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Candida and the Microbiome

The role of the gut microbiome in the treatment and prevention of candida overgrowth


Antibiotics can lead to life-threatening fungal infection because of disruption to the gut microbiome. Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria (May 2022, mice & humans)


Fungus from the intestinal mucosa can affect lung health. With this observation, we were able to show for the first time how a single member of the microbiome, Candida albicans, influences the specific immune response to a large group of other microbes Human Anti-fungal Th17 Immunity and Pathology Rely on Cross-Reactivity against Candida albicans (Feb 2019).

Candida tropicalis infection modulates the gut microbiome and confers enhanced susceptibility to colitis in mice (Dec 2021)


Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi (2018): - study shows that fungi (candida) do not colonize the gut, and instead come from diet/environment via mouth. And the conclusion I see is that it's a matter of missing microbes allowing candida to flourish in the gut. It also says "levels of Candida albicans in stool were dramatically reduced by more frequent cleaning of teeth".

That is also supported by this study from a few months ago which suggested that it's dysbiosis of the gut allowing oral bacteria to proliferate in the gut and cause problems:

"The intestinal expansion of pathogenic Candida spp. was associated with a substantial loss in bacterial burden and diversity, particularly in the anaerobes. Thus, simultaneous analysis of intestinal fungi and bacteria identifies dysbiosis states across kingdoms that may promote fungal translocation and facilitate invasive disease" (Jan 2020)

Review, 2018: The mammalian mycobiome: A complex system in a dynamic relationship with the host "healthy mice are generally resistant to C. albicans colonization in the gut, but this resistance is lost upon broad-spectrum antibiotics treatment"

Review, 2018: The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis: - Candida albicans being found in 96.8%, 88.3%, and 80.8% of the samples of healthy subjects. But an increased presence in unhealthy people (IE: people with gut dysbiosis - so correct gut dysbiosis and you fix candida overgrowth).

"At molecular levels, S. boulardii is able to secrete enzymes, such as proteases or phosphatases, which can inactivate toxins produced by highly inflammatory intestinal pathogens such as C. difficile and E. coli [59,60]. This yeast also directly inhibits the growth and dissemination of several intestinal pathogens, such as C. albicans, Salmonella typhimurium, and Yersinia enterocolitica [61]."

Newly identified yeast could prevent fungal infections by outcompeting rivals. Competitive fungal commensalism mitigates candidiasis pathology (Mar 2024)

Fungi as Part of the Microbiota and Interactions with Intestinal Bacteria (2018): - - fungal and bacterial abundance in the gut appear to be negatively correlated and disruption of the bacterial microbiota is a prerequisite for fungal overgrowth (2018 book chapter).

The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics (May 2020, mice) "Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species"

Similar thing happens with a common dust fungi:

Expansion of a certain species of house dust fungus (Wallemia mellicola) can occur in the intestines of mice after they are treated with antibiotics and exposed to the fungus. By contrast, mice with an intact and healthy intestinal microbiota resist this expansion. After expansion of this fungal population, the mice are more prone to develop asthma-like inflammation in their lungs when exposed to allergens. (2018):

Case report:

"For years I suffered from Candida and avoided all mushrooms and fungi like the plague. But later realized my mistake. Once I incorporated beneficial fungi like reishi, lions maine, and cordyceps many of my digestive issues went away, and I no longer have Candida. Apparently the cure for fungal overgrowth is fungi that outcompete the bad fungi and help restore gut flora balance"


Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection (2018): "donor-derived fungal colonization in recipients is associated with FMT response. FMT “nonresponders” and individuals treated with antibiotics display a dominant presence of Candida. High abundance of C. albicans in donor stool also correlates with reduced FMT efficacy. Furthermore, C. albicans reduces FMT efficacy in a mouse model of CDI, while antifungal treatment reestablishes its efficacy"

"The patient had high levels of Candida and Streptococci that have normalized after the FMT."

83 - Fecal Microbiota Transplantation alters the GUT Mycobiome (Fungome) which Correlates with Treatment Outcome in Clostridium Difficile Infection (2018):

"High gut Candida before FMT is associated with clinical response in ulcerative colitis" (Apr 2020, n=39(?))

So candida overgrowth is a symptom of gut dysbiosis and gut dysbiosis is fixed via FMT.


Multifactorial inhibition of Candida albicans by combinations of lactobacilli and probiotic Saccharomyces cerevisiae CNCM I-3856 (Apr 2024, in vitro)

Probiotic yeast may offer an effective treatment for drug-resistant fungal infections. Study shows that yeasts derived from food are effective in preventing infections and reducing the virulence of several Candida species Probiotic Yeasts Inhibit Virulence of Non-albicans Candida Species (Oct 2019).

Inhibition of Candida albicans morphogenesis by chitinase from Lactobacillus rhamnosus GG (Feb 2019): "we found that the closely related taxa L. rhamnosus, L. casei and L. paracasei showed stronger activity against Candida hyphae formation compared to other Lactobacillus species tested"

Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans (Aug 2022, in vitro) B. adolescentis in particular. "increasing the pH of both bacterial supernatants and mixtures of fermentation acids reduced their anti-Candida effects, indicating a combinatorial effect of prevailing pH and fermentation acids"

2019: - probiotics and herbs.

Bacillus Subtilis inhibits candida:

E. faecalis inhibits candida: