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.

    Reply

  • 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.

    Reply

    • Dr. Steve Chaney

      |

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

      Reply

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Latest Article

Does Magnesium Optimize Vitamin D Levels?

Posted February 12, 2019 by Dr. Steve Chaney

The Case For Holistic Supplementation

Author: Dr. Stephen Chaney

 

Does magnesium optimize vitamin D levels?

magnesium optimize vitamin dOne of the great mysteries about vitamin D is the lack of correlation between vitamin D intake and blood levels of its active metabolite, 25-hydroxyvitamin D. Many people who consume RDA levels of vitamin D from foods and/or supplements end up with low blood levels of 25-hydroxyvitamin D. The reason(s) for this discrepancy between intake of vitamin D and blood levels of its active metabolite are not currently understood.

Another great mystery is why it has been so difficult to demonstrate benefits of vitamin D supplementation. Association studies show a strong correlation between optimal 25-hydroxyvitamin D levels and reduced risk of heart disease, cancer, and other diseases. However, placebo-controlled clinical trials of vitamin D supplementation have often come up empty. Until recently, many of those studies did not measure 25-hydroxyvitamin D levels. Could it be that optimal levels of 25-hydroxyvitamin D were not achieved?

The authors of the current study hypothesized that optimal magnesium status might be required for vitamin D conversion to its active form. You are probably wondering why magnesium would influence vitamin D metabolism. I had the same question.

The authors pointed out that:

  • Magnesium status affects the activities of enzymes involved in both the synthesis and degradation of 25-hydroxyvitamin D.
  • Some clinical studies have suggested that magnesium intake interacts with vitamin D intake in affecting health outcomes.
  • If the author’s hypothesis is correct, it is a concern because magnesium deficiency is prevalent in this country. In their “Fact Sheet For Health Professionals,” the NIH states that “…a majority of Americans of all ages ingest less magnesium from food than their respective EARs [Estimated Average Requirement]; adult men aged 71 years and older and adolescent females are most likely to have low intakes.” Other sources have indicated that magnesium deficiency may approach 70-80% for adults over 70.

If the author’s hypothesis that magnesium is required for vitamin D activation is correct and most Americans are deficient in magnesium, this raises some troubling questions.

  • Most vitamin D supplements do not contain magnesium. If people aren’t getting supplemental magnesium from another source, they may not be optimally utilizing the vitamin D in the supplements.
  • Most clinical studies involving vitamin D do not also include magnesium. If most of the study participants are deficient in magnesium, it might explain why it has been so difficult to show benefits from vitamin D supplementation.

Thus the authors devised a study (Q Dai et al, American Journal of Clinical Nutrition, 108: 1249-1258, 2018 ) to directly test their hypothesis.

 

How Was The Study Designed?

magnesium optimize vitamin d studyThe authors recruited 180 volunteers, aged 40-85, from an ongoing study on the prevention of colon cancer being conducted at Vanderbilt University. The duration of the study was 12 weeks. Blood was drawn at the beginning of the study to measure baseline 25-hydroxyvitamin D levels. Three additional blood draws to determine 25-hydroxyvitamin D levels were performed at weeks 1, 6, and 12.

Because high blood calcium levels increase excretion of magnesium, the authors individualized magnesium intake based on “optimizing” the calcium to magnesium ratio in the diet rather than giving everyone the same amount of magnesium. The dietary calcium to magnesium ratio for most Americans is 2.6 to 1 or higher. Based on their previous work, they considered an “ideal” calcium to magnesium ratio to be 2.3 to 1. The mean daily dose of magnesium supplementation in this study was 205 mg, with a range from 77 to 390 mg to achieve the “ideal” calcium to magnesium ratio. The placebo was an identical gel capsule containing microcrystalline cellulose.

Two 24-hour dietary recalls were conducted at baseline to determine baseline dietary intake of calcium and magnesium. Four additional 24-hour dietary recalls were performed during the 12-week study to assure that calcium intake was unchanged and the calcium to magnesium ratio of 2.3 to 1 was achieved.

In short this was a small study, but it was very well designed to test the author’s hypothesis.

 

Does Magnesium Optimize Vitamin D Levels?

 

does magnesium optimize vitamin d levelsThis was a very complex study, so I am simplifying it for this discussion. For full details, I refer you to the journal article (Q Dai et al, American Journal of Clinical Nutrition, 108: 1249-1258, 2018).

