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- Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov., isolated from kimchi, a traditional Korean fermented food
- Min Ji Lee, Jisu Lee, Sohee Nam, Mi-Ja Jung, Yeon Bee Kim, Yujin Kim, Jeong Ui Yun, Seong Woon Roh, Tae Woong Whon, Che Ok Jeon, Se Hee Lee
- J. Microbiol. 2025;63(11):e2507007. Published online November 30, 2025
- DOI: https://doi.org/10.71150/jm.2507007
- 188 View
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Abstract
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Supplementary Material -
Two Gram-stain-positive, facultatively anaerobic, rod-shaped, and non-motile lactic acid bacterial strains, designated as strains CBA3605T and CBA3606T, were isolated from kimchi, a traditional Korean fermented food. Both strains were oxidase- and catalase-negative, non-spore-forming, non-hemolytic, and non-gas-producing. Optimal growth conditions for the two strains were observed at 30°C, pH 5.0, and 0% NaCl. The two genomes were composed of a circular chromosome and three plasmids and the DNA G + C content of 43.0%, respectively. Strains CBA3605T and CBA3606T were most closely related to Lactiplantibacillus (Lp.) pingfangensis 382-1T with 16S rRNA sequence similarity of 99.4% and 99.1%, respectively. However, the orthologous average nucleotide identities between CBA3605T and CBA3606T were 91.7%, and those with strain 382-1T were 76.9% and 76.5%, respectively. Digital DNA–DNA hybridization values between CBA3605T and CBA3606T were 45.0%, and those with strain 382-1T were 21.4% and 21.0%, respectively. The major fatty acids detected in both strains included C16:0, C18:1 ω9c, and summed features 7 (C19:1 ω7c, C19:1 ω6c, C19:0 cyclo ω10c, and/or C19:0 ω6c). The peptidoglycan of both strains CBA3605T and CBA3606T contained meso-diaminopimelic acid and was classified as A4α type (L-Lys–D-Asp). In polar lipid analyses, only strain CBA3605T contained aminophosphoglycolipid, which was absent in CBA3606T, although both strains harbored same major polar lipids (diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine). Based on phenotypic, phylogenetic, genomic, biochemical, and chemotaxonomic analyses, strains CBA3605T and CBA3606T represent two novel species of the genus Lactiplantibacillus, for which the names Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov. are proposed, with CBA3605T (= KACC 81073BPT = JCM 37965T), and CBA3606T (= KACC 81074BPT = JCM 37966T) as the type strains.
Journal Articles
- Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt
- Hye Seon Song , Juseok Kim , Yeon Bee Kim , Se Hee Lee , Tae Woong Whon , Seong Woon Roh
- J. Microbiol. 2022;60(9):899-904. Published online July 14, 2022
- DOI: https://doi.org/10.1007/s12275-022-2137-5
- 329 View
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- 8 Web of Science
- 8 Crossref
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- Two novel halophilic archaeal strains, CBA1133T and CBA- 1134, were isolated from solar salt in South Korea. The 16S rRNA gene sequences of the isolates were identical to each other and were closely related to the genera Natronomonas (92.3–93.5%), Salinirubellus (92.2%), Halomarina (91.3– 92.0%), and Haloglomus (91.4%). The isolated strains were coccoid, Gram-stain-negative, aerobic, oxidase-positive, and catalase-negative. Growth occurred under temperatures of 25–50°C (optimum, 45°C), NaCl levels of 10–30% (optimum, 15%), pH levels of 6.0–8.5 (optimum, 7.0), and MgCl2 concentrations of 0–500 mM (optimum, 100 mM). Digital DNADNA hybridization values between the strains and related genera ranged from 18.3% to 22.7%. The major polar lipids of the strains were phosphatidyl glycerol, phosphatidyl glycerol phosphate methyl ester, and phosphatidyl glycerol sulfate. Genomic, phenotypic, physiological, and biochemical analyses of the isolates revealed that they represent a novel genus and species in the family Halobacteriaceae. The type strain is CBA1133T (= KACC 22148T = JCM 34265T), for which the name Sala cibi gen. nov., sp. nov. is proposed.
