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Salem Health: Infectious Diseases & Conditions, 2nd Edition

Microbiome

by Marianne M. Madsen, M.S.

Category: Immune response

Definition

“Microbiome” generally refers to all the microbes (extremely small organisms that cannot be seen by the naked eye, such as bacteria, fungi, and viruses) that live in a community. Our bodies have several microbiomes; for example, the gut contains a microbiome, the nasal cavity and mouth have a different microbiome, and the skin has an even different microbiome. These communities of microbes help with many bodily functions, including keeping the body healthy and fighting off infectious diseases.

Functions

We are born with a certain microbiome that we acquire from our birth environment, both from our mother’s womb and from the environment surrounding us at birth. Even the circumstances of our birth individualizes our microbiome—babies who are born vaginally get microbes from the birth canal, while babies who are born by C-section get more microbes from skin; babies who are born at the hospital have a different microbiome profile than those born at home. As we grow and develop, our microbiomes change based on our changing environment, including the foods we eat and the air we breathe. By the time we become an adult, all our microbiomes are very different from those we had at birth. Even the microbiomes of one individual are very different. For example, the skin microbiome usually contains microbes that do well in dry conditions and can be very different from the mouth or nasal microbiome, which contains microbes that need a moist and damp environment.

However, one common thread through all the different microbiomes is that they contain microbes. Many of these microbes are helpful for us; they help us with many bodily functions, such as digestion, cell division, vitamin production, metabolism, and protection from disease.

Impact

Our different microbiomes help us fight off infectious diseases in many ways. Helpful microbes can release anti-microbials that keep harmful bacteria, fungi, and viruses away. For example, the microbiome of our skin covers us with a protective shield made of helpful microbes. Microbes help keep the skin soft and flexible, creating a strong barrier that cannot be penetrated. Harmful microbes must fight their way through this shield to get into the body to cause disease. Similarly, a healthy colony of microbes in the nasal cavity and mouth can keep harmful bacteria, such as the kind that cause colds or sinus infections, away. Some kinds of bacteria, such as Streptomyces, produce natural compounds that have even been used in making medicines. Healthy bacteria can also signal the body to produce other types of molecules that fight infection.

Sauerkraut, or fermented cabbage, can provide healthy probiotics like lactobacilli which can increase microbial diversity and promote growth of gut flora. Photo by Gandydancer via Wikimedia Commons.

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Another way that our microbiome uses to help fight off infections is by changing the environment in the body. For example, in the vagina, lactobacillus bacteria help to create an extremely acidic environment by releasing lactic acid. Harmful bacteria, yeast, and viruses often cannot survive in the acidic environment. The microbiome of our skin also produces byproducts that lower the pH of the skin, creating an acidic environment that keeps bacteria from growing and penetrating into our body.

Some helpful bacteria, such as bifidobacteria, keep toxins from passing through the intestinal wall and into the bloodstream. For example, E. coli, a type of disease-causing bacteria, can release toxins into the bloodstream that damage kidneys and destroy red blood cells, but helpful bacteria from the gut microbiome can prevent these toxins from leaving the gut. Our gut microbiome can even help deactivate toxic molecules that we ingest with the food we eat.

Microbes can also help the body avoid infection by helping to “train” the immune system. Gut and skin microbes stimulate immune tissues and increase antibodies that fight pathogens. The body can learn to recognize and attack harmful pathogens and, at the same time, recognize and encourage healthy microbes.

Our microbiome can also help promote healing when we are infected with some type of pathogen. When our gut microbiome is damaged, the bacteria living there release chemicals that signal our cells to begin dividing faster to help us heal.

Sometimes, we need antibiotics to kill infections. Our various microbiomes can be negatively affected by these medications (and others). Antibiotics are unable to differentiate between helpful and dangerous microbes. As a result, antibiotics can kill some of the helpful bacteria that we need to keep our microbiomes healthy. For example, antibiotics can interfere with the vaginal microbiome, so women may be left with an overgrowth of yeast (Candida) after taking a course of antibiotics.

To keep our microbiomes healthy, or to restore them after they have been compromised from antibiotics or other medications, diseases, or even from an unhealthy diet, one should eat fiber (whole grains, fruits, and vegetables, especially greens), fermented foods that contain probiotics (sauerkraut, kimchi, tempeh, kefir), and yogurt. If necessary, one can also take prebiotics or probiotics as a supplement. Limiting sugar intake can also help keep the microbiome healthy.

Further Reading

1 

Blaser, Martin J. Missing Microbes. New York: Henry Holt and Co., 2014.

2 

Harris, Vanessa C., Haak, Bastiaan W., Boele van Hensbroek, Michael, Wiersing, Willem J. “The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field.” Open Forum Infectious Diseases. Published online 2017 Jul 8. doi: [10.1093/ofid/ofx144].

3 

Honda, Kenya, Littman, Dan R. “The Microbiome in Infectious Disease and Inflammation.” Annual Review of Immunology. Published online 2012 Jan 6. doi: [10.1146/annurev-immunol-020711-074937].

4 

Ragab, Gaafar, Atkinson, T. Prescott, Stoll, Matthew L. (eds). The Microbiome in Rheumatic Diseases and Infection. Springer, 2018.

5 

Shreiner, Andrew B., Kao, John Y., Young, Vincent B. “The Gut Microbiome in Health and in Disease.” Current Opinion in Gastroenterology. Published 2015 Jan; 31(1): 69–75. doi: [10.1097/MOG.0000000000000139]

6 

Young, Vincent B., Britton, Robert A., Schmidt, Thomas M. The Human Microbiome and Infectious Diseases: Beyond Koch. Interdisciplinary Perspectives on Infectious Disease. Hindawi Publishing Company, 2008. https://www.hindawi.com/journals/ipid/si/861658/

Web Sites of Interest

National Institutes of Health: Human Microbiome Project

https://commonfund.nih.gov/hmp

BioMedCentral: Microbiome Journal

https://microbiomejournal.biomedcentral.com/

See also: Antibodies; Bacteria: Classification and types; Immunity; Immune response to bacterial infections; Microbiology; Microscopy.

Citation Types

Type
Format
MLA 9th
Madsen, Marianne M. "Microbiome." Salem Health: Infectious Diseases & Conditions, 2nd Edition, edited by H. Bradford Hawley, Salem Press, 2020. Salem Online, online.salempress.com/articleDetails.do?articleName=Infect2e_0358.
APA 7th
Madsen, M. M. (2020). Microbiome. In H. B. Hawley (Ed.), Salem Health: Infectious Diseases & Conditions, 2nd Edition. Salem Press. online.salempress.com.
CMOS 17th
Madsen, Marianne M. "Microbiome." Edited by H. Bradford Hawley. Salem Health: Infectious Diseases & Conditions, 2nd Edition. Hackensack: Salem Press, 2020. Accessed September 16, 2025. online.salempress.com.