Woman smiling


When thinking about oral health, we must consider fungal species, not just bacteria. The oral mycobiome can be a friendly player, hanging out harmlessly behind the scenes. But under the right conditions, it can bloom out of control causing oral thrush, cavities, sores at the corners of the lips, or a burning mouth. The oral-gut connection tells us that the mouth and the gut are inseparable. Indeed, problems with Candida or yeast overgrowth in the mouth are a surefire sign of issues in the gut. Fungal imbalance can be a whole-body issue, affecting the lungs, skin, or the genitourinary tract.  Risk factors can set you up for yeast overgrowth, including a sugary diet, antibiotics, stress, and steroid medications. A weakened immune system leaves you wide open for fungal infection. Clinicians and patients should be on the lookout for signs of fungal overgrowth and use Candida overgrowth tests to guide treatment. Follow the tips in this blog for getting rid of Candida and work with an integrative and functional medicine provider to address fungal dysbiosis for once and for all.

What is the Oral Mycobiome?

“Oral mycobiome” may be a strange word to your ears. Unlike the oral microbiome, which includes all of the microorganisms living in the mouth, the oral mycobiome refers to only the fungi that live in the mouth. Specifically, the oral microbiome includes bacteria, fungi, parasites, bacteriophages, and viruses, whereas the oral mycobiome only includes fungi in the mouth. Compared to bacteria, fungi in healthy people make up a very small percentage of the oral microbiome; perhaps as little as 0.004% of the total oral microbiome according to one source,1 or less than 400 colony forming units per milliliter saliva.2 However, even small amounts of Candida and some other fungi can cause problems in the mouth when the conditions are right. The oral mycobiome has been largely ignored while oral bacteria have been studied intensively. In fact, 2010 was the first time the “core oral mycobiome” was characterized.3 There is more for us to learn in the coming decades.

Candida: Friend or Foe?

Fungus is a normal, natural inhabitant of the oral microbiome. Candida is the most well-known oral fungus. Sometimes called “yeast,” Candida lives in people’s mouths, intestines, and on their skin. One in two adults has Candida species living in their mouth.4 In small to moderate amounts, it is normal and does not cause a problem as long as the immune system is in good working order. However, Candida can get out of balance for people at risk. Certain factors make a person more likely to have Candida overgrowth.

When people have very weak immune systems, Candida infections can take over the bloodstream (called “invasive candidiasis”) and can be deadly. Hospitals see these infections sometimes and they are dangerous. However, for most people, fungal overgrowth shows up with mild, bothersome symptoms. Most people have had, or know someone who has had, oral thrush, vaginal yeast infections, jock itch, and/or athlete’s foot. These are common yeast overgrowth symptoms that point to an imbalance of fungi and bacteria in your microbiome.

In a group of disorders known as chronic mucocutaneous candidiasis, a person may have poor immune defenses against Candida species. They will experience Candida infections that won’t go away, affecting the skin, mucous membranes, and nails.

What Puts You at Risk for Fungal Overgrowth?

  • Alcohol
  • Antibiotics5
  • Chronic stress
  • Diabetes
  • Disturbed oral microbiome or poor oral microbiome diversity
  • Higher plaque levels2
  • Inhaled or systemic steroids2
  • Oral contraceptive use
  • Poor dental hygiene2
  • Poor immune defenses5
  • Removable dental prosthesis2
  • Smoking2
  • Sugary diet
  • Weak mouth lining barrier/leaky gums

Candida Infections in the Mouth

Candida overgrowth affects the skin and mucous membranes. It can cause problems in the mouth, esophagus, corners of the mouth, and genitals. It may harm the gut, as we will discuss later.

Candida is well-known to cause mouth infections such as thrush. When Candida overgrows in the lining of the mouth, white plaques show up on the tongue, insides of the cheeks, roof of the mouth, and corners of the mouth. A white coating in the mouth may be seen in infants. Candida may also cause a burning, sore mouth, especially if the fungal overgrowth is due to poorly fitting dentures.4

Candida is the only group of fungi that grows to significant amounts in the mouth and creates a distinct ecology of its own. Candida loves an acidic pH.2 However, oral infections of Candida are usually caused by Candida working together in concert with bacteria.2 In oral microbiomes where Candida takes center stage, the oral bacteria are less diverse. Good bacteria are at lower levels. There are more acid-producing bacteria, such as Lactobacillus and Propionibacterium.2 Streptococcus oralis and Streptococcus mutans thrive in a Candida-dominant fungal infection.2

