product claims.

Some Companies Get Ahead Of What Good Science Supports: Their claims sound amazing, but they aren’t supported by clinical proof. They call it marketing. I call it lying.

In some cases, the lying is clear because they don’t provide you with clinical studies published in peer-reviewed journals.

However, if their claims sound too good to be true and they have provided clinical studies published in peer-reviewed journals, my advice is to read the studies. You don’t need to be an expert. The abstracts for every published article are available online. Read the abstract and see what health claims it makes. [Reviewers of peer-review articles generally insist that the claims match the evidence.] If a company’s marketing claims exceed the claims from the published studies backing their product, they are probably lying to you.

Rule #3: If a company’s marketing claims exceed the claims from the published studies backing their product, run the other direction. They are lying to you.

It Takes A Village: While it is useful to have one or more “hero bacteria” in your probiotic supplement, don’t assume that is all you need. Remember that you have many more than one or two bacteria in your gut. You have a thousand or more different species. For every “hero bacteria” that has gone through the clinical review process, there are dozens more that provide the same benefit, and they all work together. More importantly, they work by different mechanisms. You need a holistic approach to creating a healthier microbiome.

My recommendation is to choose probiotic supplements that contain several species that work together rather than just a single “hero bacteria.” I also recommend following a diet that supports a healthy microbiome. Based on what we currently know, that would be a primarily plant-based diet containing all five food groups.

Rule #4: Choose probiotic supplements that contain several species that work together rather than a single “hero bacteria”.


The Bottom Line


Because I know how confusing the term “microbiome” is to most of you I have written a brief overview of our microbiome and what it does. Topics I have covered are:

  • What is our microbiome?
  • How do the foods we eat influence our microbiome?
  • How does our microbiome influence the metabolism of the foods we eat?
  • How does our microbiome influence our health?
  • How do you select a good probiotic supplement?

If any of these topics interest you, read the article above.


These statements have not been evaluated by the Food and Drug Administration. This information is not intended to diagnose, treat, cure or prevent any disease.

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Comments (3)

  • Mary Romer


    Thank you so much for all of your articles. Found this one to be especially informative.


  • Brenda Anderberg


    This was helpful for me. I have been wondering about the fairly new ‘craze’ is about probiotics & which one to purchase. Then PRE biopics began their hard sell marketing and confused me more as I did not know the difference. Still working on that one.


    • Dr. Steve Chaney


      Dear Brenda,
      You will find guidelines in tomorrow’s health tip.
      Dr. Chaney


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Latest Article

The Truth About Vitamin D

Posted December 11, 2018 by Dr. Steve Chaney

Does Vitamin D Reduce Risk Of Heart Disease & Cancer?

Author: Dr. Stephen Chaney


the truth about vitamin dYou have every right to be confused. One day you are told that vitamin D reduces your risk of heart disease and cancer. The next day you are told vitamin D makes has no effect on those diseases. You are told vitamin D is a waste of money. What should you believe?  What is the truth about vitamin D?

In mid-November a major clinical study called VITAL was published. It examined the effect of vitamin D and omega-3s on heart disease and cancer risk. Last week I wrote about the omega-3 portion of the study. This week I will cover the vitamin D portion of the study.

Once again, if you rely on the media for your information on supplementation, you are probably confused. Headlines ranged from “Vitamin D Is Ineffective For Preventing Cancer And Heart Disease to “Vitamin D Lowers Odds Of Cancer Death.” What is the truth?

The problem is that reporters aren’t scientists. They don’t know how to interpret clinical studies. What they report is filtered through their personal biases. That is why I take the time to carefully evaluate the clinical studies, so I can provide you with accurate information. Let me sort through the dueling headlines and give you the truth about vitamin D, cancer, and heart disease.

How Was The Study Designed?

the truth about vitamin d studyThe VITAL study (JE Manson et al, New England Journal of Medicine, DOI: 10.1056/NEJMoa1811403) enrolled 25,871 healthy adults (average age = 67) in the United States. The study participants were 50% female, 50% male, and 20% African American. None of the participants had preexisting cancer or heart disease. The characteristics of the study group were typical of the American population at that age, namely:

  • The average BMI was 28, which means that most of the participants were significantly overweight.
  • 7% of them had diabetes.

Study participants were given questionnaires on enrollment to assess clinical and lifestyle factors including dietary intake. Blood samples were taken from about 65% of the participants to determine 25-hydroxyvitamin D levels (a measure of vitamin D status) at baseline and at the end of the first year. The participants were given either 2,000 IU of vitamin D/day or a placebo and followed for an average of 5.3 years.

There were two important characteristics of the participants in this study that may have influenced the outcome.

  • The average 25-hydroxyvitamin D level of participants at the beginning of the study was 31 ng/ml (78 nmol/L). The NIH considers 20-50 ng/ml (50-125 nmol/L) to be the optimal level of 25-hydroxyvitamin D for most physiological functions. This means that study participants started in the middle of the optimal range with respect to vitamin D status.

[Note: The NIH defines the 20-50 ng/ml range as “adequate.”  However, I know many of my readers like to aim beyond adequate to reach what they consider to be “optimal.”  In the case of vitamin D, that might not be a good idea. The NIH considers anything above 50 ng/ml as associated “with potentially adverse effects.”  For that reason, I will refer to the 20-50 ng/ml range as optimal for this article. I wouldn’t want to encourage my readers to be aiming for above 50 ng/ml.]

  • Only 12.7% of participants had 25-hydroxyvitamin D levels below 20 ng/ml, which the NIH considers to be inadequate. The results with this group were not statistically different from the study participants with optimal vitamin D status, but it is not clear that there were enough people in this subgroup for a statistically valid comparison with participants starting with an optimal vitamin D status.
  • At the end of the first year, 25-hydroxyvitamin D levels in the treatment group increased to 42 ng/ml (105 nmol/L), which is near the upper end of the optimal range. Thus, for most of the participants, the study was evaluating whether there was a benefit of increasing vitamin D status from the middle to the upper end of the optimal range.
  • The study allowed subjects to continue taking supplements that contained up to 800 IU of vitamin D. While the authors tried to correct for this statistically, it is a confounding variable.

Does Vitamin D Reduce The Risk Of Cancer?


the truth about vitamin d and cancerYou may remember from last week that omega-3s were more effective for reducing heart disease risk than for reducing cancer risk. What is the truth about vitamin D and cancer risk?   The results are reversed for vitamin D, so I will discuss cancer first.

The study reported that vitamin D supplementation did not reduce a diagnosis of invasive cancer of any type, breast cancer, prostate cancer, or colon cancer during the 5.3-year time-period of this study. This was the result that was reported in the abstract and was what lazy journalists, who never read past the abstract, reported.

However, the rest of the study was more positive. For example, occurrence of invasive cancer of any type was reduced by:

  • 23% in African-Americans.
  • 24% in patients with a healthy body weight.

Several previous studies have suggested that vitamin D may be more effective at preventing cancer in people with a healthy body weight, but the mechanism of this effect is currently unknown.

Most previous studies have not included enough African-Americans to determine whether they respond more favorably to vitamin D supplementation. However, African-Americans have a higher risk of cancer, so this finding deserves follow-up.

In addition, when the study looked at deaths from cancer, the results were very positive. For example:

  • Cancer deaths during the 5.3-year study period were reduced by 17%.
  • The longer vitamin D supplementation was continued the more effective it became at reducing cancer deaths. For example,
  • When the authors excluded cancer deaths occurring during the first year of supplementation, vitamin D reduced cancer deaths by 21%.
  • When the authors excluded cancer deaths occurring during the first two years of supplementation, vitamin D reduced cancer deaths by 25%.

Finally, no side effects were noted in the vitamin D group.


Does Vitamin D Reduce The Risk Of Heart Disease?


the truth about vitamin d and heart diseaseThe VITAL study also looked at the effect of vitamin D on heart disease risk. What is the truth about vitamin D and heart disease?  The results from this study were uniformly negative. There was no effect of vitamin D supplementation on all major cardiovascular events combined, heart attack, stroke, or death from heart disease. Does that mean vitamin D has no role in reducing heart disease risk? That’s not clear.

The authors had a thought-provoking explanation for why the results were negative for heart disease, but positive for cancer. Remember that the participants in this trial started with a 25-hydroxyvitamin D level of 31 ng/ml and increased it to at least 42 ng/ml with vitamin D supplementation.

The authors stated that previous studies have suggested the 25-hydroxyvitamin D level associated with the lowest risk for heart disease is between 20 and 25 ng/ml. If that is true, most of the participants in this trial were already in the lowest possible risk for heart disease with respect to vitamin D status before the study even started. There would be no reason to expect additional vitamin D to further reduce their risk of heart disease.

In contrast, the authors said that previous studies suggest the 25-hydroxyvitamin D level associated with the lowest risk of cancer deaths is above 30 ng/ml. If that is true, it would explain why vitamin D supplementation in this study was effective at reducing cancer deaths.

However, previous placebo-controlled clinical studies have also been inconclusive with respect to vitamin D and heart disease. My recommendation would be to think of adequate vitamin D status as part of a holistic approach to reducing heart disease – one that includes a heart-healthy diet and a heart-healthy lifestyle – rather than a “magic bullet” that decreases heart disease risk by itself.

As for heart-healthy diets, I discuss the pros and cons of various diets in my book, “Slaying The Food Myths.”  As I discuss in my book, the weight of scientific evidence supports primarily plant-based diets that include omega-3s as heart healthy. As an example, the Mediterranean diet is primarily plant-based and is rich in healthy oils like olive oil and omega-3s. It is associated with reduced risk of both heart disease and cancer.


