Journal of Microbiology

Journal Articles

Description of Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp. nov., and Luteibacter aegosomatissinici sp. nov. isolated from the Intestines of Aegosoma sinicum Larvae: Hae-In Joe , Jee-Won Choi , June-Young Lee , Hojun Sung , Su-Won Jeong , Yun-Seok Jeong , Jae-Yun Lee , Jin-Woo Bae; J. Microbiol. 2023;61(6):603-613. Published online May 5, 2023; DOI: https://doi.org/10.1007/s12275-023-00051-7

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Three novel bacterial strains, 321T, 335T, and 353T, were isolated from the intestines of Aegosoma sinicum larvae collected from Paju-Si, South Korea. The strains were Gram-negative, obligate aerobe and had rod-shaped cells with a single flagellum. The three strains belonged to the genus Luteibacter in the family Rhodanobacteraceae and shared < 99.2% similarity in their 16S rRNA gene sequence and < 83.56% similarity in thier whole genome sequence. Strains 321T, 335T, and 353T formed a monophyletic clade with Luteibacter yeojuensis KACC 11405T, L. anthropi KACC 17855T, and L. rhizovicinus KACC 12830T, with sequence similarities of 98.77–98.91%, 98.44–98.58%, and 97.88–98.02%, respectively. Further genomic analyses, including the construction of the Up-to-date Bacterial Core Gene (UBCG) tree and assessment of other genome-related indices, indicated that these strains were novel species belonging to the genus Luteibacter. All three strains contained ubiquinone Q8 as their major isoprenoid quinone and iso-C15:0 and summed feature 9 ( C16:0 10-methyl and/or iso-C17:1 ω9c) as their major cellular fatty acids. Phosphatidylethanolamine and diphosphatidylglycerol were the major polar lipids in all the strains. The genomic DNA G + C contents of strains 321T, 335T, and 353T were 66.0, 64.5, and 64.5 mol%, respectively. Based on multiphasic classification, strains 321T, 335T, and 353T were classified into the genus Luteibacter as the type strains of novel species, for which the names Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp. nov., and Luteibacter aegosomatissinici sp. nov. are proposed, respectively.

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Luteibacter sahnii sp. nov., A Novel Yellow-Colored Xanthomonadin Pigment Producing Probiotic Bacterium from Healthy Rice Seed Microbiome
Gagandeep Jaiswal, Rekha Rana, Praveen Kumar Nayak, Rekha Chouhan, Sumit G. Gandhi, Hitendra K. Patel, Prabhu B. Patil
Current Microbiology.2024;[Epub] CrossRef
Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species: Thao Thi Nguyen , Tae-Soo Chon , Jaehan Kim , Young-Su Seo , Muyoung Heo; J. Microbiol. 2017;55(7):568-582. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7085-0

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Abstract

Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM) – based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.

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Proteomics approaches: A review regarding an importance of proteome analyses in understanding the pathogens and diseases
Muhammad Zubair, Jia Wang, Yanfei Yu, Muhammad Faisal, Mingpu Qi, Abid Ullah Shah, Zhixin Feng, Guoqing Shao, Yu Wang, Qiyan Xiong
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Characterisation of Pythium aristosporum Oomycete—A Novel Pathogen Causing Rice Seedling Blight in China
Jinxin Liu, Ruisi Zhang, Chuzhen Xu, Chunlai Liu, Yanyan Zheng, Xue Zhang, Shasha Liu, Yonggang Li
Journal of Fungi.2022; 8(9): 890. CrossRef
Bacterial Panicle Blight and Burkholderia glumae: From Pathogen Biology to Disease Control
Laura Ortega, Clemencia M. Rojas
Phytopathology®.2021; 111(5): 772. CrossRef

Research Support, Non-U.S. Gov'ts

Genetic Analysis of the Capsid Region of Norovirus GII.4 Variants Isolated in South Korea: Ju-Eun Kim , Sung-Geun Lee , Han-Gil Cho , Sang-Ha Han , Lae-Hyung Kang , Youn-Mi Lee , Chul-Jong Park , Soon-Young Paik; J. Microbiol. 2014;52(5):427-434. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3538-x

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Abstract

Norovirus is one of the major causes of non-bacterial gas-troenteritis in humans. The aim of this study was to analyze the amino acid variation of open reading frame 2 of GII.4 variants in South Korea during the period from November 2006 to December 2012. Sixty-nine complete nucleotide se-quences of open reading frame 2 were obtained from 113 GII.4 strains. The GII.4 2006b variants were detected pre-dominantly between 2006 and 2009; however, new GII.4 variants, which were termed the 2010 variant and the 2012 variant, emerged in 2010 and 2012, respectively. The num-ber of GII.4 2006b variants steadily decreased until 2012, whereas the number of gastroenteritis cases caused by the new variants increased between 2010 and 2012. The amino acid sequence in the ORF2 region obtained in this study was compared with other GII.4 variants isolated in various countries. Amino acid variations were observed primarily at epitope sites and the surrounding regions. Amino acids 294, 359, 393, and 413 of the P2 subdomain were the most variable sites among the GII.4 variants. The information in this study can be useful in basic research to predict the emergence and determine the genetic functions of new GII.4 variants.

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Determining the efficacy of 27 commercially available disinfectants against human noroviruses
Jae-Woong Lee, Lae-Hyung Kang, Min-Kyeong Kim, Jeong-Soon Kim, Myung L. Kim, Sung-Geun Lee, In-Hye Choi, Chul-Jong Park, Soon-Young Paik
Journal of Infection and Public Health.2021; 14(2): 244. CrossRef
Evolutionary changes in the capsid P2 region of Australian strains of the norovirus GII.Pe_GII.4
Leesa D. Bruggink, Jean M. Moselen, Jason A. Roberts, John A. Marshall
Journal of Medical Microbiology.2017; 66(7): 1014. CrossRef
A norovirus intervariant GII.4 recombinant in Victoria, Australia, June 2016: the next epidemic variant?
Leesa Bruggink, Michael Catton, John Marshall
Eurosurveillance.2016;[Epub] CrossRef
Complete Nucleotide Sequence Analysis of the Norovirus GII.4 Sydney Variant in South Korea
Ji-Sun Park, Sung-Geun Lee, Ji-Young Jin, Han-Gil Cho, Weon-Hwa Jheong, Soon-Young Paik
BioMed Research International.2015; 2015: 1. CrossRef
Molecular epidemiology of norovirus GII.4 variants in children under 5 years with sporadic acute gastroenteritis in South Korea during 2006–2013
Han-Gil Cho, Sung-Geun Lee, Ju-Eun Kim, Kyeong-Sin Yu, Deog-Yong Lee, Po-Hyun Park, Mi-hye Yoon, Eek-Hoon Jho, Jaehong Kim, Soon-Young Paik
Journal of Clinical Virology.2014; 61(3): 340. CrossRef

Molecular Cloning, Purification, and Characterization of a Superoxide Dismutase from a Fast-Growing Mycobacterium sp. Strain JC1 DSM 3803: Ji-Sun Nam , Jee-Hyun Yoon , Hyun-Il Lee , Si Wouk Kim , Young-Tae Ro; J. Microbiol. 2011;49(3):399-406. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-1046-9