Image by Sabrina B. from Pixabay

Got Cavities? Think Candida

Streptococcus mutans, the bacteria often blamed for cavities, has a partner in crime- Candida. Both Streptococcus mutans and Candida have been found in tooth cavities.6 Candida species work together with acid-producing bacteria to cause cavities. In the process, they usually crowd out other friendly bacteria in the oral microbiome such as Streptococcus sanguinis.7 The acidic conditions breakdown or “demineralize” teeth.7

Candida has virulence factors, or harmful substances, that can damage the surrounding cells. Examples include multifunctional adhesins, enzymes that break down host cells, and toxins. Candida also makes biofilms, a perfect place for oral bacteria to hide. Biofilms help Candida attach and survive in the mouth, as well as avoid destruction by the immune system.8 Candida’s virulence factors can breakdown the mouth lining barrier in people who are susceptible.2

There is a strong association of Candida albicans with advanced dental caries.2,9 When Candida is present, cavities are more severe.7 Cavities in children known as “early childhood caries” are especially related to Candida albicans overgrowth.9,10 Candida plays a critical role in root cavities (root caries) where the tooth root is more exposed, which affects the elderly population.7 Dental professionals working with patients with chronic tooth decay that won’t resolve should look for clinical signs of Candida, test for it, and treat it. Integrative and functional medicine practitioners should ask about a history of cavities, thrush, as well as other systemic signs of fungal dysbiosis.

Fungi can also do good! Certain fungi may protect children against cavity-causing bacteria including Debaromyces, Rhodotorula, or Malassezia.2 Unfortunately, there isn’t a lot of research about friendly fungi in the mouth. Medical and dental research is way more geared toward researching pathogens and disease-causing microbiota. There is probably more to this that will unfold in the coming years.


What is Oral Thrush?

Oral thrush happens when Candida species in the mouth, usually Candida albicans, grows out of control and causes symptoms. Thrush symptoms include a white-coated tongue and mouth, multiple white flecks on the tongue, under the tongue, on the inside of the cheeks, and on the roof of the mouth.5  The flecks can grow in size to be large patches. When the patches are scrubbed off, they usually leave a red, inflamed base and they may bleed. Thrush is also known as “acute pseudomembranous candidiasis.”

Oral thrush usually affects infants, newborns, the elderly, patients on antibiotics or steroids, and people with hormone disorders or immune suppression.

Nearly 40% of newborns develop thrush during their first months of life. Children on inhaled steroids have an easier time getting thrush. Babies with thrush may also have Candida diaper rash, which may come from Candida living in the intestines that also affects the diapered skin.5 Read more about intestinal candidiasis below.

Treatments for Oral Thrush

Most antifungal agents are effective in treating thrush. Treatments for thrush include oral nystatin, which can be swished and swallowed.5 Nystatin is safe and well-tolerated and stays in the intestines, unlike systemic antifungals. A systemic antifungal medication recommended for thrush is fluconazole. Gentian violet solution is a second-line therapy for thrush when it doesn’t respond to treatment with nystatin or fluconazole. If thrush keeps coming back, then consider that you may have a fungal imbalance that goes beyond the mouth. Read the treatment suggestions later in this blog for addressing Candida infection that won’t go away.

Figure 1. Two mycotypes have been identified in the mouth: the Candida mycotype and the Malessezia mycotype. Factors that influence the fungal communities are listed across the top. The Candida mycotype is less diverse, whereas the Malassezia mycotype includes a diversity of other fungi.2


Move Over Candida, There Are Other Fungi in the Mouth!

Candida gets all of the attention for the health problems it can cause us. However, there are other fungi in the oral mycobiome that deserve some attention. Malassezia is a runner-up to Candida. Malassezia is the most abundant friendly fungus found on human skin, and the same species is found in the mouth.2 Malassezia fungus in the mouth is very common and can be found in saliva and mouth tissue samples. Many people can either have a Candida-dominant oral mycobiome or a Malessezia-dominant oral mycobiome. When Malassezia is the dominant fungi on the scene, a spread of other fungi are present (unlike with Candida), but it is rich with inflammation-loving bacteria such as Fusobacterium, Porphyomonas, Prevotella, and Leptotrichia.

In rare cases, other fungi besides Candida can wreak havoc. Cryptococcus species and filamentous fungi (Aspergillus species) have caused oral mucosal lesions and systemic infections.2 Remember, a weakened immune system is almost always necessary for fungi to take over. Unfortunately, weak immune systems are more widespread than we once thought.

