Journal of Microbiology

Full articles

Effects of sequencing platforms on the profiling of root mycorrhizal communities in Pinus densiflora: Ki Hyeong Park, Seung-Yoon Oh, Shinnam Yoo, Yoonhee Cho, Ji Seon Kim, Chang Wan Seo, Chang Sun Kim, Young Woon Lim; J. Microbiol. 2026;64(1):e2509008. Published online January 31, 2026; DOI: https://doi.org/10.71150/jm.2509008

11 View
1 Download

Abstract PDF Supplementary Material: Next-generation sequencing (NGS) has become a powerful and efficient tool for surveying mycorrhizal mycobiome diversity, surpassing classical methods in accuracy and throughput. Long-read NGS techniques are increasingly applied under the assumption that they provide better taxonomic resolution, yet their use often lacks a balanced evaluation against the established strengths and limitations of widely used short-read NGS technologies. This study compares Illumina MiSeq and PacBio Sequel platforms in analyzing the mycorrhizal mycobiome of Pinus densiflora roots, focusing on how sequencing platforms and database choice influence taxonomic resolution and diversity patterns. Both platforms detected mycorrhizal taxa with similar taxonomic resolution, recovering nearly all taxa previously reported from pine roots. Most mycorrhizal taxa were shared between datasets, although several taxa were detected exclusively by one platform. In terms of diversity, the short-read dataset showed higher diversity due to greater sequencing depth, whereas the long-read dataset offered improved identification of rare or closely related taxa owing to longer sequence information. Moreover, supplementing reference databases with locally derived sequences enhanced taxonomic resolution and the detection of native taxa in both approaches, with a stronger effect for the long-read dataset. Overall, our results emphasize that short- and long-read sequencing each have distinct advantages for mycorrhizal community analysis, and that the use of curated local reference databases is essential to maximize taxonomic resolution and improve the detection of regionally unique taxa.

FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis: Chang Wan Seo, Shinnam Yoo, Yoonhee Cho, Ji Seon Kim, Martin Steinegger, Young Woon Lim; J. Microbiol. 2025;63(4):e2411017. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2411017

5,019 View
172 Download
3 Web of Science
5 Crossref

The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.

Citations

Citations to this article as recorded by

Hidden diversity of crust-like Sebacinaceae (Sebacinales, Agaricomycetes) in Asia
Hannah Suh, Chang Wan Seo, Ki Hyeong Park, Shinnam Yoo, Dohye Kim, Yoonhee Cho, Young Woon Lim
IMA Fungus.2026;[Epub] CrossRef
Exploring Macrofungal Biodiversity and Distribution on Kyodong Island, Republic of Korea
Hannah Suh, Abel Severin Lupala, Hae Jin Cho, Sumin Jo, Jiyun Choi, Young Woon Lim
Mycobiology.2025; 53(4): 466. CrossRef
Expanding the Inventory of Seven Unrecorded Marine Penicillium with Morphological Descriptions and Phenotypic Variability
Wonjun Lee, Ji Seon Kim, Sumin Jo, Young Woon Lim
Mycobiology.2025; 53(5): 648. CrossRef
Exploring Fungal Diversity in Marine Plastic (PET) Wastes and Seafoam in Udo Island, South Korea, with Reports of Two New Species ( Leptospora conidiifera and Neodevriesia oceanoplastica )
Wonjun Lee, Sumin Jo, Soo Hyun Maeng, Ji Seon Kim, Myung Kyum Kim, Young Woon Lim
Mycobiology.2025; 53(6): 770. CrossRef
Potential of Trichoderma asperellum against root-rot caused by Fusarium equiseti in tomato plants
Louis Antoniel Joseph, Manoucheca Jean, Frantzdy Luc, Kerley-Vivaldi Jean, Bento Gil Uane, Marisa Aida Diogo Matsinhe, Meque Samuel Tivane, Inocêncio Oliveira Mulaveia
Research, Society and Development.2025; 14(12): e62141250223. CrossRef

Journal Articles

Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea: Ki Hyeong Park , Seung-Yoon Oh , Yoonhee Cho , Chang Wan Seo , Ji Seon Kim , Shinnam Yoo , Jisun Lim , Chang Sun Kim , Young Woon Lim; J. Microbiol. 2023;61(8):729-739. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00073-1