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Abstract: A cytosolic superoxide dismutase (SOD) was purified and characterized from a fast-growing Mycobacterium sp. strain JC1 DSM 3803 grown on methanol. The native molecular weight of the purified SOD was estimated to be 48 kDa. SDS-PAGE revealed a subunit of 23 kDa, indicating that the enzyme is a homodimer. The enzyme activity was inhibited by H2O2 and azide. The purified SOD contained 1.12 and 0.56 g-atom of Mn and Fe per mol of enzyme, respectively, suggesting that it may be a Fe/Mn cambialistic SOD. The apo-SOD reconstitution study revealed that Mn salts were more specific than Fe salts in the SOD activity. The gene encoding the SOD was identified from the JC1 cosmid genomic library by PCR screening protocol. The cloned gene, sodA, had an open reading frame (ORF) of 624 nt, encoding a protein with a calculated molecular weight of 22,930 Da and pI of 5.33. The deduced SodA sequence exhibited 97.6% identity with that of Mycobacterium fortuitum Mn-SOD and clustered with other mycobacterial Mn-SODs. A webtool analysis on the basis of SOD sequence and structure homologies predicted the SOD as a tetrameric Mn-SOD, suggesting that the protein is a dimeric Mn-SOD having tetramer-specific sequence and structure characteristics.

Journal Article

Sequence Analysis of the Gene Encoding H Antigen in Escherichia coli Isolated from Food in Morocco: Samira Badri , Aziz Fassouane , Ingrid Filliol , Mohammed Hassar , Nozha Cohen; J. Microbiol. 2010;48(2):184-187. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-9182-1

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Abstract: In order to develop other molecular method useful for typing of motile and non motile Escherichia coli strains, a total of 207 strains of E. coli (133 reference strains, 74 food strains) were characterized by analysis of sequences of their amplified flagellin-encoding (fliC) gene products. The collection of reference strains was used for database building of fliC gene sequences. Application of this identification system to 74 E. coli food isolates revealed a reproducible and clear cut classification with very good correlation to results obtained by HhaI restriction of the amplified flagellin gene. The proposed determination of fliC sequences variations should be helpful for epidemiological studies.

Sequence Analysis of the Cytochrome b Gene of Trimorphomyces papilionaceus Mitochondria: Kim, Young Hyun , Kang, Young Won , Jung, Hack Sung; J. Microbiol. 1995;33(1):5-9.

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Abstract: The DNA sequence of the cytochrome b (cob) gene region of Trimorphomyces papilionaceus mitochondrial DNA has been determined. The cob gene is interrupted by an intron of 1267 bp, which has an open reading frame of 897 bp contiguous to to the upstream exon. The intron belongs to group IB and contains a reading frame with a GIY-10-YVG motif. The deduced amino acid sequence shows 52~60% homology with those of other reported fungi. The phylogenetic relationship of T. papilionaceus with Neurospora crassa, Podospora adserina, Aspergillus nidulans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Homo sapiens were inferred through sequence alignment and homology comparison of amino acids deduced from cob genes. When Homo sapiens was set as an outgroup, two ascomycetous yeasts S. cerevisiae and S. pombe made one group and three ascomycetous fungi N. crassa, P. anserine, and a basidiomycetous fungus T. papilionaceus the other group, suggesting that the former group evolved first and then the latter group separated into ascomycetous and basidiomycetous fungi right after that.

Cloning and Sequence Analysis of Two Catechol-degrading Gene Clusters from a Phenol-utilizing Bacterium Pseudomonas putida SM25: Young-Hee Jung , Jong-Ok Ka , Choong-Ill Cheon , Myeong-Sok Lee , Eun-Sook Song , Soon-Young Choi , Daeho Cho , Sang-Ho Choi , Kwon-Soo Ha , Young Mok Park , Jong-Soon Choi , Kyung-Hee Min; J. Microbiol. 2003;41(2):102-108.

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Abstract: A 6.1 kb Sph I fragment from the genomic DNA of Pseudomonas putida SM 25 was cloned into the vector pUC19. The open reading frame of catB was found to consist of 1,122 nucleotides. The sequence alignment of the catB gene products from different kinds of bacteria revealed an overall identity ranging from 40 to 98%. The catC gene contained an open reading frame of 96 codons, from which a protein with a molecular mass of about 10.6 kDa was predicted. The amino acids in the proposed activesite region of CatC were found to be almost conserved, including the charged residues. Since the catBC genes in P. putida SM25 were tightly linked, they could be regulated under coordinate transcription, and transcribed from a single promoter located upstream of the catB gene, as in P. putida RB1.

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