A List of Fungal Species Found in the Human Oral Mycobiome Based on 21 Studies2

(in order of most to least common)

    1. Candida
    2. Cladosporium/Davidiella
    3. Saccharomyces
    4. Penicillium/Talaromyces
    5. Malassezia
    6. Alternaria/Lewia
    7. Pichia/Cyberlindnera
    8. Aspergillus/Emericella/Eurotium
    9. Crypococcus/Cystofilobasidium
    10. Aureobasidium
    11. Rhodotorula
    12. Trichosporon
    13. Debaromyces
    14. Wallemia
    15. Clavispora
    16. Meyerozima
    17. Mycosphaerella
    18. Phaeosphaeria
    19. Saccharomycetales (unclassified)
    20. Trichoderma
    21. Epicoccum
    22. Toxicocladosporium

Image by Daniel Albany from Pixabay

“Brushing teeth after every meal significantly decreased Candida levels in the saliva and stool,

much more than brushing one time per day.”


Fungal Dysbiosis in the Gut

Candida does not just create problems in the mouth. Fungal overgrowth- or yeast overgrowth- in the gastrointestinal tract is considered to be a significant and often overlooked cause of illness by integrative and functional medicine practitioners. It started many years ago with a famous book called the Yeast Connection by William Crook, MD. Candida is a normal inhabitant of the gut, and is found in 40–80% of normal stool specimens.11,12 However, having too much fungus can not only appear in the gut as constipation, diarrhea,11 or bloating, it can also cause systemic symptoms such as fatigue, brain fog, and susceptibility to infections. Many practitioners target the gut when a person has symptoms of fungal imbalance anywhere in the body, since the gut is a reservoir for fungi such as Candida.

Different names- intestinal candidiasis, “yeast syndrome,” or “Candida sensitivity”- have been suggested to cause a cluster of symptoms for which no etiology has been established, including: gastrointestinal complaints, fatigue, lethargy, skin rashes, urinary frequency, muscle or joint pain, abdominal pain, diarrhea, constipation, flatulence, allergies, and vaginitis. Mainstream medicine does not acknowledge this type of dysbiosis and high-quality studies to support it do not exist. However, studies that identify patients as high risk for fungal overgrowth (past history of antibiotic use), respond dramatically to a low-sugar, low-starch diet and antifungal medications.13 Dr. Carol Jessop reported a dramatic improvement in 1,100 patients with chronic fatigue syndrome after giving oral nystatin and a special diet (low sugar, alcohol, fruit, fruit juice) for 3–12 months.13,14

I have seen fungal dysbiosis repeatedly in my consulting role for laboratories and I have also experienced it personally. Fungal overgrowth on stool tests can indicate that a patient has a gastrointestinal fungal dysbiosis. Although rigorous evidence is not yet available, countless practitioners see excellent results in clinical practice when they treat patients with lifestyle changes and supplements to reduce fungal imbalances in the gut.

Symptoms of Fungal Overgrowth:

  • Athlete’s foot
  • Bloating
  • Brain fog
  • Constipation
  • Diarrhea
  • Esophagitis
  • Fatigue
  • Gastritis
  • Itchy ears
  • Jock itch
  • Reflux
  • Skin rashes
  • Sweet cravings
  • Vaginal yeast infections

The Gut Mycobiome

We are still learning about fungi in the gastrointestinal tract. Much like the mouth, fungi make up a very small percentage when compared to the trillions of bacteria they share the stage with. In a study of the human gut mycobiome, these yeasts dominated the healthy gut:

  • Saccharomyces cerevisiae (96.8%)
  • Malassezia restricta (88.3%)
  • Candida albicans (80.8%)

Because these fungi were so common, they were considered normal, or “commensals.”15 As long as someone has a healthy diet, a strong microbiome, and a good immune system, these fungi can hang around without causing disease. It’s when systems start to break down and a fungus like Candida albicans can move in, take over, and spark illness. Authors stated that diet, environment, daily rhythms, and host genetics likely influence the human gut mycobiome. One of the strong negative associations detected was between Candida and Saccharomyces. In other words: The more Saccharomyces present, the less Candida in the gut.15 This explains why so many integrative and functional medicine practitioners use Saccharomyces boulardii, a friendly yeast, to ward off intestinal yeast overgrowth.

In one study, researchers said that fungal numbers found in the stool are more reflective of fungi from the mouth and from eating foods than actual fungal dysbiosis in the gut. Researchers showed that fungi in the stool and saliva were high when eating certain foods, but when avoiding them, the levels dropped. The study found these foods to be high in fungi: bread, cheese, beer, corn, and nuts.16 Brushing teeth after every meal significantly decreased Candida levels in the saliva and stool, much more than brushing one time per day.16 The study measured 148 Human Microbiome specimens and 4 volunteers with controlled diets for extended periods of time. Tests were done by PCR and culture.

