Mycobiome

The mycobiome, mycobiota, or fungal microbiome, is the fungal community in and on an organism.[1][2][3]

There is a low abundance of fungi associated with most human body sites, such as the gastrointestinal tract, where fungi typically compose just 0.001 - 0.1% of the microbial community.[4][5] However, fungi compose a significant fraction of the microbiome at some locations, such as the ear canal.[6]

The mycobiome is relevant to human physiology as fungi may be important in maintaining microbial community structure, metabolic function, and immune-priming.[7][8] Mutualism between humans and fungi is not yet well understood, and there is much to be learned about how fungi interact with the nonfungal constituents of the microbiome.

Human Diseases

Many human diseases, including hepatitis, cystic fibrosis, obesity, and inflammatory bowel disease have been associated with changes in the human mycobiome,[9][10] and it has been proposed that any fungal colonization of the GI tract is a sign of disease.[4]

Fungal Biota Present

Vaginal Mycobiome
  • Candida (16 taxonomic units)
  • Ascomycota
  • Saccharomycetales
  • Ascomycota Davidiellaceae
  • Cladosporium
  • Eurotium
  • Alternaria
  • Basidomycota Rhodotorula

Intestinal Mycobiome[11]

(Infant) Intestinal Mycobiome
  • Saccharomycetales (infant)
  • Cladosporium
  • Cryptococcus
  • Saccharomyces cerevisiae
  • Malasseziales
  • Eurotiales
  • Botryosphaeriales
  • Filobasidiales[12]

Oral Mycobiome
  • Candida
  • Saccharomyces
  • Penicillium
  • Aspergillus
  • Scopulariopsis
  • Genotrichum[13][14][15][16]
  • Cryptococcus
  • Histoplasma
  • Mucor[17]
  • Cladosporium
  • Fusarium
  • Alternaria[18]
  • Malassezia
  • Epicoccum
  • Aureobasidium
  • Irpex
  • Cytospora
  • Lenziles
  • Sporobolomyces
  • Dothioraceae
  • Teratosphaeria
  • Glomus[19][18]
  • Pichia

Lung Mycobiome
  • Aspergillus
  • Penicillium
  • Davidiellaceae
  • Candida[20]

