Fungal Microbiome (Mycobiome): ​The Fungus Among Us

The community of fungi on the skin can determine its health

Credits: Annie Spratt at Unsplash.com
Edited By:
Raja Sivamani , MD, MS, AP

Our body is covered and contains many micro-organisms including not only bacteria but also fungi. The microbiome refers to the bacteria that live inside and on the surface of our bodies and the byproducts that they make; the mycobiome refers to the fungi that live inside and on the surface of our bodies.[1]


Fungal Microbiome vs Bacterial Microbiome

Fungi can be found all around the world and can even digest materials few other organisms are able to break down such as plastics.[2] The fungal microbiome of the human body is not as well studied as the bacterial microbiome in health and disease. One reason is that fungi can be tricky to identify, particularly as they are more difficult to grow in a laboratory as they require often near perfect conditions to grow, such as in your gastrointestinal tract or on your skin.[3]

While many of these fungi can make you sick, others are common in a healthy body.[2,4] The fungal microbiome has been studied in a wide variety of species ranging from insects to humans, and even dogs. The studies show that fungal communities are stable and are personalized to each species.[5]


Fungi Can Cause Infections

In the cases of dangerous and infectious fungi, your body can normally and properly defend itself against these tiny intruders and allow you to live a healthy life. However, if you have an underlying medical condition, it could cause overgrowth of the fungi in and around your body, usually referred to as an opportunistic infection.[6] These infections can range from skin infections commonly known as “roundworm” and “athlete’s foot” to deeper fungal deadlier infections that can spread throughout the body.


How Does the Fungal Microbiome Hurt Us?

Fungi that grow out of balance can lead to unpleasant symptoms and skin conditions if not treated. Three commonly associated diseases with fungal infections include:

1)    Seborrheic Dermatitis

Often described as dandruff, or cradle cap, this common skin disorder that can affect the face and scalp have been linked to the Malassezia yeast. Seborrheic Dermatitis occurs more commonly in men as well as adolescents, young adults, and increasing incidences after age 50.[7] While there is no cure for this disease, the treatments to control acute flares and maintain remission often include anti-fungal treatments such as ketoconazole and ciclopirox.[8,9]

2)    Tinea Versicolor

This condition often presents as whitish or slightly dark scaling spots on the areas of the skin that are rich in oil glands (back, chest, shoulders, neck).[10] This infection usually appears in times of sweating or when in hot, humid weather. Infected areas can have loss of color in the affected areas, even after treating with topical and oral treatments such as a sulfur based shampoo or itraconazole.[11]

3)    Vaginal Yeast Infections

Approximately greater than 70% of all women will develop a vaginal yeast infection during their lifetime, especially during pregnancy.[12] The most common culprit is the yeast Candida albicans, which is part of the normal community of yeast and bacteria in the vagina. Women are at increased risk of developing a vaginal yeast infection if they are using oral contraceptives, IUDs, spermicide, or condoms.[13] In addition, poor hygiene and wearing non-breathable clothing can help contribute to the development of this disease as well.

Patients have described an abnormal “cottage-cheese” like discharge during infections which can be treated with topical or oral agents such as fluconazole.[14] If you are pregnant and develop a vaginal yeast infection, your care provider can help determine a safe and effective topical treatment plan to help clear the infection.[15] While it may also seem tempting to buy an over-the-counter antifungal agent to help clear your infection, please first consult with your care provider.


Other Infections can be Common and Normal

Usually, most people are not even aware they even have fungi growing in their GI tract or all over their skin until it becomes a problem. Your immune system, however, does not ignore the fungi in and around your body, but recognizes the different fungi, often developing a symbiotic relationship that can wax and wane between tolerant and inflammatory responses.[16]


Where Do These Fungi Come From?

While many of the organisms can come from the environment such as food or contact, others come at a much earlier age, specifically from a parent. At birth, when a newborn passes through the vaginal canal, this is the first initial exposure to microorganisms.[16] This exposure, as well as initial feeding of the newborn, can help develop the micro and mycobiome. Feces samples from even extremely low birthweight babies have contained the DNA from fungi, suggesting that these fungi are a part of your body from a very early age.[17]


How Does the Fungal Microbiome Help Us?

In a study examining yeast fungi in the gut, the fungi Saccharomyces may occur naturally in the body and help limit immune response and increase immune health.[18] Other fungi that help break down complex carbohydrates such as cellulose and lignin have also been reported in human fecal samples.[19] Some species of fungi in the GI tract such as Candida sake and Debaryomyces hansenii are types of fungi that do not usually grow at body temperature, but rather are ingested through a wide variety of food including grape juice, sauerkraut, frozen salmon, cheese, and preserved/fermented meats.[20,21] Probiotic cultures for the gut designed to help aid in digestion have included fungi such as Aspergillus oryzae in addition to the usual bacteria in probiotic cultures.[22] 

While the thought of microorganisms inside and on your body may appear unnerving, your body manages to continue living a healthy life, with the complex ecological systems of your microbiome and your fungal mycobiome.