Candida Overgrowth Tests

Testing for Candida overgrowth or fungal imbalance isn’t easy or widely available. Dental professionals use saliva tests to detect fungal dysbiosis or Candida in the mouth, such as OraRisk Candida by OralDNA Labs. Since mainstream medicine doesn’t recognize subclinical fungal imbalance as a real problem, practitioners don’t run tests for it. However, integrative and functional medicine practitioners run advanced stool tests to measure fungi such as Candida or Rhodotorula species, which may be high in the intestines. One example is the GI-MAP by Diagnostic Solutions. Some of the other tests to detect yeast overgrowth are fecal microscopy, Candida blood antibodies, or urinary fungal metabolites such as D-arabinitol. In hospital settings where invasive candidiasis is a risk, physicians measure Candida by blood culture.

Unfortunately, it is difficult to test fungi. They don’t always grow well in cell culture tests. Their cell walls are very strong and that can help them evade measurement by DNA-based studies. Special procedures must be used to destroy their cell walls to free up their DNA so it can be measured accurately.2


Treatments for Candida Overgrowth in the Gut

Common treatments for fungal overgrowth in the gut include an anti-fungal diet, probiotics, Saccharomyces boulardii (a friendly yeast), and anti-fungal herbs. Oregano oil can effectively kill fungus and many integrative and functional medicine practitioners use it to treat fungal gut dysbiosis. Other anti-fungal herbs include caprylic acid, olive leaf extract, ginger, and berberine. Some clinicians use nystatin to treat gut dysbiosis. They might give it in a tablet or for a child, as a liquid. Nystatin is gentle and well-tolerated by adults and children. The only problem is that they often add sweetener to the liquid. Otherwise, this antifungal is a fave of many integrative and functional practitioners, as it stays in the gut and is gentle on the liver. Fluconazole (Diflucan), is a powerful systemic antifungal that can eradicate yeast overgrowth, but liver enzymes should be monitored. With chronic antifungal use, it is possible to build drug-resistant fungi or “superbugs.”

The Best Diet to Get Rid of Candida

The most common diet to help someone combat a fungal overgrowth is an anti-Candida diet. Candida species feed on sugars, simple carbohydrates, and starches. By greatly limiting sugar and carbohydrates, Candida and other fungi cannot grow. Instead, a diet of eggs, fish, chicken, seafood, tofu, nuts, and seeds, non-starchy vegetables, and plain yogurt with live cultures is recommended. This takes away their fuel and helps to remove Candida and other fungi from the mouth and gut.

There are many, many foods in our diet that contain fungus. This is not a bad thing, but if you have a fungal overgrowth, it can be a bad thing until your fungal overgrowth is under control. Examples are cheese, vinegar, mushrooms, nuts, beer, and wine. An anti-fungal diet will often limit these foods to help “starve out” Candida or other fungi in the gut.


Fungal Overgrowth in the Mouth and the Whole Body

Bacteria are not the only cause of mouth infections. Fungus can be the real issue lurking in the shadows. The oral mycobiome makes up the fungal microorganisms that live in the mouth. As long as your immune system is strong, you don’t eat a sugary diet, and you aren’t taking antibiotics, the fungi in your mouth can be harmless, even helpful players. However, when conditions are thrown out of balance, Candida can rise to power and cause oral thrush, cavities, sores at the corners of the lips, or a burning mouth. Candida can encourage bad bacteria, build biofilms where they can hide, and secrete substances that harm the mouth. Not just an oral or gut problem, fungal imbalance can be a whole-body issue. Practitioners and consumers should be on the lookout for signs of fungal imbalance in the mouth.  There are many natural treatments to balance fungus and get you feeling great again.


Treatments to Decrease Fungal Dysbiosis in the Mouth

  • Eat an anti-Candida diet; mostly vegetables and meat with little to no sugar, starches, fruit juice, or fungal foods. Use stevia or xylitol as sweeteners. Avoid high-fungus foods such as bread, cheese, beer, corn, and nuts.
  • Test the mouth for Candida and fungal dysbiosis
  • Run a stool test to detect yeast overgrowth in the intestines
  • Maintain oral hygiene and dental cleanings as directed
  • Brush your teeth after every meal
  • Work with a practitioner if antifungal agents are needed. Examples of natural antifungals are oregano oil, berberine, and caprylic acid. There are liquids to swish and toothpaste products that address oral dysbiosis. Pharmaceuticals are nystatin or fluconazole.
  • Take dental probiotics for the mouth, including Streptococcus salivarius
  • Take oral probiotics for the gut: Lactobacillus, Bifidobacteria, and Saccharomyces boulardii
  • Treat both the mouth and the gut if fungus is suspected
  • Avoid unnecessary antibiotics. When necessary, take precautions so as not to throw off the balance of fungus and bacteria in your microbiome.
  • Mothers, address vaginal dysbiosis/yeast infections before conceiving and giving birth, when possible.
  • If you have chronic illnesses or unexplained symptoms, find an integrative and functional medicine practitioner to work with and investigate fungal imbalance.



