When we talk about gut health, bacteria usually steal the spotlight. But there's another kingdom of microscopic organisms calling your intestines home: fungi. Known collectively as the gut mycobiome, these yeasts and molds play a surprisingly big role in digestion, immunity, and even brain health.
Research is only beginning to uncover how fungal communities in our gut influence disease risk and overall wellbeing. From associations with multiple sclerosis to changes during COVID-19 infection, the fungi living in your gut may be more important than you think [1][2].
Key takeaways
- The gut mycobiome contains fungi like Candida, Saccharomyces, and Aspergillus that interact with gut bacteria and your health.
- Candida overgrowth may be associated with conditions like multiple sclerosis, lupus, and severe COVID-19.
- The balance between fungi and bacteria in the gut appears important—disruptions may contribute to disease.
- COVID-19 research has revealed increased fungal diversity and opportunistic pathogens in infected individuals.
- Probiotic yeasts like Saccharomyces boulardii may offer health benefits by supporting microbial balance.
What Is the Gut Mycobiome?
The gut mycobiome refers to the entire community of fungi residing in your gastrointestinal tract. While less diverse than bacterial populations, these fungi still number in the hundreds of species [3].
Common genera found in the human gut include Candida, Saccharomyces, Aspergillus, and Malassezia [4]. Among these, Candida is one of the most studied—it's also one of the most cited fungal genera in scientific research overall [3].
These fungi don't just passively occupy space; they interact with your gut bacteria, your immune system, and even your diet. The balance between different fungal species, and between fungi and bacteria, appears to matter for health outcomes.
Candida: The Famous Fungus in Your Gut
Candida is perhaps the best-known gut fungus, and for good reason. It's normally present in small amounts in most healthy individuals, but it can become opportunistic under certain conditions.
Studies have found that Candida levels can vary significantly depending on health status. In patients with multiple sclerosis (MS), researchers observed an increased abundance of Candida compared to healthy controls, along with decreased Saccharomyces [2]. Similarly, in mouse models of systemic lupus erythematosus (SLE), increased Candida was observed in the gut, along with an elevated Basidiomycota-to-Ascomycota ratio that correlated with disease activity [8].
COVID-19 research has also highlighted Candida. One study found oral fungal carriage was three times higher in COVID-19 patients compared to healthy controls, with Candida albicans being the most frequently isolated species (90.79%) [12].
The Fungal-Bacterial Balance
Your gut doesn't contain fungi in isolation—they exist alongside trillions of bacteria. The ratio between these populations may matter for health.
In multiple sclerosis patients, researchers found an increased fungal-to-bacterial ratio (measured by ITS2/16S ratio) compared to healthy controls, along with more diverse fungal-bacterial interactions [2]. This suggests that disruptions in the bacterial microbiome may allow fungi to expand, or vice versa.
This fungal-bacterial interplay appears relevant in several conditions. In COVID-19 patients, fecal microbiome dysbiosis has been reported alongside increased opportunistic pathogens [1]. Similarly, in chronic respiratory diseases like COPD, the pulmonary mycobiome is dominated by Candida, with differences between oral and lung samples [4][13].
Gut Fungi and Autoimmune Conditions
Emerging research suggests gut fungi may influence autoimmune diseases beyond the gut itself. The connection appears to involve immune system modulation.
In multiple sclerosis patients, the gut mycobiome showed distinct changes: increased Basidiomycota and decreased Ascomycota at the phylum level, plus altered fungal-bacterial associations and functional profiles [2]. These changes were specific enough that researchers suggested the mycobiome could eventually serve as a biomarker.
In lupus-prone mouse models, active disease states were associated with elevated gut fungal populations and specific changes in fungal composition—particularly increased Candida species [8]. The Basidiomycota-to-Ascomycota ratio specifically correlated with lupus activity markers.
Fungi, COVID-19, and Respiratory Health
The relationship between gut fungi and respiratory health became particularly evident during the COVID-19 pandemic. Research revealed significant changes in fungal communities during SARS-CoV-2 infection.
In nasopharyngeal samples from COVID-19 patients, researchers found significantly increased population and diversity of fungi, including a high proportion of opportunistic pathogens. Notably, 37% of fungal species were exclusively associated with SARS-CoV-2 infection [10].