For Further Reading on the different microbiomes and environmental effects, click on the article links below:

Top 8 Foods that Harm the Microbiome

The Gut Microbiome and the Skin

You and Your Dog Might Share a Microbiome

The Skin Microbiome in Eczema


What's Your Skin Type

Each article on Dermveda is unique, just like you. Find your skin type and save your results to get articles that are compatible with you.


  1. Lederberg J, McCray AT. Ome SweetOmics--A Genealogical Treasury of Words. The Scientist.2001;15(7):8-8.
  2. Hallen-Adams HE, Kachman SD, Kim J, et al. Fungi inhabiting the healthy human gastrointestinal tract: A diverse and dynamic community. Fungal Ecology.2015(15):9-17; PMID: Link to research.
  3. Bickers DR, From the Department of Dermatology CUCoPaS, New York, Lim HW, et al. The burden of skin diseases: 2004. Journal of the American Academy of Dermatology.2006;55(3):490-500; PMID: Link to research.
  4. Hallen-Adams HE, Suhr MJ. Fungi in the healthy human gastrointestinal tract. Virulence.2017;8(3):352-358; PMID: 27736307 Link to research.
  5. Ott SJ, Kühbacher T, Musfeldt M, et al. Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scandinavian journal of gastroenterology.2008;43(7):831-841; PMID: 18584522 Link to research.
  6. Gudlaugsson O, Gillespie S, Lee K, et al. Attributable mortality of nosocomial candidemia, revisited. Clin Infect Dis.2003;37(9):1172-1177; PMID: 14557960 Link to research.
  7. Seborrheic dermatitis in children and adults | DynaMed Plus. 2017; Link to research.
  8. Clark GW, Pope SM, Jaboori KA. Diagnosis and treatment of seborrheic dermatitis. Am Fam Physician.2015;91(3):185-190; PMID: 25822272 Link to research.
  9. Rosen T. Mycological Considerations in the Topical Treatment of Superficial Fungal Infections. J Drugs Dermatol.2016;15(2 Suppl):s49-55; PMID: 26885799 Link to research.
  10. Schwartz RA. Superficial fungal infections. Lancet.2004;364(9440):1173-1182; PMID: 15451228 Link to research.
  11. Tinea versicolor | DynaMed Plus. 2017; Link to research.
  12. Goncalves B, Ferreira C, Alves CT, et al. Vulvovaginal candidiasis: Epidemiology, microbiology and risk factors. Crit Rev Microbiol.2016;42(6):905-927; PMID: 26690853 Link to research.
  13. Pappas PG, Kauffman CA, Andes DR, et al. Clinical Practice Guideline for the Management of Candidiasis: 2016 Update by the Infectious Diseases Society of America. Clin Infect Dis.2016;62(4):e1-50; PMID: 26679628 Link to research.
  14. Vulvovaginal candidiasis | DynaMed Plus. 2017; Link to research.
  15. Aguin TJ, Sobel JD. Vulvovaginal candidiasis in pregnancy. Curr Infect Dis Rep.2015;17(6):462; PMID: 25916994 Link to research.
  16. Bozena DK, Iwona D, Ilona K. The mycobiome - a friendly cross-talk between fungal colonizers and their host. Ann Parasitol.2016;62(3):175-184; PMID: 27770757 Link to research.
  17. LaTuga MS, Ellis JC, Cotton CM, et al. Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants. PLoS One.2011;6(12):e27858; PMID: 22174751 Link to research.
  18. Kourelis A, Kotzamanidis C, Litopoulou-Tzanetaki E, et al. Immunostimulatory activity of potential probiotic yeast strains in the dorsal air pouch system and the gut mucosa. J Appl Microbiol.2010;109(1):260-271; PMID: 20059615 Link to research.
  19. Finegold SM, Attebery HR, Sutter VL. Effect of diet on human fecal flora: comparison of Japanese and American diets. Am J Clin Nutr.1974;27(12):1456-1469; PMID: 4432829 Link to research.
  20. Romano P, Capece A, Jespersen L. Taxonomic and Ecological Diversity of Food and Beverage Yeasts. In: Querol A, Fleet G, eds. Yeasts in Food and Beverages;10.1007/978-3-540-28398-0_2. Berlin, Heidelberg: Springer Berlin Heidelberg; 2006:13-53.
  21. The Yeasts: A Taxonomic Study. Vol 1. 5 ed: Elsevier; 2011.
  22. Parvez S, Malik KA, Ah Kang S, et al. Probiotics and their fermented food products are beneficial for health. Journal of applied microbiology.2006;100(6):1171-1185; PMID: 16696665 Link to research.