The most significant finding was that magnesium supplementation did affect blood levels of 25-hydroxyvitamin D. However, the effect of magnesium supplementation varied depending on the baseline 25-hydroxyvitamin D level at the beginning of the study.

  • When the baseline 25-hydroxyvitamin D was 20 ng/ml or less (which the NIH considers inadequate), magnesium supplementation had no effect on 25-hydroxyvitamin D levels.
  • When the baseline 25-hydroxyvitamin D was 20-30 ng/ml (which the NIH considers the lower end of the adequate range), magnesium supplementation increased 25-hydroxyvitamin D levels.
  • When the baseline 25-hydroxyvitamin D level approached 50 ng/ml (which the NIH says may be “associated with adverse effects”), magnesium supplementation lowered 25-hydroxyvitamin D levels.

The simplest interpretation of these results is:

  • When vitamin D intake is inadequate, magnesium cannot magically create 25-hydroxyvitamin D from thin air.
  • When vitamin D intake is adequate, magnesium can enhance the conversion of vitamin D to 25-hydroxyvitamin D.
  • When vitamin D intake is too high, magnesium can help protect you by lowering 25-hydroxyvitamin D levels.

The authors concluded: “Our findings suggest that optimal magnesium status may be important for optimizing 25-hydroxyvitamin D status. Further dosing studies are warranted…”

 

What Does This Study Mean For You?

magnesium optimize vitamin d for youThis was a groundbreaking study that has provided novel and interesting results.

  • It provides the first evidence that optimal magnesium status may be required for optimizing the conversion of vitamin D to 25-hydroxyvitamin D.
  • It suggests that optimal magnesium status can help normalize 25-hydroxyvitamin D levels by increasing low levels and decreasing high levels.

However, this was a small study and, like any groundbreaking study, has significant limitations. For a complete discussion of the limitations and strengths of this study I refer you to the editorial (S Lin and Q Liu, American Journal of Clinical Nutrition, 108: 1159-1161, 2018) that accompanied the study.

In summary, this study needs to be replicated by larger clinical studies with a more diverse study population. In order to provide meaningful results, those studies would need to carefully control and monitor calcium, magnesium, and vitamin D intake. There is also a need for mechanistic studies to better understand how magnesium can both increase low 25-hydroxyvitamin D levels and decrease high 25-hydroxyvitamin D levels.

However, assuming the conclusions of this study to be true, it has some interesting implications:

  • If you are taking a vitamin D supplement, you should probably make sure that you are also getting the DV (400 mg) of magnesium from diet plus supplementation.
  • If you are taking a calcium supplement, you should check that it also provides a significant amount of magnesium. If not, change supplements or make sure that you get the DV for magnesium elsewhere.
  • I am suggesting that you shoot for the DV (400 mg) of magnesium rather than reading every label and calculating the calcium to magnesium ratio. The “ideal” ratio of 2.3 to 1 is hypothetical at this point. A supplement providing the DV of both calcium and magnesium would have a calcium to magnesium ratio of 2.5, and I would not fault any manufacturer for providing you with the DV of both nutrients.
  • If you are taking high amounts of calcium, I would recommend a supplement that has a calcium to magnesium ratio of 2.5 or less.
  • If you are considering a magnesium supplement to optimize your magnesium status, you should be aware that magnesium can cause gas, bloating, and diarrhea. I would recommend a sustained release magnesium supplement.
  • Finally, whole grains and legumes are among your best dietary sources of magnesium. Forget those diets that tell you to eliminate whole food groups. They are likely to leave you magnesium-deficient.

Even if the conclusions of this study are not confirmed by subsequent studies, we need to remember that magnesium is an essential nutrient with many health benefits and that most Americans do not get enough magnesium in their diet. The recommendations I have made for optimizing magnesium status are common-sense recommendations that apply to all of us.

 

The Case For Holistic Supplementation

 

magnesium optimize vitamin d case for holistic supplementationThis study is one of many examples showing that a holistic approach to supplementation is superior to a “magic bullet” approach where you take individual nutrients to solve individual problems. For example, in the case of magnesium and vitamin D:

  • If you asked most nutrition experts and supplement manufacturers whether it is important to provide magnesium along with vitamin D, their answer would likely be “No”. Even if they are focused on bone health, they would be more likely to recommend calcium along with vitamin D than magnesium along with vitamin D.
  • If your doctor has tested your 25-hydroxyvitamin D levels and recommended a vitamin D supplement, chances are they didn’t also recommend that you optimize your magnesium status.
  • Clinical studies investigating the benefits of vitamin D supplementation never ask whether magnesium intake is optimal.

