An Introduction to the Human Microbiome

An Introduction to the Human Microbiome

What is the Microbiome?

The Microbiome - “micro” meaning small and “biome” meaning living - is the name used to describe all of the microbes that live in our gut, on our skin, in our mouth, and all over our body.

The term “microbiome” encompasses the diversity of microbes with bacteria vastly outnumbering all the other microbes in our microbiome including viruses, yeast, fungi, and protozoans. The location of these microbes are generally described by putting an organ system name in front of them (i.e. gut microbiome, skin microbiome, vaginal microbiome, etc). Within each organ, there can be niche environments. That means that a bacterial species, like Lactobacillus, may grow more in one spot in the gut and a different species, like E. coli, may grow more in another location. These niche environments are important for microbes to grow happily together in order to maintain a healthy ecosystem in each site they inhabit.

A Diverse Ecosystem

The ecosystem aspect of the microbiome adds a level of complexity. Each microbe is in constant interaction and communication with each other (i.e. environmental microbes), and our own human cells. Microbes cooperate with us (their hosts) and compete with pathogenic microbes for nutrients and space. The constant turnover of cells requires that microbial offspring are quickly able to replace their parents. In addition, there is redundancy in the system – no one microbe can be responsible for a product or reaction. Instead, guilds form and several microbes can complete an action, such as production of short chain fatty acids.

“Microbes cooperate with us and compete with pathogenic microbes for nutrients and space.”

Characterizing the microbes on our body has shown us that microbes are in more places than we previously thought they were. While science has been aware of microbes since the mid 1800s, initially, we thought they were dangerous. As it turns out, of the hundreds of thousands of bacteria that are on us and around us, only 68 are considered pathogenic. The vast majority of bacteria are beneficial. Commensal bacteria evolved with humans and are tolerated by our immune system, unless they are out of balance (overgrown or in the wrong location).

Furthermore, commensals do much more than we previously thought. While we’ve known that commensal microbes were involved in the digestion of food it has recently been discovered, in the last 10 years or so, that they also mediate the metabolism of some essential micronutrients.1 They are pivotal in the production of neurotransmitters such that they impact everything from our mood to our memory.2-4 They shape our immune development and have profound effects on our immune response to infections.5-7

“We often discover how important something is by observing what happens when it’s missing…”

We often discover how important something is by observing what happens when it’s missing, and the same thing is true with the microbiome. When there is dysbiosis or microbes are missing, we see the development of infections, allergies, inflammatory bowel disease, obesity, diabetes, and neurological disease.8

Now that we know how important the microbiome is, we need to be more conscious of developing practices that protect the tiny creatures that live on and in us.

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  1. Hughes RL, Kable ME, Marco M, Keim NL. The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models. Part II: Results. Adv Nutr. 2019;10(6):979-998. doi:10.1093/advances/nmz049
  2. Kelly JR, Minuto C, Cryan JF, Clarke G, Dinan TG. Cross Talk: The Microbiota and Neurodevelopmental Disorders. Front Neurosci. 2017;11:490. doi:10.3389/fnins.2017.00490
  3. Flux MC, Lowry CA. Finding intestinal fortitude: Integrating the microbiome into a holistic view of depression mechanisms, treatment, and resilience. Neurobiol Dis. 2020;135:104578. doi:10.1016/j.nbd.2019.104578
  4. Ojeda J, Ávila A, Vidal PM. Gut Microbiota Interaction with the Central Nervous System throughout Life. J Clin Med. 2021;10(6):1299. doi:10.3390/jcm10061299
  5. Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16(6):341-352. doi:10.1038/nri.2016.42
  6. Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30(6):492-506. doi:10.1038/s41422-020-0332-7
  7. Takiishi T, Fenero CIM, Câmara NOS. Intestinal barrier and gut microbiota: Shaping our immune responses throughout life. Tissue Barriers. 2017;5(4):e1373208. doi:10.1080/21688370.2017.1373208
  8. Khan R, Petersen FC, Shekhar S. Commensal Bacteria: An Emerging Player in Defense Against Respiratory Pathogens. Front Immunol. 2019;10:1203. Published 2019 May 31. doi:10.3389/fimmu.2019.01203