Journal of Microbiology

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Chemokine CCL6 Plays Key Role in the Inhibitory Effect of Vitamin A on Norovirus Infection: Heetae Lee , Giljae Lee , You-Hee Cho , Youngcheon Song , GwangPyo Ko; J. Microbiol. 2023;61(5):579-587. Published online May 26, 2023; DOI: https://doi.org/10.1007/s12275-023-00047-3

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Abstract: Norovirus (NoV) is the most common viral cause of acute gastroenteritis worldwide. Vitamin A has demonstrated the potential to protect against gastrointestinal infections. However, the effects of vitamin A on human norovirus (HuNoV) infections remain poorly understood. This study aimed to investigate how vitamin A administration affects NoV replication. We demonstrated that treatment with retinol or retinoic acid (RA) inhibited NoV replication in vitro based on their effects on HuNoV replicon-bearing cells and murine norovirus-1 (MNV-1) replication in murine cells. MNV replication in vitro showed significant transcriptomic changes, which were partially reversed by retinol treatment. RNAi knockdown of CCL6, a chemokine gene that was downregulated by MNV infection but upregulated by retinol administration, resulted in increased MNV replication in vitro. This suggested a role of CCL6 in the host response to MNV infections. Similar gene expression patterns were observed in the murine intestine after oral administration of RA and/or MNV-1.CW1. CCL6 directly decreased HuNoV replication in HG23 cells, and might indirectly regulate the immune response against NoV infection. Finally, relative replication levels of MNV-1.CW1 and MNV-1.CR6 were significantly increased in CCL6 knockout RAW 264.7 cells. This study is the first to comprehensively profile transcriptomes in response to NoV infection and vitamin A treatment in vitro, and thus may provide new insights into dietary prophylaxis and NoV infections.

UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis: Jihyeon Kim , Seong-In Na , Dongwook Kim , Jongsik Chun; J. Microbiol. 2021;59(6):609-615. Published online May 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1231-4

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Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2.

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Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi: Young Joon Oh , Joon Yong Kim , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi; J. Microbiol. 2021;59(5):460-466. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-0513-1

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Abstract

To date, all species in the genus Salicibibacter have been isolated in Korean commercial kimchi. We aimed to describe the taxonomic characteristics of two strains, NKC5-3T and NKC21-4T, isolated from commercial kimchi collected from various regions in the Republic of Korea. Cells of these strains were rod-shaped, Gram-positive, aerobic, oxidase- and catalase- positive, non-motile, halophilic, and alkalitolerant. Both strains, unlike other species of the genus Salicibibacter, could not grow without NaCl. Strains NKC5-3T and NKC21-4T could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and grow at pH 7.0–10.0 (optimum 8.5) and 8.0–9.0 (optimum 8.5), respectively; they showed 97.1% 16S rRNA gene sequence similarity to each other and were most closely related to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively). The genome of strain NKC5-3T was nearly 4.6 Mb in size, with 4,456 protein-coding sequences (CDSs), whereas NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs. OrthoANI values between the novel strains and S. kimchii NKC1-1T were far lower than the species demarcation threshold. NKC5-3T and NKC21-4T clustered together to form branches that were distinct from the other Salicibibacter species. The major fatty acids in these strains were anteiso-C15:0 and anteiso-C17:0, and the predominant menaquinone was menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and five unidentified phospholipids (PL), and those of NKC21-4T included DPG, PG, seven unidentified PLs, and an unidentified lipid. Both isolates had DPG, which is the first case in the genus Salicibibacter. The genomic G + C content of strains NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic analyses, strains NKC5-3T (= KACC 22040T = DSM 111417T) and NKC21-4T (= KACC 22041T = DSM 111418T) represent two novel species of the genus Salicibibacter, for which the names Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov. are proposed.

