Understanding The Gut Microbiome

Understanding The Gut Microbiome
Photograph by Michelle Ramirez of Tres Misterios Salinos, oil in canvas by Fernando Ureña Rib, 2001.

Understanding the gut microbiome and the importance of your intestinal flora


I hope everyone is enjoying these holiday days and, hopefully, a little time off! This week I wanted to talk about those friendly bacteria that live in our gut and the impact these guys can have on our health. I am a big fan of probiotics and have been for years. As the research accumulates, we discover more conditions that our intestinal flora affects. Therefore, understanding the gut microbiome is key to our health and wellness. We have introduced the concept of the microbiome in a previous post, which you can check out here.


There is so much to talk about, I will divide this into a two-part series. On this first part, we will talk about the microbiome, what it is and why it is important. We will also focus specifically on the gut microbiome and we will talk all about probiotics. Next week, we will discuss all the health conditions our friendly intestinal neighbors can have and all the information the latest research is showing (click here to read it).  So, without further delay, let’s talk about the microbiome!


MICROBIOME – What is it?


Microbiome is the term used to describe all the microorganisms that naturally reside in/on our bodies. It relates to fungi, viruses and a large number of bacteria. We have so many “roommates” symbiotically living with us!  In fact, the genes in our microbiome outnumber our own genetic material by a factor of 100 to 1. We have more bacteria in our bodies than human cells! We are true ambulating ecosystems. While it’s unclear, sources estimate as many 100 trillion bacteria make up our microbiome!


The organisms that live in our bowel are referred to as the intestinal or gut microbiome/flora. There are some that are friendly and helpful and others, not so much. The friendly and unfriendly (also known as pathogenic) bacteria are kept in a steady balance. However, diet, living conditions, disease and medications can modify these guys. When we are born, our initial microbiome is determined by birthing route (vaginal births populate us with friendly bacteria much more that cesarean section births), breast feeding (important to populate our gut with healthy bacteria) and whether or not we received antibiotics soon after birth.


Microbiome – where is it?


These bacteria live everywhere in our bodies: skin, mouth and bowel to name a few. Why do our bodies allow for these potentially dangerous organisms to live in our bodies? Since the beginning of time, animals developed and allowed this relationship because it was beneficial to both parties involved. The bacteria that live in our bowel, for example, produce enzymes that allow us to break down and absorb nutrients from food that we would be unable to obtain otherwise. These friendly organisms can also produce chemicals that keep us safe from the potentially bad bacteria.  


Microbiome – what  more does it do?


As I mentioned, the gut microbiome differs from one person to the next. The foods we eat and our environment, among other things, contribute to those differences in our gut flora. These gut microbes help dictate many processes in our bodies, including the body’s response to insulin, our appetite and even weight gain. They also help make vitamins in our bodies (guess who makes the B vitamins?)


It is important to mention that both our large and small bowel play a vital role in our immune system. Both contain lymphoid tissue, called Peyer’s patches in the small bowel and colon patches in the large bowel. These patches contain T-cells, B-cells and dendritic cells, vital cells for our immune function. Guess who stimulates these immune cells in our bowel? Yep! All those friendly bacteria in our gut! They increase the production of antibodies, which helps keep those pathogenic bacteria in check. It also helps our bodies tolerate our friendly bacteria, which in turn, helps our bodies tolerate our own cells. Why is this important? Because otherwise we may suffer from autoimmune disorders where our bodies attack our own cells. In doing this, they also keep inflammation at bay. We know chronic inflammation in our bodies can have terrible effects and we will talk more about this on part II. I think that’s pretty awesome relationship we have with these guys!!



All right, we will now embark in a mini crash course in embryology, which is important in understanding the gut microbiome a bit more. I actually really enjoyed studying our development from a single cell to a full human when I was in med school. I think you will find this fascinating as well!  Check this out:


During our formation in utero, our brain and spinal cord are formed from a structure called the neural tube. Some cells located at the dorsal portion of the neural tube are called the neural crest cells. The brain and the spinal cord form what we call the Central Nervous System. The neural crest cells migrate from their spot in the neural tube to from several structures in our body, one of which is called the enteric nervous system. 


The enteric nervous system consists of a large number of neurons (the same types of cells that make up our brain) and glial cells (another type of cell present in our nervous system). These cells are located all along our gastrointestinal tract. This system is capable of controlling the functions of our intestinal tract independently from our brain. You may have heard our gut called our second brain, and this is why. Phrases like “I know this in my gut” or “I can feel it in my gut” may be more accurate than other old adages!




Let’s talk a bit about probiotics and what they are. Most likely you have seen them or heard someone talk about them. In the last few years, they became super popular and there is TONS of research going on.


An easy way to keep the best microbiome is to eat a diet rich in whole foods and fiber and low in processed and high sugar foods. You can also make sure to eat foods that are rich in probiotics. Kefir and other fermented foods, such as kombucha or pickled veggies (like sauerkraut and kimchi) contain a good number of probiotics. By the way, making fermented veggies is super easy, feel free to drop me a line if you need instructions ☺.



But just what exactly are probiotics?


Probiotics are live microorganisms, bacteria for the most part, but also some yeast. They are very similar to those friendly organisms that make up the gut microbiome. They are available in concentrated amounts in pill or powder form, but we can also get them from the foods we eat as we mentioned before. Some of the supplements are heat sensitive, so need to be refrigerated, while other are not.


Most probiotic supplements contain Lactobacillus, BifidobacteriumBacillus coagulens, or a mix of several different bacteria and yeast. 


Research has been conducted on different strains of bacteria and the different strains may have different effects on our health. It can also vary by geographic region. For example, for treatment of acute gastroenteritis (sudden diarrhea) in Europe, Latin America and the US, L. rhamnosus GG and S. boulardi seem to be the most effective bacterial strains. However, in other parts of the world, the before mentioned strains, plus Indian Dahi (Indian curd/yogurt) seem to be most effective.


Since we are not aware what is the best strain mix or the best number of live bacteria that a probiotic supplement should have, the jury is still not out on official recommendations. We also don’t know how long term ingestion of probiotics can help us. It seems much work remains in understanding the gut microbiome.


So, what’s next?


We have a large number of studies on particular bacterial strains, on the microbiome in general and its health effects on multiple disease processes. We will be discussing these next week (click here to read it). Make sure you tune in (or subscribe to our blog if you haven’t already!) to find out the multiple potential health benefits probiotics and building a solid microbiome can have!


In the meantime, if you take probiotics, feel free to drop a comment on your favorite probiotic supplement (I will tell you mine next week!) and have an amazing, happy and healthy start to 2018!!


10 thoughts on “Understanding The Gut Microbiome”

Leave a Reply