The Microbiome

The Microbiome

I am sure by now most people have heard or seen the term “microbiome” on social media, in the news, on podcasts, or via word of mouth. It has definitely become one of the new hot topics, and for good reason. It is very possible that, as research advances in this area, the human microbiome will become the answer to solving many of today’s health concerns.

What is the human microbiome?

In the not too distant past, scientists began to realize that our bodies contained trillions of microbiota, all of which play a role in creating a complex ecosystem. Microbiota aka microbes are a collective term for microflora (any type of minute organism) that may be found within a given environment. The term microbiome refers to all of the genetic material associated with the microbiota within a given environment. The human microbiome consists of a diverse array of microbes including bacteria, archaea, fungi, protozoans, and nonliving viruses. The vast majority of these microbes inhabit the gastrointestinal tract, with the greatest number of them located in the colon.  In fact, there are so many bacterial cells in our body that they slightly outnumber our human cells. With numbers like that, there’s no wonder why the microbiome has gained so much popularity.

Good Bacteria vs Bad Bacteria

There are some estimates that the human microbiome consists of 900-1,000 different species of microbes. Within the gut microbiome there are many microbes that can cause infection if the opportunity arises. However, in a healthy gut, they are usually kept in check by a greater abundance of beneficial microbes. Clostridium difficile (C. diff) for example is a bacteria that lives naturally within the human gut without causing problems. However, after a course of antibiotics, it is possible to experience a C. diff infection as a result of the antibiotics wiping out too many beneficial bacteria. This creates an opportunity for the C. diff to flourish.  It is important for our immune system to have potentially harmful bacteria around, because this exposure allows for the development of a stronger defense system. Scientists have compared mice raised in a germ free environment to those raised in a natural setting, and the germ free mice had much higher levels of inflammatory markers than the naturally raised mice. This means that the mice exposed to more microbes in the environment were healthier and experienced much less inflammation. When the body is placed in a state of chronic inflammation, the immune system can begin to work against us rather than for us. This is part of what leads to diseases such as autoimmunity.

Germ Theory vs Hygiene Hypothesis

The Germ Theory is the idea that certain diseases are caused by the invasion of specific microbes within the body. This theory was developed and gained gradual acceptance in the middle 1800s, and started a huge shift in the medical mindset. The development of drugs for the treatment of infectious diseases was now a major focus. In 1928, Sir Alexander Fleming discovered penicillin, and it gained great popularity after its use in World War II. With penicillin, there were fewer deaths from amputations and serious infections such as endocarditis, meningitis, pneumonia, tuberculosis, etc. This quickly led to a number of pharmaceutical industries searching for additional antibacterial agents.

Following this, many public health measures were taken to limit the spread of infections. These included; decontamination of water supplies, pasteurization and sterilization of dairy and other food products, the development of vaccinations, and the widespread use of antibacterial products and antibiotics. As a result, the U.S. has seen a significant decline in people suffering from infectious diseases. However, this is where one must ask, “when does too much of a good thing become bad?” According to the hygiene hypothesis, the decreasing incidence of infections is resulting in an increasing incidence of digestive disorders, autoimmunity, and allergies. The leading idea is that some infectious agents, especially those that co-evolved with us are able to protect us against a large spectrum of immune-related disorders. Now that we have been limiting our exposure to so many microbes, we are basically weakening our immune system and causing bigger problems.

The microbiome at birth

I remember when I first started becoming passionate about the microbiome. It was during my second year of medical school, and my gastroenterology professor started talking about the impact of a cesarean delivery on gut flora. She talked about how an infant’s first exposure to beneficial bacteria is usually during its passage through the vaginal canal. She explained how important this step was, because it allows the bacteria to colonize within the baby’s body. When a cesarean section occurs, the first bacteria that the baby is exposed to tends to be that of the skin and whatever is present in the hospital setting. Prior to all of the research discovering the role of the microbes within our system, we wouldn’t have given a second thought to the difference between a vaginal or cesarean section.

This information was especially interesting to me because of the fact that I was delivered via cesarean. When my professor went on to say that correlations had been made showing an increased risk of allergies, asthma, autoimmune disease, obesity, mood disorders, and type 2 diabetes with cesarean delivery, I began to wonder if this was the root cause to all of my problems. Some studies have shown that the mode of delivery resulted in disturbances to the gut flora of the infant for up to 6 months of life, and another study showed alterations as long as 7 years. The reason this is important is because our immune systems are going through the most critical stages of development during infancy, and our gut flora play a key role in this development. Therefore, it appears that by altering the gut flora we are initially exposed to during delivery, we are creating an immune system with an enhanced inflammatory response.

The importance of the microbiome

The gut microbiota maintain a symbiotic relationship with the gut mucosa (the cells that line the digestive tract) and play many metabolic, immune supportive, and gut protective functions in a healthy individual. The gut flora derive their nutrients from some of the carbohydrates that we consume. These carbohydrates (specifically fiber) get fermented and turned into short chain fatty acids (SCFA), such as butyrate, proprionate and acetate. These SCFAs are a rich source of energy for our cells, and play a role in regulating inflammation, gut motility, the immune system, and metabolism. A healthy gut flora is important for lipid and protein metabolism, and the synthesis of vitamin K and many B vitamins. They also aid in breaking down and activating various plant polyphenols, which would normally remain inactive without the presence of the gut flora. These polyphenols are the medicinal components of plants, and are very useful in preventing disease and optimizing health.