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Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef

Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax: Mohamed El-Agamy Farh , Yeon-Ju Kim , Priyanka Singh , Sun Young Jung , Jong-Pyo Kang , Deok-Chun Yang; J. Microbiol. 2017;55(10):767-774. Published online September 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7033-z

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Abstract

Gram-staining-negative, uniflagellated, rod-shaped, designated as DCY110T, was isolated from sludge located in Gangwon province, Republic of Korea. The phylogenetic tree of 16S rRNA gene sequence showed that the strain DCY110T belonged to the genus Rhodoferax with a close similarity to Rhodoferax saidenbachensis DSM 22694T (97.7%), Rhodoferax antarcticus DSM 24876T (97.5%), Rhodoferax ferrireducens DSM 15236T (97.3%), and Rhodoferax fermentans JCM 7819T (96.7%). The predominant isoprenoid quinine was ubiquinone (Q-8). DNA G + C content was 62.8 mol%. The major polar lipids were phosphatidylethanolamine and two unidentified phospholipids. The major fatty acids (> 10%) were C12:0, C16:0, summed feature 3 (which comprised C16:1 ω7c and/or C16:1 ω6c). The DNA-DNA relatedness values between the strain DCY110T and the closely related relatives used in this study were lower than 70%. Based on the following polyphasic analysis, the strain DCY110T is considered as a novel species of the genus Rhodoferax, for which the name Rhodoferax koreense sp. nov. is proposed. The type strain is DCY- 110T (= KCTC 52288T = JCM 31441T).

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Azohydromonas riparia sp. nov. and Azohydromonas ureilytica sp. nov. isolated from a riverside soil in South Korea: Tuan Manh Nguyen , Jaisoo Kim; J. Microbiol. 2017;55(5):330-336. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6519-z

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Abstract

White and pale yellow coloured bacteria were isolated from the riverside soil, Daejeon, South Korea, and were designated UCM-11T, UCM-F25, and UCM-80T. We found that all strains were able to reduce nitrate, and the cells were aerobic and motile. The DNA G+C contents of UCM-11T, UCM-F25, and UCM-80T were between 68.9 to 71.2 mol% and the main ubiquinone was observed as Q-8. Based on16S rRNA gene sequences, strains UCM-11T and UCM-F25 were found to closely match with Azohydromonas australica IAM 12664T (98.48–98.55%), and the strain UCM-80T was the closest match with Azohydromonas lata IAM 12599T (98.34%). The presence of summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0, summed feature 8 (C18:1ω7c and/or C18:1ω6c) as well as twokinds of hydroxyfatty acids consisting of C10:0 3-OH and C12:0 2-OH, and branched fatty acids containing C16:0 iso and C17:0 cyclo were detected in all the strains. Phosphatidy-lethanolamine was a major polar lipid. DNA–DNA related-ness confirmed UCM-11T, UCM-F25 and UCM-80T as novel members of the genus Azohydromonas. Based on the mor-phological, physiological, biochemical and genotypic char-acteristics, we suggest that strains UCM-11T, UCM-F25, and UCM-80T represent novel species within the genus Azohy-dromonas. The names Azohydromonas riparia sp. nov., and Azohydromonas ureilytica sp. nov. are proposed for the type strains UCM-11T (=KACC 18570T =NBRC 111646T) and UCM-80T (=KACC 18576T =NBRC 111658T), respectively.

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Research Support, Non-U.S. Gov't

Effects of Nutritional Input and Diesel Contamination on Soil Enzyme Activities and Microbial Communities in Antarctic Soils: Jiwon Han , Jaejoon Jung , Seunghun Hyun , Hyun Park , Woojun Park; J. Microbiol. 2012;50(6):916-924. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2636-x

