Table 3.
Summary of mycobiomes in different body sites
| 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] |