295 View
1 Download
1 Crossref

Abstract PDF

Mycorrhizal fungi are key components of forest ecosystems and play essential roles in host health. The host specificity of mycorrhizal fungi is variable and the mycorrhizal fungi composition for the dominant tree species is largely known but remains unknown for the less common tree species. In this study, we collected soil samples from the roots of six understudied ectomycorrhizal tree species from a preserved natural park in the Republic of Korea over four seasons to investigate the host specificity of mycorrhizal fungi in multiple tree species, considering the abiotic factors. We evaluated the mycorrhizal fungal composition in each tree species using a metabarcoding approach. Our results revealed that each host tree species harbored unique mycorrhizal communities, despite close localization. Most mycorrhizal taxa belonged to ectomycorrhizal fungi, but a small proportion of ericoid mycorrhizal fungi and arbuscular mycorrhizal fungi were also detected. While common mycorrhizal fungi were shared between the plant species at the genus or higher taxonomic level, we found high host specificity at the species/OTU (operational taxonomic unit) level. Moreover, the effects of the seasons and soil properties on the mycorrhizal communities differed by tree species. Our results indicate that mycorrhizal fungi feature host-specificity at lower taxonomic levels.

Citations

Citations to this article as recorded by

Effects of elevated temperatures on soil enzymatic activities and bacterial and fungal community composition and diversity
Precious Mutambara, Kabwe Nkongolo
Ecological Genetics and Genomics.2025; 36: 100382. CrossRef

Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyung Park , Shin Nam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(2):189-197. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00017-9

440 View
1 Download
3 Web of Science
2 Crossref

Abstract PDF

Indoor fungi obtain carbon sources from natural sources and even recalcitrant biodegradable materials, such as plastics and synthetic dye. Their vigorous activity may have negative consequences, such as structural damage to building materials or the destruction of precious cultural materials. The animal specimen room of the Seoul National University stocked 36,000 animal resources that had been well-maintained for over 80 years. Due to abandonment without the management of temperature and humidity during the rainy summer season, many stuffed animal specimens had been heavily colonized by fungi. To investigate the fungal species responsible for the destruction of the historical specimens, we isolated fungi from the stuffed animal specimens and identified them at the species level based on morphology and molecular analysis of the β-tubulin (BenA) gene. A total of 365 strains were isolated and identified as 26 species in Aspergillus (10 spp.), Penicillium (14 spp.), and Talaromyces (2 spp.). Penicillium brocae and Aspergillus sydowii were isolated from most sections of the animal specimens and have damaged the feathers and beaks of valuable specimens. Our findings indicate that within a week of mismanagement, it takes only a few fungal species to wipe out the decades of history of animal diversity. The important lesson here is to prevent this catastrophe from occurring again through a continued interest, not to put all previous efforts to waste.

Citations

Citations to this article as recorded by

Investigating the Role of Microclimate and Microorganisms in the Deterioration of Stone Heritage: The Case of Rupestrian Church from Jac, Romania
Dorina Camelia Ilieș, Andrei-Ionuț Apopei, Cristina Mircea, Alexandru Ilieș, Tudor Caciora, Berdenov Zharas, Lucian Barbu-Tudoran, Nicolaie Hodor, Alexandru Turza, Ana Cornelia Pereș, Thowayeb H. Hassan, Bahodirhon Safarov, Ioan-Cristian Noje
Applied Sciences.2024; 14(18): 8136. CrossRef
Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation
Geoffrey Michael Gadd, Marina Fomina, Flavia Pinzari, Mark D. Rose
Microbiology and Molecular Biology Reviews.2024;[Epub] CrossRef

Diversity and Dynamics of Marine Arenicolous Fungi in Three Seasides of the Korean Peninsula: Jun Won Lee , Chang Wan Seo , Wonjun Lee , Ji Seon Kim , Ki Hyeong Park , Yoonhee Cho , Young Woon Lim; J. Microbiol. 2023;61(1):63-82. Published online January 30, 2023; DOI: https://doi.org/10.1007/s12275-023-00011-1