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Abstract: Pollution of Antarctic soils may be attributable to increased nutritional input and diesel contamination via anthropogenic activities. To investigate the effect of these environmental changes on the Antarctic terrestrial ecosystem, soil enzyme activities and microbial communities in 3 types of Antarctic soils were evaluated. The activities of alkaline phosphomonoesterase and dehydrogenase were dramatically increased, whereas the activities of β-glucosidase, urease, arylsulfatase, and fluorescein diacetate hydrolysis were negligible. Alkaline phosphomonoesterase and dehydrogenase activities in the 3 types of soils increased 3- to 10-fold in response to nutritional input, but did not increase in the presence of diesel contamination. Consistent with the enzymatic activity data, increased copy numbers of the phoA gene, encoding an alkaline phosphomonoesterase, and the 16S rRNA gene were verified using quantitative real-time polymerase chain reaction. Interestingly, dehydrogenase activity and 16S rRNA gene copy number increased slightly after 30 days, even under diesel contamination, probably because of adaptation of the bacterial population. Intact Antarctic soils showed a predominance of Actinobacteria phylum (mostly Pseudonorcarida species) and other phyla such as Proteobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Verrucomicrobia were present in successively lower proportions. Nutrient addition might act as a selective pressure on the bacterial community, resulting in the prevalence of Actinobacteria phylum (mostly Arthrobacter species). Soils contaminated by diesel showed a predominance of Proteobacteria phylum (mostly Phyllobacterium species), and other phyla such as Actinobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes were present in successively lower proportions. Our data reveal that nutritional input has a dramatic impact on bacterial communities in Antarctic soils and that diesel contamination is likely toxic to enzymes in this population.

Journal Article

NOTE] Arenimonas aquaticum sp. nov., a Member of the Gammaproteobacterium, Isolated from a Freshwater Reservoir: A-Ram Kim , Siwon Lee , Kyudong Han , Tae-Young Ahn; J. Microbiol. 2012;50(2):354-358. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1301-8

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6 Scopus

Abstract: A novel bacterial strain, designated NA-09T, was isolated from a freshwater sample collected from the Cheonho reservoir, Republic of Korea. Colonies were creamy-white pigmented, translucent, and circular with convex shape. The isolate was Gram-staining negative, strictly aerobic, motile, and rod-shaped. The 16S rRNA gene sequence analysis revealed that strain NA-09T belonged to the genus Arenimonas and showed the highest sequence similarities with Arenimonas malthae CC-JY-1T (95.4%), A. oryziterrae YC6267T (94.9%), A. composti P2-12-1T (94.8%), and A. donghaensis H03-R19T (94.1%). The major fatty acids were iso-C16:0 (20.8%), iso-C15:0 (16.9%), summed feature 1 (13.2%), and iso-C16:1ω7c alcohol (10.2%). The major isoprenoid quinone of the isolate was ubiquionone-8. On the basis of the data from the polyphasic characterization, the strain NA-09T represents a novel species, for which the name Arenimonas aquaticum sp. nov. is proposed (type strain NA-09T =KACC 14663T =NBRC 106550T).

Research Support, Non-U.S. Gov't

NOTE] Pigmentiphaga soli sp. nov., a Bacterium Isolated from Soil: Jae-Jin Lee , Sathiyaraj Srinivasan , Myung Kyum Kim; J. Microbiol. 2011;49(5):857-861. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1375-8

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Abstract: Strain BS12T, a Gram-negative motile bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain belonged to the family Alcaligenaceae in the class Betaproteobacteria. The highest degree of sequence similarities of strain BS12T were found with Pigmentiphaga litoralis JSM 061001T (98.3%), Pigmentiphaga daeguensis K110T (98.2%), and Pigmentiphaga kullae K24T (98.1%). Chemotaxonomic data revealed that strain BS12T possessed ubiquinone-8, which is common in the family Alcaligenaceae, and the predominant fatty acids were C16:0, C17:0 cyclo, summed feature 3 (C16:1 ω6c/ω7c), and summed feature 8 (C18:1 ω6c/ω7c). The major polar lipids of strain BS12T were phosphatidylethanolamine and phosphatidylglycerol. Based on these data, BS12T (=KCTC 23577T =JCM 17666T =KEMB 9004-082T) should be classified as a type strain of a novel species, for which the name Pigmentiphaga soli sp. nov. is proposed.