In chronic lung diseases like COPD, the pulmonary mycobiome is less stable than the oral mycobiome over time, with Candida dominating samples from both patients and healthy controls [13]. This suggests that fungi may play a role in respiratory disease progression or severity.
Can Probiotic Fungi Help?
Not all fungi in the gut are problematic—some may actually benefit health. This has led to interest in yeast-based probiotics.
Saccharomyces boulardii is the most studied probiotic yeast, with demonstrated benefits including prevention and treatment of diarrhea, production of antimicrobial agents, prevention of pathogen adherence, and immune system modulation [7].
Other yeast candidates like Kluyveromyces lactis and Debaryomyces hansenii are also being evaluated for potential health applications [7]. These probiotic yeasts may help maintain microbial balance in the gut, potentially keeping opportunistic fungi like Candida in check.
Frequently asked questions
What is the gut mycobiome?
The gut mycobiome is the community of fungi living in your gastrointestinal tract. It includes species like Candida, Saccharomyces, and Aspergillus, which interact with gut bacteria and your immune system [3][4].
Is Candida in the gut normal?
Yes, Candida is normally present in small amounts in most healthy individuals. Problems arise when it overgrows, which can happen due to antibiotic use, immune suppression, or other factors that disrupt the microbial balance [2][12].
How does the gut mycobiome affect autoimmune diseases?
Research suggests gut fungi may influence autoimmune conditions through immune system interactions. Studies in multiple sclerosis and lupus have found specific fungal composition changes, including increased Candida and altered fungal-bacterial ratios [2][8].
Does COVID-19 affect gut fungi?
Yes, studies have found significant changes in fungal communities during COVID-19. One study found oral fungal carriage was three times higher in COVID-19 patients, with increased opportunistic pathogens detected in the nasopharyngeal tract [10][12].
Can probiotic yeasts improve gut health?
Saccharomyces boulardii is a well-studied probiotic yeast that may help prevent diarrhea, modulate the immune system, and maintain microbial balance. Other yeasts are also being investigated for potential health benefits [7].
References
- The human microbiome and COVID-19: A systematic review — Yamamoto S et al., 2021, PloS one
- Multiple sclerosis patients have an altered gut mycobiome and increased fungal to bacterial richness — Yadav M et al., 2022, PloS one
- What are the 100 most cited fungal genera? — Bhunjun CS et al., 2024, Studies in mycology
- The pulmonary mycobiome-A study of subjects with and without chronic obstructive pulmonary disease — Martinsen EMH et al., 2021, PloS one
- The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives — de Dios Caballero J et al., 2022, Microorganisms
- Multilocus sequence typing of Candida albicans oral isolates reveals high genetic relatedness of mother-child dyads in early life — Alkhars N et al., 2024, PloS one
- Advances in Yeast Probiotic Production and Formulation for Preventative Health — Moonsamy G et al., 2024, Microorganisms
- Fungal microbiome in gut of systemic lupus erythematosus (SLE)-prone mice (pristane and FCGRIIb deficiency), a possible impact of fungi in lupus — Cheibchalard T et al., 2024, PloS one
- Microbial profile in bile from pancreatic and extra-pancreatic biliary tract cancer — Di Carlo P et al., 2024, PloS one
- Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients — Hoque MN et al., 2023, PloS one
- Microbiota in cancer: current understandings and future perspectives — Yao Y et al., 2026, Signal transduction and targeted therapy
- Assessment of species distribution and virulence factors of oral fungal carriage among hospitalized patients with COVID-19: a case-control study — Ramezanalipour Z et al., 2024, Annals of medicine and surgery (2012)
- A longitudinal study of the pulmonary mycobiome in subjects with and without chronic obstructive pulmonary disease — Martinsen EMH et al., 2022, PloS one
- Do Malassezia yeasts colonize the guts of people living with HIV? — Abdillah A et al., 2025, PloS one
- The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies — Warren A et al., 2026, Alzheimer's & dementia : the journal of the Alzheimer's Association
- Diagnostic, prognostic, and therapeutic potentials of gut microbiome profiling in human schistosomiasis: A comprehensive systematic review — Oyono MG et al., 2025, PLoS neglected tropical diseases