Journal of Microbiology

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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

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Abstract PDF Supplementary Material: 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.

Journal Article

Pedobacter aquicola sp. nov., isolated from freshwater: Yochan Joung , Hye-jin Jang , Miri Park , Jaeho Song , Jang-Cheon Cho; J. Microbiol. 2018;56(7):478-484. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7499-3

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A non-motile, pink-pigmented bacterial strain designated IMCC25679T, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679T formed a lineage within the genus Pedobacter. The strain IMCC25679T was closely related to Pedobacter daechungensis Dae 13T (96.4% sequence similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter lentus DS-40T (94.3%). The major fatty acids of IMCC- 25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE), an unidentified sphingolipid (SL), an unidentified aminolipid (AL) and three unidentified polar lipids (PL). The DNA G + C content of IMCC25679T was 32.2 mol%. Based on the evidence presented in this study, the strain IMCC25679T represents a novel species within the genus Pedobacter, with the proposed name Pedobacter aquicola, sp. nov. The type strain is IMCC25679T (= KACC 19486T = NBRC113131T).

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Genome-Based Classification of Pedobacter albus sp. nov. and Pedobacter flavus sp. nov. Isolated from Soil
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Haejin Woo, Geeta Chhetri, Inhyup Kim, Yoonseop So, Sunho Park, Yonghee Jung, Taegun Seo
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Screening of potential microbial markers for lung cancer using metagenomic sequencing
Qiang Chen, Kai Hou, Mingze Tang, Shuo Ying, Xiaoyun Zhao, Guanhua Li, Jianhui Pan, Xiaomin He, Han Xia, Yuechuan Li, Zheng Lou, Li Zhang
Cancer Medicine.2023; 12(6): 7127. CrossRef
Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water
Le Tran Tien Chau, Yong-Seok Kim, Chang-Jun Cha
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Pedobacter riviphilus sp. nov., isolated from stream sediment
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International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Complete Genome Sequence of Pedobacter sp. PAMC26386 and Their Low Temperature Application in Arabinose-containing Polysaccharides Degradation
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Current Microbiology.2021; 78(3): 944. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
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Xiao-yan He, Na Li, Xiu-lan Chen, Yu-zhong Zhang, Xi-ying Zhang, Xiao-yan Song
Antonie van Leeuwenhoek.2020; 113(3): 357. CrossRef
Leeia aquatica sp. nov., isolated from freshwater
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International Journal of Systematic and Evolutionary Microbiology .2020; 70(11): 5848. CrossRef
Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake
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Research Support, Non-U.S. Gov'ts

NOTE] Molecular Phylogenetic Status of Korean Strain of Podosphaera xanthii, a Causal Pathogen of Powdery Mildew on Japanese Thistle (Cirsium japonicum) in Korea: Hyang Burm Lee; J. Microbiol. 2012;50(6):1075-1080. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2618-z

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Abstract: Powdery mildew diseases are sensitive to climate change and spread can be favored by increased temperature and low moisture. During 2011 to 2012, a powdery mildew disease by a Podosphaera species was observed on the leaves of Japanese thistle (Cirsium japonicum) in Korea. The initial sign of this disease included scattered superficial white mycelia on leaves. As the disease progressed, abundant necrotic black spots exhibiting chasmothecia were formed on the leaves. rDNA ITS and 28S homologies of the fungus (EML-CSPW1) showed 100% identity values with those regions from many strains of P. xanthii (syn. P. fusca) via NCBI BLASTN search.

Predicting Genetic Traits and Epitope Analysis of apxIVA in Actinobacillus pleuropneumoniae: Min-Kyoung Shin , Seung-Bin Cha , Won-Jung Lee , Han Sang Yoo; J. Microbiol. 2011;49(3):462-468. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0449-y

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Abstract

Actinobacillus pleuropneumoniae causes a severe hemorrhagic pneumonia in pigs. Fifteen serotypes of A. pleuropneumoniae express four different Apx toxins that belong to the pore-forming repeats-in-toxin (RTX) group of toxins. ApxIV, which is conserved and up-regulated in vivo, could be an excellent candidate for the development of a protective cross-serotype immunity vaccine, and could aid in the differential diagnosis of diseases caused by A. pleuropneumoniae. We identified and sequenced apxIVA from A. pleuropneumoniae serotype 2 isolated in Korea (Kor-ApxIVA). The Kor-ApxIVA was closely related to Switzerland (AF021919), China (CP000687), and China (GQ332268), showing 98.6%, 98.4%, and 97.2% amino acid homology, respectively. The level of amino acid homology, however, was higher than the nucleotide homology. The structural characteristics of ApxIVA showed RTX proteins, including N-terminal hydrophobic domains, signature sequences for potential acylation sites, and repeated glycine-rich nonapeptides in the C-terminal region of the protein. Thirty glycine-rich nonapeptides with the consensus sequence, L/V-X-G-G-X-G-N/D-D-X, were found in the C-terminus of the Kor-ApxIVA. In addition, the Kor-ApxIVA was predicted for the linear B-cell epitopes and conserved domains with determined peptide sequences. This genetic analysis of the Kor-ApxIVA might be an important foundation for future biological and functional research on ApxIVA.

