Current Taxonomy and Nomenclature of Fungi

Öz

Fungi are eukaryotic microorganisms that can cause a wide spectrum of clinical diseases in humans, ranging from superficial infections to severe, life-threatening systemic mycoses. Owing to their complex cellular organization, diverse life cycles, and distinct pathogenic mechanisms, fungi occupy a unique position within clinical microbiology. Medical mycology has evolved from early morphology-based classifications to a modern discipline shaped by molecular biology, phylogenetics, and standardized nomenclature. The increasing use of molecular diagnostic methods has profoundly altered the taxonomy of medically important fungi, enabling accurate genus- and species-level identification and improving the understanding of epidemiology, pathogenicity, and antifungal resistance patterns. The adoption of the “One Fungus, One Name” principle has eliminated dual nomenclature systems and contributed to greater consistency in fungal naming. In recent years, extensive taxonomic revisions have affected major groups of clinically relevant fungi, including yeasts, molds, dimorphic fungi, dematiaceous fungi, and Mucorales. These changes have direct implications for clinical diagnosis, laboratory reporting, epidemiological surveillance, and patient management. This review summarizes the historical development of medical mycology, outlines key principles of fungal nomenclature and taxonomy, and provides an updated overview of major taxonomic revisions among clinically important fungi, emphasizing the critical role of molecular approaches in contemporary fungal classification.

Anahtar Kelimeler

• Medical mycology
• Fungal taxonomy
• fungi
• nomenclature

Mantarların Güncel Taksonomisi ve Nomenklatürü

Öz

Mantarlar, insanlarda yüzeyel enfeksiyonlardan ağır ve yaşamı tehdit eden sistemik mikozlara kadar uzanan geniş bir klinik hastalık spektrumuna yol açabilen ökaryotik mikroorganizmalardır. Kompleks hücresel organizasyonları, çeşitli yaşam döngüleri ve kendine özgü patojenik mekanizmaları nedeniyle mantarlar, klinik mikrobiyoloji içerisinde özgün bir konuma sahiptir. Tıbbi mikoloji, erken dönemlerde morfolojiye dayalı sınıflandırmalardan günümüzde moleküler biyoloji, filogenetik analizler ve standartlaştırılmış nomenklatür ile şekillenen modern bir disipline evrilmiştir. Moleküler tanı yöntemlerinin giderek artan kullanımı, tıbbi açıdan önemli mantarların cins ve tür düzeyinde doğru tanımlanmasını mümkün kılmış; epidemiyoloji, patojenite ve antifungal direnç paternlerinin daha iyi anlaşılmasına önemli katkılar sağlamıştır. “Tek Mantar/Tek İsim” ilkesinin kabulü, çift adlandırma sistemlerini ortadan kaldırarak mantar nomenklatüründe tutarlılığı artırmıştır. Son yıllarda mayalar, küf mantarları, dimorfik mantarlar, dematiyöz mantarlar ve Mucorales gibi klinik açıdan önemli gruplarda kapsamlı taksonomik revizyonlar gerçekleştirilmiştir. Bu değişiklikler; klinik tanı, laboratuvar raporlaması, epidemiyolojik sürveyans ve hasta yönetimi açısından doğrudan klinik sonuçlar doğurmaktadır. Bu derleme, tıbbi mikolojinin tarihsel gelişimini özetlemekte, mantar nomenklatürü ve taksonomisinin temel ilkelerini ele almakta ve klinik açıdan önemli mantarlarda meydana gelen başlıca taksonomik değişikliklere güncel bir bakış sunarak, çağdaş mantar sınıflandırmasında moleküler yaklaşımların kritik rolünü vurgulamaktadır.

Anahtar Kelimeler

• Tıbbi mikoloji
• Fungal taksonomi
• Fungus
• Nomenklatür

Kaynakça

1. Murray PR, Rosenthal KS, Pfaller MA. Medical microbiology. 9th ed. Elsevier; 2020.
2. Ryan KJ, editor. Sherris & Ryan’s Medical Microbiology. 8th ed. New York: McGraw Hill; 2022.
3. Hawksworth DL. The naming of fungi. In: McLaughlin DJ, McLaughlin EG, Lemke PA, editors. The Mycota. Vol. 7B, Systematics and Evolution. Berlin, Heidelberg: Springer; 2001. p. 171-92.
4. Du H, Bing J, Hu T, Ennis CL, Nobile CJ, Huang G. Candida auris: epidemiology, biology, antifungal resistance, and virulence. PLoS Pathog. 2020;16(10):e1008921.
5. Kidd SE, Abdolrasouli A, Hagen F. Fungal nomenclature: managing change is the name of the game. Open Forum Infect Dis. 2023;10(1):ofac559.
6. UK Health Security Agency. UK Standards for Microbiology Investigations: Introduction to the preliminary identification of medically important bacteria and fungi from culture. London: UK Health Security Agency; 2024.
7. Lücking R, Aime MC, Robbertse B, et al. Fungal taxonomy and sequence-based nomenclature. Nat Microbiol. 2021;6(5):540-548.
8. Wang F, Wang K, Cai L, et al. Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy. Nucleic Acids Res. 2023;51(D1):D708-716.

