‌‌‌‌What is the Microbiome?

The microbiome is a community of a large variety of microorganisms such as bacteria, fungi, and viruses, contained within the gastrointestinal (GI) tract. It is a complex and integrated ecosystem that contains at least 1,000 different types of organisms belonging to more than 2,000 species.1

The microbiome exhibits a huge diversity, which is shaped by numerous factors including:

  • Genetics
  • Gender
  • Age
  • Immune System
  • Health Conditions
  • Geographic Location
  • Socioeconomic Factors (Access To Water, Sanitation)
  • Treatments
  • Diet

‌‌‌‌What Does the Gastrointestinal (GI) Tract do? 

The GI tract has many functions. It’s responsible for breaking down our food (digesting), making sure that food is absorbed properly so it can turn that steak dinner into the muscle of your thigh. It also eliminates the unwanted waste that the body doesn’t need. Red blood cells that are no longer functional give our excreted waste its brown color.

 The GI tract also protects us, as there are many bacteria and other unwanted things in the food we eat, or from touching our mouths with our hands. The GI tract makes sure these bacteria don’t harm us (or cause food poisoning). 

In addition to its many functions, the GI system also has many parts. This system starts at the mouth and ends at the anus. The stomach and small intestine are responsible for digestion and absorption, while the large intestine’s function is to remove water and compact the waste, while the sigmoid colon and rectum store the waste before it’s elimination from the body.2

‌‌‌‌Where Does Our Microbiome Come From? 

Recent research has found that colonization of the GI tract actually starts before birth as the placenta contains good bacteria. Also, the meconium, or first bowel movement, of an infant is not sterile, meaning that even in the womb, an unborn baby’s GI tract is already developing its microbiome.3

After birth, if a baby is born vaginally, they have a microbiota containing species derived from the vaginal microbiome of their mothers. On the other hand, if a baby is born via C-section, their microbiome is more similar to their mother’s skin. 

Breastfeeding also plays a role in forming the GI microbiome and the development of the immune system. Human milk has a protective role for babies. For example, antibodies like IgA and anti-microbial agents like lactoferrin protect babies from gastrointestinal and respiratory infections.

‌‌‌‌Why is the Microbiome Important? 

All of the microbes that make up the community or microbiome in your gut do many positive things for us. The microbiome is involved in harvesting energy and storing that energy. One of the ways it does this is by fermenting fibers such as butyrate to create short-chain fatty acids (SCFAs). 

These compounds promote a healthy GI tract by contributing to intestinal repair. They also serve as the main energy source for colonocytes, or cells in the colon. Many of the bacteria in the GI tract are key to synthesize vitamins like B1, B2, B5, B6B12Kfolic acid, and biotin.4

The microbiome also stimulates the immune system, just after birth.

‌‌‌‌How Does the Microbiome Influence the Immune System?

The GI tract has its own layer of protection called the mucosal immune system to regulate and guard against any foreign substances that we may ingest. This system is separate from the larger immune system of the body. The bacterial colonization of the GI tract dramatically changes our body’s immune system.

One of the most important steps to mature the immune system is to “teach” it the difference between what to attack and what to leave alone. Specialized cells in the digestive system interact with our bacteria (the good ones) and pathogenic bacteria (the bad ones), so the immune system can learn what to tolerate and what must be destroyed, as it could cause infection or harm to the body.

In addition to “teaching” the immune system what to attack and what to leave alone, the microbiome also helps immune cells mature and directs them where they are needed in the body. For example, the microbiome differentiates specific T cells in the immune system to perform various functions. For example, T cells can be Th1, Th2, or Th17. 

Th 1 and 2 release specific chemicals throughout their lives call cytokines. These chemicals “call” other immune cells to fix problems in the body. Th17 cells are much more diverse in their function: they change the types of chemicals they secrete, making them adaptable to many situations in the body. In other words, the Th17 cells are the MVPs of the immune system, and they can play many positions.

A lot of our immune system lives in our gut. Specific areas in our gut called Peyer’s patches are very rich in lymphoid tissue, which houses many of our defense immune cells. Think of all of the potential things we can eat that could harm us. Having this immune location in our gut is the perfect way to protect the body from harm.

With poor diets, some medication use, or from natural aging, the number of bad bacteria in the gut can start to outweigh the good bacteria. This is called dysbiosis or an imbalance of good to bad bacteria. When the amount of good bacteria decreases in the gut, the immune system doesn’t get the support it needs. There are theories that dysbiosis in the gut may contribute to an overactive immune system, and this overactivity may be the cause of autoimmune centered disease.

‌‌‌‌Supplements to Support a Healthy Microbiome

Probiotics - the "Good" Bacteria 

Probiotics, according to both the Food and Agricultural Organization of the United Nations and the World Health Organization, are defined as living microorganisms that provide health benefits.5 Scientist Elie Metchnikoff introduced the concept of probiotics through his studies of these good bacteria in milk. 

His research showed that when eaten, these good bacteria could benefit human health. Since then, probiotics have been vastly marketed and consumed, mainly as dietary supplements or functional foods. Benefits of probiotics include increasing “good bacteria” in intestinal microbial communities, supporting the suppression of bad bacteria, supporting the immune system, and contributing to a healthy intestinal lining.

Many consumers report many positive benefits of taking probiotics. For example when on antibiotics, many people experience diarrhea. Probiotics may help to stave off this unwanted side effect. Some studies have shown that probiotics rich in Lactobacillus strains can help support a better mood. Other probiotic strains have been linked to supporting heart health. Probiotics may also help to reduced allergy symptoms and some strains have been shown to improve poor skin health. The use of some strains has been correlated with managing weight and symptoms of digestive disorders. 

Probiotics are available in supplement form, in capsules, tablets, and/or liquid. These supplements can help support a healthy microbiome and are an easy way to get in needed microbes to support gut and immune health.

Butyrate - an Anti-inflammatory

Butyrate is a short-chain fatty acid derived from the fermentation of indigestible fiber in the GI tract. This compound is known for its anti-inflammatory properties and for its ability to provide energy to colonocytes.6 When dysbiosis occurs, the body may have difficulty producing this important energy source. Butyrate is available as a supplement and is often taken in conjunction with probiotics.

The microbiome is a diverse ecosystem that lives in our GI tracts. This combination of microorganisms supports the immune system in many ways. Thankfully, supplements like probiotics and butyrate can easily be incorporated into our daily routines to support the optimal health of both our GI and immune systems.


  1. Lazar, V., Ditu, L. M., Pircalabioru, G. G., Gheorghe, I., Curutiu, C., Holban, A. M., Picu, A., Petcu, L., & Chifiriuc, M. C. (2018). Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Frontiers in immunology, 9, 1830.
  2. Cheng, L. K., O'Grady, G., Du, P., Egbuji, J. U., Windsor, J. A., and Pullan, A. J. (2010). Gastrointestinal system. Wiley interdisciplinary reviews. Systems biology and medicine, 2(1), 65-79.
  3. Abba13. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A (2010) 107:11971-5.10.
  4. Wong JM, de Souza R, Kendall CW, Emam A, Jenkins DJ. Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol. 2006;40(3):235-243.
  5. Hemarajata, P., and Versalovic, J. (2013). Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therapeutic advances in gastroenterology, 6(1), 39-51.
  6. Canani, R. B., Costanzo, M. D., Leone, L., Pedata, M., Meli, R., & Calignano, A. (2011). Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World journal of gastroenterology, 17(12), 1519-1528.