What Is The Truth About Vitamin D?


the truth about vitamin d signThere is a lot of confusion around the question of whether vitamin D reduces the risk of cancer. This study strengthened previous observation suggesting that vitamin D supplementation decreases cancer deaths. However, it is also consistent with previous studies that have failed to find an effect of vitamin D on cancer development. How can we understand this apparent discrepancy? The authors provided a logical explanation. They pointed out that:

  • Cancer development takes 20-30 years while this clinical study lasted only 5.3 years. That means that vitamin D supplementation only occurred at the tail end of the cancer development process. In fact, the cancer was already there in most of the patients in the study who developed cancer. It just had not been diagnosed yet. In the words of the authors: “Given the long latency for cancer development, extended follow-up is necessary to fully ascertain potential effects [of vitamin D supplementation].”
  • In contrast, none of the patients had been diagnosed with cancer when they entered the trial. That means that the patients were diagnosed with cancer during the 5.3-year study period. They were receiving extra vitamin D during the entire period of cancer treatment. Thus, the effect of vitamin D on reducing cancer deaths was easier to detect.

What Does This Study Mean For You?

the truth about vitamin d questionsVitamin D Is Likely To Decrease Your Risk Of Dying From Cancer: When you combine the results of this study with what we already know about vitamin D and cancer, the results are clear. Vitamin D appears to reduce your risk of dying from cancer. More importantly, the longer you have been supplementing with vitamin D, the greater your risk reduction is likely to be.

Vitamin D May Decrease Your Risk Of Developing Cancer: Association studies suggest that optimal vitamin D status is associated with decreased cancer risk, especially colon cancer risk. However, the long time for cancer development means that we may never be able to prove this effect through double-blind, placebo-controlled clinical trials.

Holistic Is Best: When you combine the VITAL study results with what we already know about vitamin D and heart disease, it appears that supplementing with vitamin D is unlikely to reduce your risk of developing heart disease unless you are vitamin D deficient. However, a holistic approach that starts with a healthy, primarily plant-based diet and makes sure your vitamin D status is adequate is likely to be effective.

The same is likely true for cancer. While the latest study suggests that vitamin D supplementation reduces your risk of dying from cancer, those vitamin D supplements are likely to be even more effective if you also adopt a healthy diet and lifestyle.

How Much Vitamin D Do You Need? The optimal dose of vitamin D is likely to be different for each of us. One of the things we have learned in recent years is that there are significant differences in the efficiency with which we convert vitamin D from diet and/or sun exposure into the active form of vitamin D in our cells. Fortunately, the blood test for 25-hydroxyvitamin D is readily available and is widely considered to be an excellent measure of our vitamin D status.

I recommend that you have your blood level of 25-hydroxyvitamin D tested on an annual basis. Based on the best currently available data, I recommend you aim for >20 ng/ml (50 nmol/L) if you wish to minimize your risk of heart disease and >30 ng/ml (75 nmol/L) if you wish to minimize your risk of cancer. If you can achieve those levels through diet and a multivitamin supplement, that is great. If not, I would recommend adding a vitamin D supplement until those levels are achieved.

Finally, you shouldn’t think of vitamin D as a magic bullet. If you are a couch potato and eat sodas and junk food, don’t expect vitamin D to protect you from cancer and heart disease. You should think of maintaining adequate 25-hydroxyvitamin D levels as just one component of a holistic approach to healthy, disease-free living.


The Bottom Line


There is a lot of confusion around the question of whether vitamin D reduces the risk of cancer and heart disease. A major clinical study has just been published that sheds light on these important questions. It reported:

  • Vitamin D did not decrease the risk of developing cancer during the 5.3-year study duration. The authors pointed out that cancer takes 20-30 years to develop, which means their study was probably too short to detect an effect of vitamin D on the risk of developing cancer.
  • Vitamin D did decrease the risk of dying from cancer, and the longer people were supplementing with vitamin D the bigger the protective effect of vitamin D was.
  • Vitamin D did not decrease the risk of heart disease. However, most study participants had a level of 25-hydroxyvitamin D that was optimal for reducing the risk of heart disease at the beginning of the study. There was no reason to expect that extra vitamin D would provide additional benefit.
  • With respect to both cancer and heart disease the best advice is to:
    • Get your 25-hydroxyvitamin D levels tested on an annual basis and supplement, if necessary, to keep your 25-hydroxyvitamin D levels in what the NIH considers to be an adequate range (20-50 ng/ml).
    • We do not have good dose response data for the beneficial effects of vitamin D on heart disease and cancer. However, according to this article, previous studies suggest you may want to am for 25-hydroxyvitamin D levels above 20 ng/ml to reduce the risk of heart disease and above 30 ng/ml to reduce your risk of cancer.
    • Consider vitamin D as just one component of a holistic approach to healthy, disease-free living.

For more details about the interpretation of these studies and what they mean for you, read the article above.


These statements have not been evaluated by the Food and Drug Administration. This information is not intended to diagnose, treat, cure or prevent any disease.