Without a doubt, the most important role of our gut flora is in its regulation of our immune system. Did you know that nearly 80% of the immune system is found within the digestive tract? That alone should tell you how important gut health is. One critical role of the gut flora is in maintaining the structure and permeability of our intestinal tract. When things get out of balance, this can lead to the well talked about Leaky Gut problem. Tons of research has already uncovered the many other ways in which our gut flora interplay with our immune system. The information gets really technical and science heavy, but feel free to read all about it if you are eager to know more.

Gut brain connection

There has been a lot of talk recently about the second brain found in your gut. If you think about it, when you’re feeling really nervous or anxious, where do you feel it? In your stomach. This is because there is a direct connection between our brain and our gut. It really gives meaning to the old saying, “trust your gut.” Just about everyone has heard of the neurotransmitter serotonin. It is responsible for regulating anxiety, happiness, and sleep. What you probably didn’t know is that almost 90% of it is created in the digestive tract. This is another awesome role of our gut flora, because they are responsible for signaling the cells in our intestines to increase serotonin production.

This connection between the gut and the brain is the reason that many mood disorders are accompanied by digestive complaints. I have experienced this first hand with my own health. When my bloating, candida, and heartburn have been at their worst, I was also plagued with overwhelming anxiety, pessimism, perfectionism, sadness, and a lack of motivation. I have even been able to target certain foods that I am sensitive to based on my heart rate increasing shortly after consuming them. I used to think I was going crazy because I couldn’t understand why I was anxious all of the time. Once I eliminated these foods, my anxiety went away. Because the communication between the brain and the gut runs in both directions, it creates the basis for how important stress reduction is for overall healing. I can’t tell how many times I have emphasized to my patients the need for eliminating stressors from their lives. If we are not mentally balanced, then our gut is not balanced, and then our immune system is not balanced, and then inflammation increases, and our risk of disease increases, and the vicious cycle repeats endlessly. I think you get the point.

Microbiome testing

So with all of this talk about the microbiome, you might be wondering how one goes about testing their microbiome. In general, I will tell you that we are still many years away from truly understanding the full scope of the microbiome. The testing that exists can give you some information, but it won’t be the answer to all of your problems. If you have the opportunity to see a functional doctor or a naturopathic doctor, they can order a stool analysis. As of now, the one that provides the most information about gut flora and gut health is Genova. This test does require a doctor to order it, so it won’t be something you can do on your own. However, by having a doctor order it, you will also have a doctor to interpret the information and provide you with recommendations.

If you are wanting to see how your gut flora compares to thousands of people around the world, then you can use companies like UBiome or American Gut Project. Once you pay for the kit they mail it to you with instructions for how to collect the sample and send it back. The results will basically tell you how your abundance and diversity of bacteria compares to all of the other samples they have collected. In general, the more diverse your sample is, the better. No health information will be provided with these tests, they are more informational. However, these tests are something you can do without a doctor.

There is a new option that launched in the last couple of years called Viome. They provide the greatest amount of information regarding the flora living within your gut, and some of the possible health implications that go along with it. In addition to this, they give you a list of foods to enjoy and avoid for optimal gut health. The program isn’t cheap, but the information can be interesting. This is another test that can be done without a doctor.

Ways to support your microbiome

Things to Avoid

  • Antibiotics: Try to only use antibiotics when absolutely necessary, because they deplete the abundance and diversity of your gut microbiota. If you have to take antibiotics, then make sure you are also taking a quality probiotic a few hours away from the antibiotics.
  • Stress: As I mentioned previously, stress can have a negative impact on your microbiome because of the gut-brain connection. Chronic stress leads to chronic inflammation, and chronic inflammation can lead to autoimmunity.
  • Unhealthy Foods: Decrease your consumption of sugar, processed foods, white rice, and white breads. These foods feed the bad bacteria leading to an imbalance in your gut flora in a way that promotes inflammation and disease.
  • Antibacterial Products: When you use these products in your home and on your body, you are greatly decreasing the number of good bacteria on and around you. As I have already mentioned, you need to have exposure to these microbes in order for your immune system to be strong. In addition to this, antibacterial products contribute to the promotion of superbugs.


  • Fiber: Also referred to as probiotics, and what our good bacteria live on. They can be found in root vegetable, legumes, and whole grains.
  • Exercise: Important for decreasing inflammation and relieving stress.
  • Probiotics: Help maintain a healthy population of gut bacteria. You should look for ones that have many different strains, and counts of 10 billion or more per serving.
  • Fermented Foods: These foods are full of living beneficial bacteria. So consume more kimchi, sauerkraut, kombucha, and raw organic yogurt and kefir.
  • Time In Nature: Carve out more time to get out in nature.  Not only is this very helpful for relieving stress, it is also helpful in populating your gut with good microbes from the environment. Walk around barefoot, play in the water, roll around in the dirt, make mud pies with your kids, go camping, get out in your garden, and get your hands dirty.