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Table 3 Summary of mycobiomes in different body sites

From: The human mycobiome in health and disease

Sequencing method/ specimen type
(sample size (n))
Health status
or disease
Fungal composition of the mycobiome Citation
Oral cavity
Pyrosequencing/oral rinse samples (n = 20) Healthy Candida (22.2%), Cladosporium (19.4%), Aspergillus (11.1%), Fusarium (5.6%), Glomus (5.6%), Penicillium (4.2%), Alternaria (4.2%), Saccharomycetales (13.9%), Cryptococcus (2.8%), Ophiosoma (2.8%), Phoma (2.8%), Schizosaccharomyces (2.8%), Zygosaccharomyces (2.8%) [8]
Culture and morphologic observation/
oral mucosal swabs (n = 30)
AIDS Candida (100%) [67]
Nasal cavity
Culture and morphologic observation/
nasal mucosal swabs (n = 48)
Allergies Cladosporium (29.4%), Penicillium (20.6%), Alternaria (11.7%), Aspergillus (11.7%), Rhodotorula (2.9%), Chrysonilia (2.9%), Paecilomyces (5.8%), Stemphylium (2.9%), uncultivated Ascomycota (2.9%), Cladophialophora (2.9%), others (2.9%) [35]
Lung
Pyrosequencing/
sputum samples (n = 83)
Cystic fibrosis Candida, Saccharomyces, Malassezia, Fuscoporia, Fusarium, Acremonium, Thanatephorus, Cladosporium [12]
Pyrosequencing/
sputum samples (n = 4)
  Candida (74.98%), Neosartorya (16.68%), Malassezia (2.95%), Hyphodontia (1.04%), Kluyveromyces (1.02%), Aspergillus (0.93%), Penicillium (0.70%), Peniophora (0.43%), Clavispora (0.29%), Piptoporus (0.28%), Dioszegia (0.27%), Phlebiopsis (0.09%), Stereum (0.07%), Torulaspora (0.04%), Chalara (0.04%), Physalospora (0.04%), Eurotium (0.03%), Cryptococcus (0.03%), Quambalaria (0.03%), Nectria (0.03%), Didymella (0.02%), Saccharomyces (0.02%), Sporobolomyces (0.03%), Phaeosphaeria (0.01%), Strobilurus (0.01%) [19]
DGGE/sputum samples (n = 5)   Candida dubliniensis, C. albicans, C. parapsilosis, Aspergillus fumigatus [11]
Gut
RFLP/fecal samples (n = 106) Hepatitis B cirrhosis and chronic hepatitis B Candida (33.78%), uncultured fungi (12.53%), Aspergillus (7.99%), Simplicillium (5.65%), Chaetomium (2.46%), Galactomyces (2.33%), Rhizopus (1.96%), Wallemia (1.10%), Fusarium (1.10%), Iodophanus (0.12%), Penicillium (0.49%), Saccharomyces (25.18%), uncultured Pezizomycotina (0.86%), uncultured Pucciniomycotina (1.10%), uncultured Agaricomycotina (0.74%), Aureobasidium (0.61%), Hyphozyma (0.49%), Asterotremella (0.49%), Cryptococcus (0.49%), Doratomyces (0.37%), Ophiocordyceps (0.12%) [10]
Pyrosequencing/
fecal samples (n = 10)
Healthy Wallemia, Trichocomaceae, Saccharomycetaceae, Rhodotorula, Pleosporaceae, Metschnikowiaceae, Cystofilobasidiaceae, Ascomycota, Amphisphaeriaceae, Agaricaceae [21]
Sanger sequencing/
pouch endoscopic biopsies (n = 57)
Inflammatory bowel disease (including Crohn's disease and ulcerative colitis) Rhodotorula (16.08%), Galactomyces (0.60%), Trametes (9.52%), Pleospora (7.14%), Sclerotinia (8.34%), Penicillium (7.74%), Bullera (4.17%), Ustilago (4.17%), Candida (2.38%), Chaetomium (2.38%), Flammulina (1.79%), Dacrymyces (1.79%), Exidiopsis (1.19%), Sirococcus (1.19%), uncultured basidiomycete (11.31%), Botryotinia (4.17%), Filobasidium (3.51%), Sporolobomyces (2.98%), uncultured ascomycete (2.38%), uncultured ustilaginomycete (1.79%), Trichosporon (1.19%), Aureobasidium (0.60%), Raciborskiomyces (0.60%), Dothideomycete (0.60%), Cladosporium (0.60%), Madurella (0.60%), Tricholoma (0.60%), Graphiola (0.60%) [14]
Skin
RFLP/limb skin swabs (n = 8) Psoriasis Malassezia, Paracoccidioides, Blastomyces, Histoplasma, Coccidioides, Microsporum, Trichophyton, Sporothrix, Trichoderma, Hortaea, Anguillospora, Candida, Pneumocystis, Cryptococcus, Trichosporon, Rhodotorula, Rhizopus, Absidia [68]
Sanger sequencing/face skin swabs (n = 9) Atopic dermatitis Malassezia (67.9%), Cladosporium (5.5%), Candida (5.2%), Cryptococcus (5.2%), Rhodotorula (4.0%), Trichosporon (2.6%), Meyerozyma (2.0%), Alternaria (1.9%), Debaryomyces (0.3%), Phialophora (0.3%), Aspergillus (0.2%), Davidiella (0.1%), Mrakia (0.1%), Wallemia (0.1%), Sporobolomyces (0.2%), Penicillium (0.2%), Saccharomyces (0.1%), Sympodiomycopsis (0.1%), Tilletiopsis (0.1%), Apioplagiostoma (0.1%), Toxicocladosporium (1.5%), Wickerhamomyces (0.7%), Aureobasidium (1.9%), Exophiala (0.1%), Gibellulopsis (0.1%), Persiciospora (0.1%), Trametes (0.1%) [50]
Pyrosequencing/
scalp swabs (n = 7)
Dandruff-
afflicted scalps
Filobasidium (33.85%), Penicillium (3.44%), Malassezia (1.91%), Eupenicillium (0.04%), Acremonium (57.91%), uncultured soil fungus (2.47%), Cryptococcus (0.26%), Didymella (0.05%), Rhodotorula (0.05%), Coniochaeta (0.00%), uncultured Ascomycete (0.02%) [66]
Culture and morphologic observation/
foot skin swabs (n = 129)
Foot disease in soccer athletes Trichophyton (76.4%), Candida (20.0%), others (3.6%) [69]
Vagina
Pyrosequencing/
vaginal mucosal swabs (n = 494)
Healthy Candida (34%), Pichia (2%), Eurotium (1%), Alternaria (1%), Rhodotorula (1%), Cladosporium (2%), Davidiellaceae (3%), uncultured Saccharomycetales (6%), uncultured Epicoccum (1%), other minorities (49%) [63]
Conjunctiva
Culture and morphologic identification/
conjunctiva swabs (n = 61)
Leprosy (Hansen's disease) Candida (26.67%), Aspergillus (13.33%), Geotrichum (6.67%), Acremonium (6.67%), Alternaria (6.67%), Chaetonium (6.67%), Drechslera (6.67%), Penicillium (13.33%), Cladosporium (6.67%), Phialophora (6.67%) [70]