9. Wingfield MJ, de Beer ZW, Slippers B, et al. One fungus, one name promotes progressive plant pathology. Mol Plant Pathol. 2012;13(6):604-613.
10. Hawksworth DL, Crous PW, Redhead SA, et al. The Amsterdam Declaration on Fungal Nomenclature. IMA Fungus. 2011;2(1):105-112.
11. de Hoog GS, Chaturvedi V, Denning DW, et al. Name changes in medically important fungi and their implications for clinical practice. J Clin Microbiol. 2015;53(4):1056-1062.
12. Lücking R, Aime MC, Robbertse B, et al. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus. 2020;11(1):14.
13. Index Fungorum. Index Fungorum database [Internet]. [cited 2026 Jan 05]. Available from: https://www.indexfungorum.org/
14. MycoBank. MycoBank database [Internet]. [cited 2026 Jan 11]. Available from: https://www.mycobank.org/
15. Atlas of Clinical Fungi. Nomenclature and names [Internet]. [cited 2026 Jan 15]. Available from: https://www.atlasclinicalfungi.org/nomenclaturenames/
16. Hennequin C, Coste A, Imbert C. Changes in the fungal nomenclature: why and how to manage? J Mycol Med. 2023;33(2):101404.
17. Poplin V, Smith C, Caceres DH, et al. Geographical distribution of the Cryptococcus gattii species complex: a systematic review. Lancet Microbe. 2024;5(12):100921.
18. Telles JP, Ribeiro VST, Kraft L, Tuon FF. Pseudozyma spp. human infections: a systematic review. Med Mycol. 2021;59(1):1-6.
19. Commenges A, Coucheney F, Lessard MH, Drider D, Labrie S. Trichosporon asahii: taxonomy, health hazards, and biotechnological applications. Fungal Biol Rev. 2024;49:100369.
20. Zhu HY, Shang YJ, Wei XY, et al. Taxonomic revision of Geotrichum and Magnusiomyces, with the descriptions of five new Geotrichum species from China. Mycology. 2024;15(3):400-423.
21. Peng LY, Zhuang WY, Wang XC. New species of Aspergillus in sections Cavernicolarum and Nigri from terrestrial ecosystems of China (Eurotiales, Aspergillaceae). MycoKeys. 2025;124:275-290.
22. Tsang CC, Tang JYM, Lau SKP, Woo PCY. Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era: past, present and future. Comput Struct Biotechnol J. 2018;16:197-210.
23. Luangsa-Ard J, Houbraken J, van Doorn T, et al. Purpureocillium, a new genus for the medically important Paecilomyces lilacinus. FEMS Microbiol Lett. 2011;321(2):141-149.
24. Lombard L, van der Merwe NA, Groenewald JZ, Crous PW. Generic concepts in Nectriaceae. Stud Mycol. 2015;80:189-245.
25. de Hoog GS, Dukik K, Monod M, et al. Toward a novel multilocus phylogenetic taxonomy for the dermatophytes. Mycopathologia. 2017;182(1-2):5-31.
26. García-Martín JM, Muro A, Fernández-Soto P. Diagnosis of human endemic mycoses caused by thermally dimorphic fungi: from classical to molecular methods. J Fungi (Basel). 2024;10(9):637.
27. Kirkland TN, Fierer J. Coccidioides immitis and Coccidioides posadasii: a review of their biology, genomics, pathogenesis, and host immunity. Virulence. 2018;9(1):1426-35.
28. Rodrigues AM, Beale MA, Hagen F, et al. The global epidemiology of emerging Histoplasma species in recent years. Stud Mycol. 2020;97:100095.
29. Mendoza L, Vilela R. Current taxonomic status of the cultivable and uncultivable Paracoccidioides species. Med Mycol. 2024;62(11):myae108.
30. Morgado DS, Castro R, Ribeiro-Alves M, et al. Systematic review of literature to evaluate global distribution of species of the Sporothrix genus stored in culture collections. Front Cell Infect Microbiol. 2024;14:1382508.
31. Marinelli T, Kim HY, Halliday CL, et al. Fusarium species, Scedosporium species, and Lomentospora prolificans: a systematic review to inform the World Health Organization fungal priority pathogens list. Med Mycol. 2024;62(6):myae128.
32. Spatafora JW, Chang Y, Benny GL, et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016;108(5):1028-1046.
33. Wagner L, Stielow JB, de Hoog GS, et al. A new species concept for the clinically relevant Mucor circinelloides complex. Persoonia. 2020;44:67-97.
34. Dolatabadi S, de Hoog GS, Meis JF, Walther G. Species boundaries and nomenclature of Rhizopus arrhizus (syn. R. oryzae). Mycoses. 2014;57(3):108-127.
35. Tanrıverdi ES. Taksonomi ve isimlendirme. Metin DY, editör. Tıbbi Mikolojiye Güncel Yaklaşım. 1. Baskı. Ankara: Türkiye Klinikleri; 2025
36. Unalan-Altintop T, Arikan-Akdagli S. Fungal Nomenclature: one Fungus, one Name? Infect Dis clin North Am. 2025;39(1):57-73.
37. Hui ST, Gifford H, Rhodes J. Emerging antifungal resistance in fungal pathogens. Curr Clin Microbiol Rep. 2024;11(2):43-50.