References
  1. Cui, Lijia; Morris, Alison; Ghedin, Elodie (2013). "The human mycobiome in health and disease". Genome Medicine. 5 (7): 63. doi:10.1186/gm467. PMC 3978422. PMID 23899327.
  2. Ghannoum, Mahmoud (February 1, 2016). "The Mycobiome". The Scientist. Retrieved February 5, 2016.
  3. Suhr, M. J; Hallen-Adams, H. E (2015). "The human gut mycobiome: Pitfalls and potentials--a mycologists perspective". Mycologia. 107 (6): 1057–73. doi:10.3852/15-147. PMID 26354806. S2CID 16731371.
  4. Auchtung, TA; Fofanova TY; Stewart CJ; Nash AK; Wong MC; Gesell JR; Auchtung JM; Ajami NJ; Petrosino JF (2018). "Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi". mSphere. 3 (2): e00092–18. doi:10.1128/mSphere.00092-18. PMC 5874442. PMID 29600282.
  5. Qin, Junjie; Li, Ruiqiang; Raes, Jeroen; Arumugam, Manimozhiyan; Burgdorf, Kristoffer Solvsten; Manichanh, Chaysavanh; Nielsen, Trine; Pons, Nicolas; Levenez, Florence; Yamada, Takuji; Mende, Daniel R; Li, Junhua; Xu, Junming; Li, Shaochuan; Li, Dongfang; Cao, Jianjun; Wang, Bo; Liang, Huiqing; Zheng, Huisong; Xie, Yinlong; Tap, Julien; Lepage, Patricia; Bertalan, Marcelo; Batto, Jean-Michel; Hansen, Torben; Le Paslier, Denis; Linneberg, Allan; Nielsen, H. Bjørn; Pelletier, Eric; et al. (2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.
  6. Oh, J; Byrd AL; Park M; NISC Comparative Sequencing Program; Kong HH; Segre JA (2016). "Temporal Stability of the Human Skin Microbiome". Cell. 165 (4): 854–66. doi:10.1016/j.cell.2016.04.008. PMC 4860256. PMID 27153496.
  7. Seed, P. C (2014). "The Human Mycobiome". Cold Spring Harbor Perspectives in Medicine. 5 (5): a019810. doi:10.1101/cshperspect.a019810. PMC 4448585. PMID 25384764.
  8. Pflughoeft, Kathryn J; Versalovic, James (2012). "Human Microbiome in Health and Disease". Annual Review of Pathology: Mechanisms of Disease. 7: 99–122. doi:10.1146/annurev-pathol-011811-132421. PMID 21910623.
  9. Mar Rodríguez, M; Pérez, Daniel; Javier Chaves, Felipe; Esteve, Eduardo; Marin-Garcia, Pablo; Xifra, Gemma; Vendrell, Joan; Jové, Mariona; Pamplona, Reinald; Ricart, Wifredo; Portero-Otin, Manuel; Chacón, Matilde R; Fernández Real, José Manuel (2015). "Obesity changes the human gut mycobiome". Scientific Reports. 5: 14600. Bibcode:2015NatSR...514600M. doi:10.1038/srep14600. PMC 4600977. PMID 26455903.
  10. Ackerman, A. Lenore; Underhill, David M (2017). "The mycobiome of the human urinary tract: Potential roles for fungi in urology". Annals of Translational Medicine. 5 (2): 31. doi:10.21037/atm.2016.12.69. PMC 5300854. PMID 28217696.
  11. Nash, AK; Auchtung TA; Wong MC; Smith DP; Gesell JR; Ross MC; Stewart CJ; Metcalf GA; Muzny DM; Gibbs RA; Ajami NJ; Petrosino JF (2017). "The gut mycobiome of the Human Microbiome Project healthy cohort". Microbiome. 5 (1): 153. doi:10.1186/s40168-017-0373-4. PMC 5702186. PMID 29178920.
  12. Latuga, Mariam Susan; Ellis, Joseph Christopher; Cotton, Charles Michael; Goldberg, Ronald N; Wynn, James L; Jackson, Robert B; Seed, Patrick C (2011). "Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants". PLOS ONE. 6 (12): e27858. Bibcode:2011PLoSO...627858L. doi:10.1371/journal.pone.0027858. PMC 3234235. PMID 22174751.
  13. Williams, DW; Lewis, MAO (2008). "Oral Microbiology: Isolation and identification of candida from the oral cavity". Oral Diseases. 6 (1): 3–11. doi:10.1111/j.1601-0825.2000.tb00314.x. PMID 10673781.
  14. Schuster, G. S (1999). "Oral flora and pathogenic organisms". Infectious Disease Clinics of North America. 13 (4): 757–74, v. doi:10.1016/s0891-5520(05)70107-0. PMID 10579107.
  15. Salonen, J.H; Richardson, M.D; Gallacher, K; Issakainen, J; Helenius, H; Lehtonen, O.-P; Nikoskelainen, J (2000). "Fungal colonization of haematological patients receiving cytotoxic chemotherapy: Emergence of azole-resistant Saccharomyces cerevisiae". Journal of Hospital Infection. 45 (4): 293–301. doi:10.1053/jhin.1999.0718. PMID 10973747.
  16. Jabra-Rizk, M. A; Ferreira, S. M. S; Sabet, M; Falkler, W. A; Merz, W. G; Meiller, T. F (2001). "Recovery of Candida dubliniensis and Other Yeasts from Human Immunodeficiency Virus-Associated Periodontal Lesions". Journal of Clinical Microbiology. 39 (12): 4520–2. doi:10.1128/JCM.39.12.4520-4522.2001. PMC 88577. PMID 11724873.
  17. Iatta, Roberta; Napoli, Christian; Borghi, Elisa; Montagna, Maria Teresa (2009). "Rare mycoses of the oral cavity: A literature epidemiologic review". Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontology. 108 (5): 647–55. doi:10.1016/j.tripleo.2009.07.010. PMID 19836721.
  18. Ghannoum, Mahmoud A; Jurevic, Richard J; Mukherjee, Pranab K; Cui, Fan; Sikaroodi, Masoumeh; Naqvi, Ammar; Gillevet, Patrick M (2010). "Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals". PLOS Pathogens. 6 (1): e1000713. doi:10.1371/journal.ppat.1000713. PMC 2795202. PMID 20072605.
  19. Dupuy, Amanda K; David, Marika S; Li, Lu; Heider, Thomas N; Peterson, Jason D; Montano, Elizabeth A; Dongari-Bagtzoglou, Anna; Diaz, Patricia I; Strausbaugh, Linda D (2014). "Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal". PLOS ONE. 9 (3): e90899. Bibcode:2014PLoSO...990899D. doi:10.1371/journal.pone.0090899. PMC 3948697. PMID 24614173.
  20. Charlson, Emily S; Diamond, Joshua M; Bittinger, Kyle; Fitzgerald, Ayannah S; Yadav, Anjana; Haas, Andrew R; Bushman, Frederic D; Collman, Ronald G (2012). "Lung-enriched Organisms and Aberrant Bacterial and Fungal Respiratory Microbiota after Lung Transplant". American Journal of Respiratory and Critical Care Medicine. 186 (6): 536–45. doi:10.1164/rccm.201204-0693OC. PMC 3480531. PMID 22798321.
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