468 View
2 Download
7 Web of Science
8 Crossref

Abstract PDF

Various arenicolous fungal species have been detected from the beach sand in the coastal area. However, little has been revealed regarding their distribution and dynamics. To investigate the overall diversity of marine arenicolous fungi (MAFs) in Korea and whether the composition of MAFs is affected by ocean currents, we isolated and analyzed the fungal community from the western, southern, and eastern seasides of the Korean Peninsula. In total, 603 strains were isolated and identified as 259 species based on appropriate molecular markers for each genus (ITS, BenA, CaM, tef1, and act). The composition of MAFs showed differences among the seasides. Our results indicate that many MAFs inhabit the beach sand on the Korean Peninsula, and the composition of MAFs is also affected by ocean currents flowing along each coast.

Citations

Citations to this article as recorded by

A case for monitoring fungi of clinical relevance at beaches: enterococci measures do not correlate with all disease risks
Larissa Montás-Bravo, Helena M. Solo-Gabriele, Débora F. Gil, Ayaaz Amirali, Sebastian P. Arenas, Sofia Hoffman, Adriana Jimenez, Alexandre Mendonça, Rivka Reiner, Raquel Sabino, Konstantina Sarioglou, Mark E. Sharkey, Bhavarth S. Shukla, Isabella J. Tava
Environmental Monitoring and Assessment.2026;[Epub] CrossRef
Inside out: New root endophytic Penicillium and Talaromyces species isolated from Cattleya orchids (Orchidaceae) in Brazil
T.O. Condé, D.O. Ramos, P.T.S. Nogueira, O.L. Pereira
Fungal Systematics and Evolution.2025; 15(1): 179. CrossRef
Taxonomic Study of Sixteen Unrecorded and Five New Species of Hypocreales from the Korean Marine Environment
Wonjun Lee, Ji Seon Kim, Sumin Jo, Chang Wan Seo, Young Woon Lim
Mycobiology.2025; 53(2): 144. CrossRef
Fungal frontiers in toxic terrain: Revealing culturable fungal communities in Serpentine paddy fields of Taiwan
Kai-Wen Cheng, Jiue-in Yang, Piroonporn Srimongkol, Marc Stadler, Aphichart Karnchanatat, Hiran A. Ariyawansa
IMA Fungus.2025;[Epub] CrossRef
Taxonomy, phylogeny, and bioactive potential of Xylariales (Sordariomycetes, Ascomycota) from Thailand: novel species discovery, new host and geographical records, and antibacterial properties
Achala R. Rathnayaka, K. W. Thilini Chethana, Areerat Manowong, Amuhenage T. Bhagya, Hsan Win, Zaw L. Tun, Ausana Mapook, Kevin D. Hyde
MycoKeys.2025; 120: 35. CrossRef
The genus Peniophora (Russulales, Basidiomycota) from Patagonia revisited
Mario Rajchenberg, Andrés de Errasti, Sergio Pérez Gorjón
Mycological Progress.2024;[Epub] CrossRef
Contributions to the Inocybe umbratica–paludinella (Agaricales) Group in China: Taxonomy, Species Diversity, and Molecular Phylogeny
Xin Chen, Wen-Jie Yu, Tolgor Bau, P. Brandon Matheny, Egon Horak, Yu Liu, Li-Wu Qin, Li-Ping Tang, Yu-Peng Ge, Tie-Zhi Liu, Yu-Guang Fan
Journal of Fungi.2024; 10(12): 893. CrossRef
Long-Term Investigation of Marine-Derived Aspergillus Diversity in the Republic of Korea
Jun Won Lee, Wonjun Lee, Rekhani Hansika Perera, Young Woon Lim
Mycobiology.2023; 51(6): 436. CrossRef

Published Erratum

Erratum to: Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyeong Park , Shinnam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(6):653-653.; DOI: https://doi.org/10.1007/s12275-023-00060-6

283 View
1 Download

Abstract PDF: Correction to: Journal of Microbiology (2023) 61:189–197 https://doi.org/10.1007/s12275-023-00017-9 In this article two author names are given erroneaously: Written incorrectly: Ki Hyung Park · Shin Nam Yoo It should be read: Ki Hyeong Park · Shinnam Yoo

First
Prev
Page of 1
Next
Last

Search