  1. Caselli E, Fabbri C, D’Accolti M, et al. Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture. BMC Microbiol. May 18 2020;20(1):120. doi:10.1186/s12866-020-01801-y
  2. Diaz PI, Dongari-Bagtzoglou A. Critically Appraising the Significance of the Oral Mycobiome. Journal of dental research. Feb 2021;100(2):133-140. doi:10.1177/0022034520956975
  3. Ghannoum MA, Jurevic RJ, Mukherjee PK, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. Jan 8 2010;6(1):e1000713. doi:10.1371/journal.ppat.1000713
  4. Edminister JR. Mucosal Candidiasis. Medscape. Updated May 26, 2022. Accessed July 25, 2023. https://emedicine.medscape.com/article/1075227-overview
  5. Kumar M. Thrush. Medscape. Updated June 21, 2023. Accessed July 25, 2023. https://emedicine.medscape.com/article/969147-overview
  6. Li Y, Huang S, Du J, Wu M, Huang X. Current and prospective therapeutic strategies: tackling Candida albicans and Streptococcus mutans cross-kingdom biofilm. Frontiers in cellular and infection microbiology. 2023;13:1106231. doi:10.3389/fcimb.2023.1106231
  7. Du Q, Ren B, He J, et al. Candida albicans promotes tooth decay by inducing oral microbial dysbiosis. ISME J. Mar 2021;15(3):894-908. doi:10.1038/s41396-020-00823-8
  8. Rapala-Kozik M, Surowiec M, Juszczak M, et al. Living together: The role of Candida albicans in the formation of polymicrobial biofilms in the oral cavity. Yeast. May 16 2023;doi:10.1002/yea.3855
  9. Bao J, Huang X, Zeng Y, et al. Dose-Dependent Inhibitory Effect of Probiotic Lactobacillus plantarum on Streptococcus mutans-Candida albicans Cross-Kingdom Microorganisms. Pathogens. Jun 20 2023;12(6)doi:10.3390/pathogens12060848
  10. Lu Y, Lin Y, Li M, He J. Roles of Streptococcus mutans-Candida albicans interaction in early childhood caries: a literature review. Frontiers in cellular and infection microbiology. 2023;13:1151532. doi:10.3389/fcimb.2023.1151532
  11. Hidalgo JA CB. Candidiasis. emedicine from WebMD. Accessed 5/14/2013, 2013. https://emedicine.medscape.com/article/213853-overview#showall
  12. Santelmann H, Howard JM. Yeast metabolic products, yeast antigens and yeasts as possible triggers for irritable bowel syndrome. Eur J Gastroenterol Hepatol. Jan 2005;17(1):21-6. doi:10.1097/00042737-200501000-00005
  13. Olmstead S MD, Ralson J. Candida, fungal-type dysbiosis and chronic disease: exploring the nature of the yeast connection. Townsend Letter. 2012;5
  14. Cater RE, 2nd. Chronic intestinal candidiasis as a possible etiological factor in the chronic fatigue syndrome. Med Hypotheses. Jun 1995;44(6):507-15. doi:10.1016/0306-9877(95)90515-4
  15. Nash AK, Auchtung TA, Wong MC, et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome. Nov 25 2017;5(1):153. doi:10.1186/s40168-017-0373-4
  16. Auchtung TA, Fofanova TY, Stewart CJ, et al. Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. mSphere. Mar-Apr 2018;3(2)doi:10.1128/mSphere.00092-18
  17. Ghosh K, Weiss LM. Molecular diagnostic tests for microsporidia. Interdiscip Perspect Infect Dis. 2009;2009:926521. doi:10.1155/2009/926521
  18. Wojcik A, Blaszkowska J, Kurnatowski P, Goralska K. Sandpits as a reservoir of potentially pathogenic fungi for children. Annals of agricultural and environmental medicine : AAEM. Dec 23 2016;23(4):542-548. doi:10.5604/12321966.1226843
  19. Guidara R, Trabelsi H, Neji S, et al. Rhodotorula fungemia: Report of two cases in Sfax (Tunisia). Journal de mycologie medicale. Jun 2016;26(2):178-181. doi:10.1016/j.mycmed.2016.02.020


Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.