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Citations
Citations to this article as recorded by
- Dominance and diversity of archaea in food-grade salts: insights for histamine degradation in salt-fermented foods
Jing Hou, Ya-Ling Mao, Na Li, Xiao-Yan Yang, Chidiebele Nwankwo, Heng-Lin Cui
International Journal of Food Science and Technology.2024; 59(12): 9490. CrossRef - Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef - Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat
Yao Hu, Xue Ma, Shun Tan, Xin-Xin Li, Mu Cheng, Jing Hou, Heng-Lin Cui
Antonie van Leeuwenhoek.2024;[Epub] CrossRef - Assessing the impact of heavy metals on bacterial diversity in coastal regions of Southeastern India
Chandra Veluchamy, Avinash Sharma, Kalaivani Thiagarajan
Environmental Monitoring and Assessment.2024;[Epub] CrossRef - Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively
Umakant Bhoopati Deshmukh, Aharon Oren
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef - Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef - Halorarius litoreus gen. nov., sp. nov., Halorarius halobius sp. nov., Haloglomus halophilum sp. nov., Haloglomus salinum sp. nov., and Natronomonas marina sp. nov., extremely halophilic archaea isolated from tidal flat and marine solar salt
Ya-Ping Sun, Bei-Bei Wang, Zhang-Ping Wu, Xi-Wen Zheng, Jing Hou, Heng-Lin Cui
Frontiers in Marine Science.2023;[Epub] CrossRef - Naming new taxa of prokaryotes in the 21st century
Aharon Oren
Canadian Journal of Microbiology.2023; 69(4): 151. CrossRef
- Dominance and diversity of archaea in food-grade salts: insights for histamine degradation in salt-fermented foods
- Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.
- Yujin Kim , Yeon Bee Kim , Juseok Kim , Joon Yong Kim , Tae Woong Whon , Won-Hyong Chung , Eun-Ji Song , Young-Do Nam , Se Hee Lee , Seong Woon Roh
- J. Microbiol. 2022;60(7):678-688. Published online July 4, 2022
- DOI: https://doi.org/10.1007/s12275-022-1581-6
- 327 View
- 0 Download
- 2 Web of Science
- 3 Crossref
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Abstract
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- Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104T and CBA3105T, were isolated from kimchi. Strain CBA3104T and CBA3105T grew at 10–35°C (optimum, 25°C and 30°C, respectively), at pH 6.0–8.5 (optimum, pH 6.5), and in the presence of 0–15% (w/v) NaCl (optimum, 5%). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBA3104T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105T was closely positioned with Brachybacterium halotolerans MASK1Z-5T. The 16S rRNA gene sequence similarity between strains CBA3104T and CBA3105T was 99.9%, but ANI and dDDH values between strains CBA3104T and CBA3105T were 93.61% and 51.5%, respectively. Strain CBA3104T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium, however, strain CBA3105T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5T. Among biochemical analysis results, strain CBA3104T could uniquely utilize bromo-succinic acid whereas only strain CBA3105T was positive for alkaline phosphatase and α-fucosidase among two novel strains, closely related strains, and type species of the genus Brachybacterium. Compared with strain CBA3105T and Brachybacterium halotolerans JCM 34339T, strain CBA3105T was differentially positive for acid production of D-arabinose, D-adonitol, and potassium 5-ketogluconate and enzyme activity of β-glucuronidase. Both strains contained menaquinone-7 as the dominant quinone. The cell-wall peptidoglycan of two novel strains contained meso-diaminopimelic acid. The major fatty acids of strains CBA3104T and CBA3105T were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54–62 tRNAs). Both the CBA3104T and CBA3105T strain harbored various oxidoreductase, transferase, hydrolase, and lyase as strain-specific functional genes compared to closely related strains and Brachybacterium type species. The results of biochemical/physiological, chemotaxonomic, and genomic analyses demonstrated that strains CBA3104T and CBA3105T represent a novel species of the genus Brachybacterium and a novel subspecies of B. halotolerans, respectively, for which the names Brachybacterium kimchii sp. nov. and B. halotolerans subsp. kimchii subsp. nov. are proposed. The type strains of the novel species and the novel subspecies are CBA3104T (= KCCM 43417T = JCM 34759T) and CBA3105T (= KCCM 43418T = JCM 34760T), respectively.