That’s because most doctors and nutrition experts still think of nutrients as “magic bullets.” I cover holistic supplementation in detail in my book “Slaying The Supplement Myths.”  Other examples that make a case for holistic supplementation that I cover in my book include:

  • A study showing that omega-3 fatty acids and B vitamins may work together to prevent cognitive decline. Unfortunately, most studies looking at the effect of B vitamins on cognitive decline have not considered omega-3 status and vice versa. No wonder those studies have produced inconsistent results.
  • Studies looking at the effect of calcium supplementation on loss of bone density in the elderly have often failed to include vitamin D, magnesium, and other nutrients that are needed for building healthy bone. They have also failed to include exercise, which is essential for building healthy bone. No wonder some of those studies have failed to find an effect of calcium supplementation on bone density.
  • A study reported that selenium and vitamin E by themselves might increase prostate cancer risk. Those were the headlines you might have seen. The same study showed Vitamin E and selenium together did not increase prostate cancer risk. Somehow that part of the study was never mentioned.
  • A study reported that high levels of individual B vitamins increased mortality slightly. Those were the headlines you might have seen. The same study showed that when the same B vitamins were combined in a B complex supplement, mortality decreased. Somehow that observation never made the headlines.
  • A 20-year study reported that a holistic approach to supplementation produced significantly better health outcomes.

In summary, vitamins and minerals interact with each other to produce health benefits in our bodies. Some of those interactions we know about. Others we are still learning about. When we take high doses of individual vitamins and minerals, we create potential problems.

  • We may not get the full benefit of the vitamin or mineral we are taking because some other important nutrient(s) may be missing from our diet.
  • Even worse, high doses of one vitamin or mineral may interfere with the absorption or enhance the excretion of another vitamin or mineral. That can create deficiencies.

The same principles apply to our diet. I mentioned earlier that whole grains and legumes are among the best dietary sources of magnesium. Eliminating those two foods from the diet increases our risk of becoming magnesium deficient. And, that’s just the tip of the iceberg. Any time you eliminate foods or food groups from the diet, you run the risk of creating deficiencies of nutrients, phytonutrients, specific types of fiber, and the healthy gut bacteria that use that fiber as their preferred food source.

The Bottom Line

 

A recent study suggests that optimal magnesium status may be important for optimizing 25-hydroxyvitamin D status. This is one of many examples showing that a holistic approach to supplementation is superior to a “magic bullet” approach where you take individual nutrients to solve individual problems. For example, in the case of magnesium and vitamin D:

  • If you asked most nutrition experts and supplement manufacturers whether it is important to provide magnesium along with vitamin D, their answer would likely be “No.”  Even if they are focused on bone health, they would be more likely to recommend calcium along with vitamin D than magnesium along with vitamin D.
  • If your doctor has tested your 25-hydroxyvitamin D levels and recommended a vitamin D supplement, chances are he or she did not also recommend that you optimize your magnesium status.
  • Clinical studies investigating the benefits of vitamin D supplementation never ask whether magnesium intake is optimal. That may be why so many of those studies have failed to find any benefit of vitamin D supplementation.

I cover holistic supplementation in detail in my book “Slaying The Supplement Myths” and provide several other examples where a holistic approach to supplementation is superior to taking individual supplements.

In summary, vitamins and minerals interact with each other to produce health benefits in our bodies. Some of those interactions we know about. Others we are still learning about. Whenever we take high doses of individual vitamins and minerals, we create potential problems.

  • We may not get the full benefit of the vitamin or mineral we are taking because some other important nutrient(s) may be missing from our diet.
  • Even worse, high doses of one vitamin or mineral may interfere with the absorption or enhance the excretion of another vitamin or mineral. That can create deficiencies.

The same principles apply to what we eat. For example, whole grains and legumes are among the best dietary sources of magnesium. Eliminating those two foods from the diet increases our risk of becoming magnesium deficient. And, that’s just the tip of the iceberg. Any time you eliminate foods or food groups from the diet, you run the risk of creating deficiencies.

For more details about the current study and what it means to 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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