Journal Article

Oceanicoccus sagamiensis gen. nov., sp. nov., a Gammaproteobacterium Isolated from Sea Water of Sagami Bay in Japan: Sanghwa Park , Kazuhiro Kogure , Akira Yokota; J. Microbiol. 2011;49(2):233-237. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0368-y

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Abstract: A gram-negative, motile, coccoid- and amorphous-shaped, non-pigmented chemoheterotrophic bacterium, designated strain PZ-5T, was isolated from sea water of Sagami Bay in Japan and subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate could be affiliated with the class Gammaproteobacteria. Strain PZ-5T showed below 93.9% similarity with validly published bacteria and demonstrated the highest sequence similarity to Dasania marina KOPRI 20902T (93.9%). Strain PZ-5T formed a monophyletic group with D. marina KOPRI 20902T. The DNA G+C content of strain PZ-5T was 49.8 mol%. The major isoprenoid quinone was Q-8 and redominant cellular fatty acids were C15:0 ISO 2OH (19%), C16:1 ω7c (17.4%), C17:1 ω8c (16.2%), C11:0 3OH (7.5%), and C15:1 ω8c (6.5%). Based on evidence from a polyphasic taxonomical study, it was concluded that the strain should be classified as representing a new genus and species of the class Gammaproteobacteria, for which the name Oceanicoccus sagamiensis gen. nov., sp. nov., (type strain PZ-5T =NBRC 107125T =KCTC 23278T) is proposed.

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

New Taxa in Alphaproteobacteria: Brevundimonas olei sp. nov., an Esterase-Producing Bacterium: Myungjin Lee , Sathiyaraj Srinivasan , Myung Kyum Kim; J. Microbiol. 2010;48(5):616-622. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-9367-7

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Abstract: A polyphasic taxonomic approach was used to characterize a Gram-negative, non-motile bacterium, designated MJ15T, that was isolated from soil of a GS-Caltex Oil reservoir in Korea. As shown by comparative 16S rRNA gene sequence analysis, strain MJ15T belongs to genus Brevundimonas. The 16S rRNA gene sequence similarities ranged from 95.6-99.2% between strain MJ15T and validated representatives of the genus Brevundimonas. With respect to Brevundimonas species, strain MJ15T exhibited DNA-DNA relatedness values below 40.7%. The G+C content of the genomic DNA was 61.7 mol%. Strain MJ15T contained ubiquinone Q-10. The major fatty acids were C16:0 (27.7%), C19:0 cyclo ω8c (23.2%), summed feature 8 (containing C18:1 ω7c/C18:1 ω6c) (28.5%), and major hydroxyl fatty acid was C12:0 3OH (3.7%). Based upon its phenotypic and genotypic properties, as well as its phylogenetic distinctiveness, strain MJ15T (KCTC 22461T; JCM 16237T) should be classified in the genus Brevundimonas as the type strain of a novel species. The name Brevundimonas olei sp. nov. is proposed for this new species.

Methylobacterium dankookense sp. nov., Isolated from Drinking Water: Si-Won Lee , Hyun-Woo Oh , Kang-Hyun Lee , Tae-Young Ahn; J. Microbiol. 2009;47(6):716-720. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0126-6

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Abstract: A pink-pigmented bacterium, designated SW08-7T was isolated from the drinking water of a water purifier. Cells were Gram-negative, rod-shaped, strictly aerobic, and non-spore-forming. It grew optimally at 25°C, pH 6~7. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain SW08-7T belongs to the genus Methylobacterium. The highest 16S rRNA gene sequence similarities were found to Methylobacterium mesophilicum JCM 2829T (96.9%), Methylobacterium brachiatum B0021T (96.9%), Methylobacterium phyllosphaerae CBMB27T (96.6%), Methylobacterium radiotolerans JCM 2831T (96.6%), and Methylobacterium hispanicum GP34T (96.5%). DNA-DNA hybridization experiment revealed low-level (28.5%) of DNA- DNA relatedness between strain SW08-7T and Methylobacterium hispanicum. The genomic DNA G+C content was 68.9 mol% and the major isoprenoid quinone was Q-10. The major cellular fatty acid of strain SW08-7T was C18:1 ω7c (79.8±2.1%). Results of phylogenetic, phenotypic, and biochemical analyses revealed that strain SW08-7T could be classified as representing a novel species of genus Methylobacterium, for which the name Methylobacterium dankookense sp. nov. is proposed. The type strain is SW08-7T (=KCTC 22512T =DSM 22415T).

