100 Trillion Microbes: Explaining the Microbiome

Updated: Mar 5

According to Harvard Health, about 100 trillion bacteria live in our gastrointestinal tracts. Each of us has a different combination, not one of us is the same (although our particular composition might look very similar to our friends and families). The microbiome has been called an additional organ for the wonderful things it produces for our bodies. Without the beneficial bacteria, we would die. With a combination of more harmful bacteria- we might also be more inclined to die. This is why it is important to maintain a healthy gut microbiota.

Dysbiosis, or microbial imbalance, has been associated with an ever increasing number of diseases, including IBD, Chron's, ulcerative colitis, obesity, diabetes, heart disease, liver and kidney disease, and even central nervous disorders such as autism and anxiety/depression.

While the research is new in this field, leaving many of the pathophysiologic mechanisms unexplained, there are some that we do understand. For example, we know that certain bacteria in the intestines are capable of producing TMA from choline and carnitine (found in eggs and red meat), which is then absorbed and can be converted into TMAO in the liver. TMAO damages cells throughout the body and is positively correlated with coronary artery disease, stroke, kidney disease, diabetes, and Alzheimer's. Having TMAO circulating in your body is an independent risk factor for death from cardiovascular disease and ALL causes.


Did you also know that the mass of nerve tissue surrounding our gut is often referred to as the "second brain"? Ever feel nervous and get "butterflies" in your stomach? Well, it turns out psychological stress and gastrointestinal stress may go hand in hand. There is an evolving field showing the efficacy of using psychological treatment for GI conditions like IBS, and the reverse may also be true. Science is beginning to explore the connection between too much serotonin being produced in the gut and disorders like autism.


Wait, what? Seratonin is produced in the gut? Yep, you read right. It turns out 90-95% of our serotonin resides in the gut. In case you need a biology refresher, serotonin is responsible for stabilizing mood and also helps with eating, sleeping, and digestion. I bet you never imagined that having a healthy microbiome may be the key to improving your mental health. In fact, success stories are now appearing of people who saw incredible improvements in their mental health by eating a plant-based diet, and the gut-brain axis may be why.


In case the connection between our brain and our "second brain" not interesting enough, did you know that the microbiome plays a role in food allergies?


It turns out that many food allergies might actually be triggered by what is known as a "leaky gut". Our gut is where our bodies interact most with the outside world- not our skin, eyes, or noses. It may seem like our intestinal tract is "inside of us", but the reality is that it is just a continuation of the barriers we have on the outside of our bodies. Only when particles pass through our intestinal cell membranes, do they truly become "inside of us".


We protect ourselves from harmful chemicals passing through our intestinal tract by having layers of defenses inside our GI system. The first layer is trillions of bacteria, the second is mucosa, the third is physiological (cells), and the fourth is immune. When our bacteria aren't being fed what they prefer, they may begin eating away at the mucosal layer, leading to inflammation which may lead to gaps within our intestinal cells. It is through these gaps that our body faces an infiltration of pathogens, toxins, and even food particles which then stimulate an immune response (Source: How to Eat to Relieve IBS and Heal Your Gut). This may explain why children with immature digestive tracts can end up developing allergies, and how adults can develop allergies later in life through unhealthy gut microbiomes.


I am not a gastroenterologist, so even I have to oversimplify some of this information in order to understand it myself. However, the science is compelling. We need to take care of our microbiome so that it can take care of us.


Now, what do we know about how to have a healthy microbiome?


While I won't go into the specifics of what may lead to dysbiosis, there is a small space for me to say that research is indicating that bile acids, which can be transformed by bacteria into secondary bile acids, may play a role in several types of illness. Therefore, Gastroenterologist Dr. Angie Sadeghi puts all her IBS patients on a low animal/saturated fat diet and encourages them to get fat from whole food sources like avocados, nuts, and seeds (bile is part of fat digestion).


Next, we know that there are certain foods that your microbiome LOVES. The most important of these being FIBER. Our intestinal secretions cannot digest fiber, which leaves it largely untouched until it reaches the large intestine. It is here that bacteria can do some incredible work, breaking down those carbohydrates and producing some gas (unfortunately), and some very helpful short-chain fatty acids (SCFA's), along with other compounds. SCFA's are an important fuel for our intestinal cells, so we see the symbiotic relationship most displayed through this dynamic digesting/feeding process happening in our colons (hint, this is why fiber helps prevent colon cancer).


There are certain fibers that are more fermentable by bacteria than others. As the saying goes, all prebiotics are a form of fiber, but not all fiber is prebiotic.


Here are some foods that contain highly fermentable fibers, aka prebiotics:

  • Legumes

  • Vegetables like onions, leeks, garlic, asparagus, savoy cabbage, and Jerusalem artichokes

  • Fruits like apples, bananas, watermelon, and grapefruit

  • Grains such as oats and barley

  • Nuts and seeds like almonds, pistachios, flax, chia

This may seem like a small list, but the reality is that many of us use at least one of these foods each day, be it garlic, bananas, or apples. Therefore, there's a good chance you are feeding those bacteria enough food.


Although the list of prebiotic plant foods seems short, there is reason to believe that a wider variety of fruits and vegetables are beneficial for the microbiome because of polyphenols.


Polyphenols are natural compounds found in plant foods that are known for their antioxidant, anti-inflammatory, anti-diabetic, anti-cancer, neuroprotective, and anti-adipogenic properties. The mechanism behind this is not fully known, but may perhaps have to do with polyphenols' ability to modulate the gut microbiome through prebiotic, antimicrobial, bacterial DNA modulating, and anti-inflammatory properties, among others.


Where can you get polyphenols? Try any of the following:

  • Red fruits and red wine

  • Soy foods

  • Teas and coffee

  • Citrus fruit

  • Chocolate

And those are just the ones that have been studied/identified. As the research grows, so sure will this list, I'm sure!


You may be asking, if I eat foods that aren't healthy, will my microbiome suddenly change?


The answer is that our gut microbiota is relatively stable, so if you go from one way of eating to the other, it will change for that meal, but then revert back to "normal". The key then becomes eating in a way that produces a microbiome that is "normally" healthy and balanced.


If you want to help diversify your microbiome, fermented foods are a really good source of naturally occurring probiotics, that are cheaper and more efficacious than supplements. Try eating some more kimchi, sauerkraut, pickled veggies, tempeh (fermented soy), miso, and (unsweetened) kombucha.

Lastly, how do I know if my gut is healthy?


Well, chances are, you know if it's not.


And chances are, you can always improve it by moving towards a more plant-forward diet, with less saturated fat and animal products as these are connected to more gut issues. You can also make sure to have great sources of prebiotics and polyphenols daily, along with lots of fiber in general to help move things along. Lastly, you can also try incorporating natural sources of probiotics regularly into your diet.


In conclusion, we should view our gut microbiome as another organ that we need to take care of for our health, just like we take care of our cardiovascular systems by exercising, and our renal systems by drinking lots of water and eating less animal protein. This is such an interesting field that will continue to evolve, but for now, know that you can be protecting your health by protecting those trillions of little guys living in your GI tract.



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