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Your Microbiome: The Most Promising Facts

bifidobacterium-bacterial-strain3d-illustration-picture-id1163670497 Your Microbiome: The Most Promising Facts

By Naveen Jain and Deepak Chopra™, MD

It is fair to say that the exploration of the microbiome has turned out to be the most exciting prospect in medicine since the discovery of DNA. Most people have at least heard the term “gut microbiome,” which applies to the trillions of microbes, chiefly bacteria, that live in the human digestive tract. Awareness has risen to the point that taking probiotics—over-the-counter additives of microbes to supplement and balance the gut microbiome—has become a global $5 billion-dollar market.

We’ve reached the point, after a decade of intense investigation, where the ABCs of the microbiome are known. These facts provide the groundwork for what you can do, or cannot do, to improve your own gut microbiome (the word “gut” is necessary because we have multiple microbiomes in our mouth, groin, and armpits as well as over the surface of our skin).


Here are some basic facts and the positive implications of each:

  • Every person’s microbiome is unique.

Positive implication: Individual diets can be tailored to promote the best bacterial activity in your diet.

  • Hundreds and perhaps thousands of different species of bacteria inhabit the gut microbiome. As part of a teeming community that is involved in digesting your food, some bacteria are beneficial, some are not.

Positive implication: It is possible to potentially increase the beneficial bacteria and decrease the harmful ones.

  • Through direct chemical signals sent to the immune system, the gut microbiome has a strong, perhaps the strongest, influence on your immune status.

Positive implication: All types of diseases, including cancer and the major chronic diseases of modern life (obesity, type 2 diabetes, heart disease, hypertension), might be prevented and possibly cured through maintaining a healthy gut microbiome.

  • Diet is seen as the most powerful way to change your gut microbiome, since each bacterial species feeds on specific foods.

Positive implication: Without any kind of medication, a healthy microbiome should be sustainable through proper diet alone.

You can see why the microbiome has provoked so much promise and excitement. As positive as these facts are, however, they are also very general. At present there are hundreds of studies on the gut microbiome that have reached no consensus, so the whole field remains in flux.   

Here are the major issues that need to be resolved.

  • There is no ideal microbiome and therefore no ideal diet. Much seems to depend on the individual. Even inside one person the community of micro-organisms is incredibly complex.
  • Studies show that indigenous peoples around the world have much richer gut microbiomes than in developed countries. This depletion of our microbiome has some researchers worried, but no conclusion has been reached.

With so many issues still up in the air, what can you reliably do to maintain a healthier microbiome? In your colon, the food that nourishes you isn’t what nourishes your microbiome. It feeds largely on fiber, of which there are many kinds. But essentially fiber is from vegetables, grains, and legumes. Those foods are considered “prebiotic,” meaning that they are the building blocks that the microbiome needs. A diet rich in prebiotics would include a wide variety of vegetables, fruits, grain, and nuts. This is far more important than taking a probiotic pill and buying active yogurt.

Secondly, it is now possible to test your own gut microbiome to see what is weak, deficient, or out of balance in it. To understand what such a test can tell you, we’ll delve into the biology of the gut microbiome.

Each person's gut microbiome can produce beneficial molecules such as vitamins and short chain fatty acids (SCFAs), and it can also produce harmful molecules (e.g., lipopolysaccharides and putrescine). They key is that the production of molecules is determined by the dietary ingredients in food. The micronutrients in our food are the raw materials for specific microbiome functions. Because every person’s gut microbiome is unique, the same food given to two people can cause the microbiome of one person to produce beneficial molecules and the other person harmful molecules.

By performing functional (gene expression) tests through stool samples, each person can feed their microbiome exactly what it needs to produce lots of beneficial molecules rather than the harmful ones. Presently the only such RNA (functional) microbiome test readily available is from Viome—in the interests of fair reporting, the two authors are the founder of Viome and an advisor to the company. But our larger aim is to further the practical application of microbiome research.

Let’s deepen this understanding. Your cells share a chemical language with the bacteria in your gut. They sense their environment using chemical signaling. Crucially, the immune system, senses the presence or absence of specific molecules that rigger an immune response. For example, your immune system mounts an inflammatory response if it senses the presence of lipopolysaccharide (LPS), and inflammation calms down in the presence of a different molecule, butyrate. Both LPS and butyrate can be produced by many types of bacteria under specific conditions. If we can figure out which foods a person should eat, and which ones to avoid, we can rebalance the functions of their microbiome to reduce the inflammation and chronic diseases. Because every person has a different gut microbiome, there is no one diet that is good for all people.

Only individual testing makes precise dietary recommendations possible. Your gut microbiome can be used to measure your own digestive abilities. For example, if our digestive juices are not able to process all the protein we eat, the undigested protein will make its way to the colon, where certain microbes can convert it to putrescine or cadaverine, two harmful chemicals that deserve their morbid names. If these microbial functions (processing of undigested proteins into putrescine or cadaverine) are measured by a functional stool test, it can inform a person to reduce their protein intake.

This brings up the difference between DNA and RNA tests. Let’s say that a DNA test determines that someone’s gut microbiome has the genes that ferment undigested proteins into putrescine and cadaverine. That DNA test cannot determine if those genes are active or not (in other words, is protein fermentation actually happening?). Only an RNA test can determine if harmful protein fermentation actually takes place or not, because it measures gene activity, not just the presence or absence of the genes.

Testing is a critical step in doing the most important thing, analyzing the state of your gut microbiome, since it is unique to you. There are exciting links being made with autoimmune disorders and a person’s immune response to invading pathogens (a pressing issue during the COVID-19 pandemic). With so much suspicion being directed at inflammation and stress as the root cause of chronic illness, the gut microbiome has huge implications.

We’ve given a one over lightly of the issues involved, but the important thing is that at this very moment faith, fiction, and facts are being separated out. This is some of the best medical news one can think of.

 Reprinted from San Francisco Chronicle with permission


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