Blue green microbe

Living Well & Understanding the Body:

What Is the Microbiome and Why Is It Important?

Our bodies are teaming with single-celled organisms called microbes, which include bacteria as well as archaea, fungi, viruses, and others. In fact, the number of microscopic inhabitants is roughly equivalent to the number of our own human cells. There are distinct, diverse microbial communities – or microbiomes – found in various parts of the body, including the skin, mouth, lungs, and the gut.

These complex communities work in tandem
with our immune system to protect the body
against infectious agents

Just as we provide these microorganisms with a warm, comfortable environment and plenty to eat, their presence plays a critical role in our health. These complex communities help us digest food and extract nutrients, carry out certain metabolic processes, and work in tandem with our immune system to protect the body against infectious agents. When an imbalance in their delicate ecosystem occurs, it can have serious effects on our health.

Many chronic illnesses, including obesity, type 2 diabetes, and inflammatory bowel disease, appear to be affected by the microbiome. The relationship between autoimmunity and the microbiome is still being studied intensely, but it is likely that these conditions are associated with an imbalance in the gut microbiome.

Although strong evidence is lacking, there seems to be a marked reduction in diversity of the gut microbiome amongst autoimmune disease patients. In Crohn’s disease, one study has revealed that a bacteria called Faecalibacterium prausnitzii, which is normally found in healthy individuals, was missing in Crohn’s patients. Researchers have made similar connections in other inflammatory bowel diseases, like ulcerative colitis. While these studies do not indelibly prove the connection of the microbiome to the pathophysiology of autoimmune disease, they certainly signal the need for further investigation.

To discover the complex role of the microbiome in health and disease, a growing body of research is focused on characterizing the human microbiome. One such endeavor is The Human Microbiome Project (HMP), an interdisciplinary effort by NIH to collect resources for characterizing microbial communities found in the gastrointestinal tract, nasal passages, oral cavities, skin, and the urogenital tract.

The data collected by the Human Microbiome Project is enabling researchers to study disease, diversity, biogeography, and molecular function as it relates to the human microbiome. This information – as well as other innovative microbiome research – will continue to serve as a blueprint for understanding the symbiotic relationship between microbes and the host, and the impact it can have on human health and disease.

Microbiome Facts

  • Our gut microbiome interacts with the microbiomes of our organs, including the brain
  • The functions and interactions of the microbiome differ according to the species and strains of bacteria, fungi, and viruses, their quantity, their proximity to each other, and even their location in the gut
  • Our microbiomes change in reaction to the food we eat, the time of day, and any medications we take – most importantly antibiotics
  • Being born via cesarean section adversely affects our microbiomes, as they starts developing at birth (and most likely even in utero)
  • When our microbiomes are unhealthy, we are vulnerable to allergies, infectious and autoimmune diseases, as well as neurological damage, which can cause anxiety, depression, anxiety, OCD, and movement and cognitive disorders

Trending Topics in Research

  • Effect of antibiotics on the microbiome
  • Impact of cesarean section birth on the microbiome and disease development
  • Use of probiotics to improve digestive conditions
  • Influence of the microbiome on gastrointestinal disorders such as IBS (irritable bowel syndrome), IBD (inflammatory bowel disease), Crohn’s, and ulcerative colitis
  • Effect of alterations in the microbiome on cancer treatment
  • Role of the environment on the microbiome’s composition

For more about the microbiome, check out our article: The Relationship Between Autoimmune Disease and the Gut Microbiome


  1. Article Sources and Footnotes
    1. Rose, N. R., & Mackay, I. R. (2014). The Microbiome and Autoimmunity. The Autoimmune Diseases (5th ed., pp 329-338). Oxford, UK: Elsevier Academic Press.

    2. The Body’s Ecosystem (2014, August 1). The Scientist.

    3. Sender, R., Fuchs, S., & Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS biology, 14(8), e1002533.

    4. Institute for Genome Sciences, University of Maryland School of Medicine. About the Human Microbiome.

    5. Baylor College of Medicine. The Human Microbiome Project

    6. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. (2017) Strains, functions and dynamics in the expanded Human Microbiome Project. Nature, 550:61–66. doi:10.1038/nature23889.

    7. Devaraj, S., Hemarajata, P., & Versalovic, J. (2013). The Human Gut Microbiome and Body Metabolism: Implications for Obesity and Diabetes. Clinical chemistry, 59(4), 617–628.

    8. Opazo, M. C., Ortega-Rocha, E. M., Coronado-Arrázola, I., Bonifaz, L. C., Boudin, H., Neunlist, M., … Riedel, C. A. (2018). Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases. Frontiers in microbiology, 9, 432.