**Background:** The human microbiome consists predominantly of bacteria, but advances in sequencing have revealed that fungi (the mycobiome) also play an important role in health and disease. This narrative review aims to synthesize current knowledge about commensal yeasts—primarily Candida spp., Malassezia spp., Cryptococcus spp., and Rhodotorula spp.—that colonize the human gut, skin, oral cavity, and urogenital tract, and to describe the diseases associated with mycobiome dysbiosis.
**Methods:** The authors conducted a literature search across Scielo, PubMed, and Web of Science using keywords including mycobiome, intestinal microbiota, skin yeasts, fungi, vaginal microbiota, oral microbiota, vulvovaginal diseases, and skin diseases. Inclusion criteria were articles in Portuguese or English, with text availability, and a preferred publication date within the last 5 years. The review blends findings from systematic reviews and primary studies.
**Key Results:** The review identifies Candida spp. as the most common fungal genus across all four niches (skin, vagina, intestine, oral cavity). C. albicans colonizes the vagina in approximately 20–30% of asymptomatic women by culture-dependent methods and ~65% by molecular methods. When symptomatic, 80–92% of vulvovaginal candidosis cases are caused by C. albicans. Up to 9% of women of childbearing age suffer from recurrent VVC (≥4 episodes/year). In the gut, Saccharomyces cerevisiae, Malassezia restricta, and C. albicans were identified in 96.8%, 88.3%, and 60.8% of individuals, respectively. In Crohn's disease, there is an increase in the fecal fungal burden and an elevated Basidiomycota–Ascomycota ratio, with increased abundance of C. albicans, C. tropicalis, C. glabrata, Aspergillus clavatus, Cryptococcus neoformans, and others, alongside a decrease in Saccharomyces cerevisiae. In irritable bowel syndrome (affecting 10–15% of individuals), Candida spp. (notably C. albicans), Malassezia spp., Cladosporium spp., and S. cerevisiae are increased, while Mycosphaerella spp., Aspergillus spp., Sporidiobolus spp., and Pandora spp. decrease. For Cryptococcus, an estimated 223,000 people with HIV/AIDS develop cryptococcal meningitis annually, with 181,000 deaths. C. gattii has a mortality rate of nearly 33% and can infect immunocompetent individuals. Malassezia constitutes >90% of the total fungal population on skin. In seborrheic dermatitis, prevalence increases with age (2.0% in <35 years; 3.6% in 35–64 years; 4.4% in ≥65 years), with a 14.3% prevalence reported in the Rotterdam study. Malassezia DNA is detected in ~90% of skin lesions. Among Rhodotorula infections, R. mucilaginosa accounts for 72% of cases, followed by R. glutinis (21%) and R. minuta (7%). In the oral cavity, C. albicans is the primary cause of oropharyngeal candidosis, and advanced dental caries are associated with increased C. albicans in adults and C. dubliniensis in children. In periodontitis, a decrease in microbiome diversity is observed, with reduced S. cerevisiae and increased Filobasidiales species. In obesity, Candida, Nakaseomyces, Penicillium, and other genera are increased, while Mucor racemosus and M. fuscus are more common in non-obese individuals. In diabetes, C. albicans is the most common strain in stool, with type 2 diabetes also showing increases in Cladosporium spp., Meyerozyma spp., Mortierella spp., and Aspergillus spp.
**Clinical Implications:** The review underscores that fungal communities are integral to human microbiota homeostasis across multiple body sites. Dysbiosis of the mycobiome is associated with a wide range of diseases including inflammatory bowel disease, irritable bowel syndrome, colorectal cancer, obesity, diabetes, pityriasis versicolor, seborrheic dermatitis, psoriasis, oropharyngeal candidosis, dental caries, periodontitis, vulvovaginal candidosis, and candiduria. The authors highlight emerging evidence for inter-niche connections (gut–skin axis, gut–vagina axis, oral–gut axis) that may open new preventive, diagnostic, and therapeutic possibilities. A major concern is the increasing resistance of microorganisms to antifungal drugs. The authors suggest that mycobiome-based monitoring and sanitization systems, including probiotic-containing sanitizing products, are being developed to modulate mycobiomes and reduce pathogen proliferation, particularly in hospital environments. They call for future research to include yeasts in microbiome studies to better understand their role in health and disease, and to investigate the effects of geography, diet, and age on the human mycobiome.