Citations

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Rapid detection of Actinobacillus pleuropneumoniae targeting the apxIVA gene for diagnosis of contagious porcine pleuropneumonia in pigs by polymerase spiral reaction
R. Sarkar, P. Roychoudhury, S. Kumar, S. Dutta, N. Konwar, P. K. Subudhi, T. K. Dutta
Letters in Applied Microbiology.2022; 75(2): 442. CrossRef
Development ofActinobacillus pleuropneumoniaeApxI, ApxII, and ApxIII-specific ELISA methods for evaluation of vaccine efficiency
Myunghwan Jung, Hokeun Won, Min-Kyoung Shin, Myung Whan Oh, Soojin Shim, Injoong Yoon, Han Sang Yoo
Journal of Veterinary Science.2019;[Epub] CrossRef
Carbon source utilisation and evaluation of the Biolog system in the identification of Actinobacillus pleuropneumoniae
László Makrai, Rita Sárközi, László Fodor
Acta Veterinaria Hungarica.2019; 67(3): 327. CrossRef
So sánh khả năng dự đoán chất lượng nước sông Đồng Nai bằng mạng nơ ron nhân tạo và lý thuyết xám
Nguyễn Hiền Thân, Chế Đình Lý, Phạm Văn Tất
Can Tho University, Journal of Science.2017; Môi trường: 120. CrossRef
Prevalence and Characterization ofActinobacillus pleuropneumoniaeIsolated from Korean Pigs
Ki-Eun Lee, Hwan-Won Choi, Ha-Hyun Kim, Jae-Young Song, Dong-Kun Yang
Journal of Bacteriology and Virology.2015; 45(1): 19. CrossRef
Identification and Characterization of the Insecticidal Toxin “Makes Caterpillars Floppy” in Photorhabdus temperata M1021 Using a Cosmid Library
Ihsan Ullah, Eun-Kyung Jang, Min-Sung Kim, Jin-Ho Shin, Gun-Seok Park, Abdur Khan, Sung-Jun Hong, Byung-Kwon Jung, JungBae Choi, YeongJun Park, Yunyoung Kwak, Jae-Ho Shin
Toxins.2014; 6(7): 2024. CrossRef

Reductive Divergence of Enterobacterial Repetitive Intergenic Consensus Sequences among Gammaproteobacteria Genomes: Young-Gun Zo; J. Microbiol. 2011;49(1):35-45. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1024-2

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Abstract

Enterobacterial repetitive intergenic consensus (ERIC) sequence is a transcription-modulating, nonautonomous, miniature inverted-repeat transposable element. Its origin and the mechanism of highly varying incidences, limited to Enterobacteriaceae and Vibrionaceae, have not been identified. In this study, distribution and divergence of ERICs along bacterial taxonomic units were analyzed. ERICs were found among five families of gammaproteobacteria, with the copy numbers varying with exponential increments. The variability was explained by genus (45%) and species (36%) affiliations, indicating that copy numbers are specific to subfamily taxa. ERICs were interspersed in genomes with considerable divergences. Locations of ERICs in a genome appeared to be strongly conserved in a strain, moderately in a species or a genus, and weakly in a family. ERICs in different species of a genus were from the identical population of sequences while ERICs in different genera of a family were nearly identical. However, ERICs in different families formed distinct monophylectic groups, implying vertical transmission of diverging population of sequences. In spite of large difference in copy numbers, overall intra-genome evolutionary distances among ERICs were similar among different species, except for a few genomes. The exceptions substantiated hypotheses of genetic drifts and horizontal gene transfers of mobility capacity. Therefore, the confined, variable distribution of ERIC could be explained as a two-step evolution: introduction and proliferation of ERIC in one of the progenitors of gammaproteobacteria, followed by vertical transmission under negative selection. Deterioration of sequences and reduction in copy number were concluded to be the predominant patterns in the evolution of ERIC loci.

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Functional Roles and Genomic Impact of Miniature Inverted-Repeat Transposable Elements (MITEs) in Prokaryotes
Michael F. Minnick
Genes.2024; 15(3): 328. CrossRef

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