Comamonas granuli sp. nov., Isolated from Granules Used in a Wastewater Treatment Plant: Kyoung-Ho Kim , Leonid N. Ten , Qing-Mei Liu , Wan-Taek Im , Sung-Taik Lee; J. Microbiol. 2008;46(4):390-395. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0019-0

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28 Scopus

Abstract: A Gram-negative, motile, rod-shaped, non-spore-forming bacterial strain, designated as Ko03T, was isolated from microbial granules, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The isolate was positive for catalase and oxidase, but negative for gelatinase and β-galactosidase. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evoluionary radiation occupied by the genus Comamonas, its closest neighbors being Comamonas koreensis KCTC 12005T (95.9% sequence similarity), Comamonas nitrativorans DSM 13191T (95.7%), and Comamonas odontotermitis LMG 23579T (95.7%). Strain Ko03T had a genomic DNA G+C content of 68.4 mol% and the predominant respiratory quinone was Q-8. The major fatty acids were C16:1 ω7c (44.7%), C16:0 (28.1%), C18:1 (16.1%), and C10:0 3-OH (3.5%). These chemotaxonomic results supported the affiliation of strain Ko03T to the genus Comamonas. However, low 16S rRNA gene sequence similarity values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Ko03T from recognized Comamonas species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Ko03T represents a novel species of the genus Comamonas, for which the name Comamonas granuli sp. nov. is proposed. The type strain is Ko03T (= KCTC 12199T= NBRC 101663T).

Sphingopyxis granuli sp. nov., a [beta]-Glucosidase-Producing Bacterium in the Family Sphingomonadaceae in [alpha]-4 Subclass of the Proteobacteria: Myung Kyum Kim , Wan-Taek Im , Hiroyuki Ohta , Myungjin Lee , Sung-Taik Lee; J. Microbiol. 2005;43(2):152-157.; DOI: https://doi.org/2169 [pii]

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Abstract: Strain Kw07^T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from granules in an Up-flow Anaerobic Sludge Blanket (UASB) bioreactor used in the treatment of brewery wastewater. 16S rRNA gene sequence analysis revealed that strain Kw07^T belongs to the [alpha]-4 subclass of the Proteobacteria, and the highest degree of sequence similarity was determined to be to Sphingopyxis macrogoltabida IFO 15033^T (97.8%). Chemotaxonomic data revealed that strain Kw07^T possesses a quinone system with the predominant compound Q-10, the predominant fatty acid C_18:1 w7c, and sphingolipids, all of which corroborated our assignment of the strain to the Sphingopyxis genus. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Kw07^T represents a distinct species. Based on these data, Kw07^T (= KCTC 12209^T = NBRC 100800^T) should be classified as the type strain for a novel Sphingopyxis species, for which the name Sphingopyxis granuli sp. nov. has been proposed.

Culture and Identification of Bacteria from Marine Biofilms: Yoo Kyung Lee , Kae-Kyung Kwon , Kyeung Hee Cho , Hyo Won Kim , Jae Hyun Park , Hong Kum Lee; J. Microbiol. 2003;41(3):183-188.

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Abstract: We isolated and cultured bacteria that inhabited marine biofilms, and identified them by phylogenetic analysis using 16S rDNA sequences. In the marine environment, biofilms cover most subtidal and intertidal solid surfaces such as rocks, ships, loops, marine animals, and algae. The bacteria in most biofilms are embedded in extracellular polymeric substances that comprise mainly of exopolysaccharides. The exopolysaccharides are excreted from multiple bacterial species; therefore, biofilms are a good source for screening exopolysaccharide-producing bacteria. Thirty-one strains were cultured, and a total of 17 unique strains were identified. Phylogenetic analysis using 16S rDNA sequences indicated that the 17 strains belonged to [alpha]-Proteobacteria (Ochrobactrum anthropi, Paracoccus carotinifaciens); [gamma]-Proteobacteria (Pseudoalteromonas agarovorans, P. piscicida, Pseudomonas aeruginosa, Shewanella baltica, Vibrio parahaemolyticus, V. pomeroyi); CFB group bacteria (Cytophaga latercula, Tenacibaculum mesophilum); high GC, Gram-positive bacteria (Arthrobacter nicotianae, Brevibacterium casei, B. epidermidis, Tsukamurella inchonensis); and low GC, Gram-positive bacteria (Bacillus macroides, Staphylococcus haemolyticus, S. warneri).

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