“All disease begins in the gut.”


Short of ecological catastrophe, our diet is the most important environmental interaction we experience. We are quite literally bringing the outside environment into our own bodies; every day, several times a day. As we ingest food, the only thing running interference for us is the razor thin layer of bacteria known as the gut microbiome.

This remarkable collection of commensal organisms has evolved with us over the millennia as humankind has evolved. While the human body is composed of approximately 10 trillion cells, the gut microbiome consists of approximately 100 trillion cells. That means that 90% of the cells that make up your body are not you! To give you an idea of the enormity of their foreign presence, consider the fact that there are approximately 1000 times more bacteria in your gut than there are stars in our galaxy. And this does not even begin to account for the additional fungi, protozoa, and viruses that inhabit our inner nooks and crannies.

The human gut is among the most concentrated ecosystems on the planet. Right now, there are 1-2 kg of bacteria inside you that is producing approximately 30% of your daily energy needs. There is more bacterial DNA in our metagenome (the DNA that includes everything inside us; our entire being) than human DNA.

The human genome project identified roughly 20,500 genes that make up our exclusively human genome. The study of the bacterial metagenome from our gut, revealed around 3.3 million bacterial genes, more than 150 times larger than the human gene complement. It is now hypothesized that human beings could not even survive if it were not for the existence of our gut microbiome

These bacteria are in constant communication with our gastrointestinal tract. Our gastrointestinal tract functions like our second brain. It contains over 200 million neurons; which is roughly equivalent to the brain of a dog or cat. Ask any pet owner, and they will tell you about how smart their dog or cat is.

Yet there is even more going on between, the gut, the brain and the rest of the body. While once we thought there was only a one-way, brain-derived communication through this enteric nervous system driving the biological and physiological processes; we now know there is a much richer, deeper and complex relationship. The gut communicates to the rest of our body not only through the nervous system, but through the use of hormones and neurotransmitters secreted into the blood stream. The gut microbiome is in constant contact and communication with our gut through similar chemical messengers. In fact, the gut microbiome itself can produce neurotransmitters that can alter our thoughts and moods.

For example, the gut microbiome can produce serotonin. In the gut, about 95% of the serotonin is associated with gastric transit. However, it is also associated with determining the state of immune function. This bacterially produced serotonin from the gut can also reach our brain. In the brain, serotonin is associated with the production of a positive mood in the sense of well-being. Thus a truly happy belly does quite literally make us feel happy.

Because the gut microbiome is not only populous, but active; it plays a very important role in regulating immune function of the entire body. Roughly 70% of your entire immune system is located within the gastrointestinal tract, predominately within an area known as GALT, or gut-associated lymphoid tissue. Therefore, it is essential to maintain a healthy gut microbiome. A healthy functioning gut microbiome helps keep our immune system in perfect balance. Our well-being is not an isolated endeavor, or a completely genetically prescribed phenomenon. We are fundamentally and critically dependent on our gut microbiome. They, in turn, are dependent upon what internal environment we create. The cornerstone of our internal environment is the food we choose to eat. A proper diet leads to internal balance, harmony, and health; both figuratively and literally.

However, there are many things that can upset that balance. Stress, antibiotics, and particularly the food we eat can all cause unwanted changes in the character and composition of our gut microbiome. A recently completed study demonstrated that a single typical fast food breakfast sandwich can cause an alteration of the healthy bacteria in your gut that can last for almost a week. Such artificial and highly processed foods are relatively new additions to our diet. The effects of these comestibles appear to be an unfavorable one.

Recent studies performed over the last five years have demonstrated that certain processed, ultra-processed foods and additives, while they may not affect human cells directly; can have profound effects on the bacteria within us. Unfortunately, it appears the majority of such effects are detrimental. An example is certain types ozero-calorieie artificial sweeteners. These compounds are not absorbed or processed by our human gastrointestinal tract. Thus, in theory since they would pass through our bowels unabsorbed and unaltered they would add sweetness but no caloric value. It turns out that the Law of Unintended Consequences is everywhere observed; even inside of us.

Recent research has shown that “consumption of commonly used NAS formulations drives the development of glucose intolerance through induction of compositional and functional alterations to the intestinal microbiota.” In other words, what was billed as inert turns out to alter the very fibers of our being. Add to this that such compounds are among the most widely used food additives worldwide, and the magnitude of the issue becomes immediately apparent.

One potential area of positive intervention is in the emerging science of probiotics. Probiotics are collections of presumed beneficial gut bacteria. The idea is that by ingesting them we can help maintain a healthy composition within our gut microbiome and thus a healthy gut. Preliminary studies in certain conditions have shown significant benefit. However, since many preparations vary by bacterial species, bioavailability and counts; it is extremely important to research individual brands in consideration of taking these preparations. Even when taking probiotics, however, it is important to consume healthful foods so that your inner garden can continue to grow. Once you have some wee beasties, you have to feed them. Foods that help maintain a healthy gut microbiome are known as pre-biotics. There are available options that package both together, these are known as synbiotics.

Our inner gut microbiome is not unlike growing a garden outside. When we consume the foods of the modern Western diet we change our inner soil from a rich patch of heartland loam into a homestead at Fukushima. Yet for all the potentially dismal news, the fact remains that we still have choice. For now.


Karlsson, F. H., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Backhed, F., & Nielsen, J. (2012, December for). Symptomatic Atherosclerosis Associated with an Altered Gut Metagenome. Nature, 3:1245. Retrieved July 20, 2013, from Nature Communications.

Ley, R., Turnbaugh, P., Klein, S., & Gordon, J. (2006). Microbial Ecology: Human Gut Microbes Associated with Obesity. Nature, 444:1022-1023.

Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., . . . Wang, J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65 doi:10.1038/nature08821.

Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C. A., Maza, O., . . . Elinav, E. (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature, 514, 181–186 doi:10.1038/nature13793 .

Tremaroli, V., & Backhed, F. (2012). Functional Interactions between the Gut Microbiota and Host Metabolism. Nature, 489:242-249.

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444:1027-1031 doi:10.1038/nature05414.

Wang, Z., Klipfell, E., Bennett, B., Koeth, R., Levison, B., DuGar, B., . . . Hazen, S. (2011). Gut Flora Metabolism of Phosphatidylcholine Promotes Cardiovascular Disease. Nature, 472 (7341): 57-63.

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