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Citations
Citations to this article as recorded by- Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
Alexander G. Elcheninov, Kseniya S. Zayulina, Alexandra A. Klyukina, Mariia K. Kremneva, Ilya V. Kublanov, Tatiana V. Kochetkova
Microorganisms.2023; 12(1): 16. CrossRef - Validation List no. 208. 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 .2022;[Epub] CrossRef -
Complete Genome Sequence of
Brachybacterium
sp. Strain NBEC-018, Isolated from Nematode-Infected Potatoes
Ling Chen, Yueying Wang, Nanxi Liu, Lei Zhu, Yong Min, Yimin Qiu, Yuxi Tian, Xiaoyan Liu, David Rasko
Microbiology Resource Announcements.2022;[Epub] CrossRef
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Review
- Omics in gut microbiome analysis
- Tae Woong Whon , Na-Ri Shin , Joon Yong Kim , Seong Woon Roh
- J. Microbiol. 2021;59(3):292-297. Published online February 23, 2021
- DOI: https://doi.org/10.1007/s12275-021-1004-0
- 346 View
- 0 Download
- 41 Web of Science
- 41 Crossref
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Abstract
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- Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.
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Journal Articles
- Paenibacillus psychroresistens sp. nov., isolated from the soil of an Arctic glacial retreat
- In-Tae Cha , Eui-Sang Cho , Yoo Kyung Lee , Seong Woon Roh , Myung-Ji Seo
- J. Microbiol. 2019;57(7):569-574. Published online June 27, 2019
- DOI: https://doi.org/10.1007/s12275-019-8666-x
- 364 View
- 0 Download
- 4 Web of Science
- 4 Crossref
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Abstract
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- Strain ML311-T8T was isolated from a glacial retreat area in Svalbard, Norway, and was taxonomically characterized by a polyphasic approach. Upon phylogenetic analysis, strain ML311-T8T was clustered with Paenibacillus arcticus MME2_ R6T and P. contaminans CKOBP-6T with 98.3–98.6 and 93.5– 93.9% 16S rRNA gene sequence similarities, respectively. DNA-DNA hybridization values between strain ML311-T8T and P. arcticus MME2_R6T was 19.9%. The genomic DNA G+C content was 41.1 mol%. The isolated strain was Gramstain- positive, strictly aerobic and rod-shaped, and grew in 0–0.5% (w/v) NaCl, at 4–23°C and pH 6.0–10.0, with optimal growth in 0% (w/v) NaCl, at 20°C and pH 7.0–8.0. The predominant respiratory quinone of strain ML311-T8T was MK- 7 and the major fatty acids were anteiso-C15:0 and C16:0. The polar lipids of strain ML311-T8T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified amino lipids, and three unidentified lipids. On the basis of polyphasic taxonomic analysis, the strain ML311-T8T is proposed to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus psychroresistens sp. nov. is proposed. The type strain is ML311-T8T (= KCCM 43190T = JCM 31243T).
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Citations
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Maikel Gilberto Fernández-López, Ayixon Sánchez-Reyes, Marcos Eduardo Rosas-Ramírez, Edgar Balcázar-López
Water, Air, & Soil Pollution.2024;[Epub] CrossRef -
Paenibacillus dendrobii sp. nov., an indole-3-acetic acid-producing endophytic bacterium isolated from Dendrobium nobile
Yadong Hu, Hongjie Li, Yaoyi Chen, Qiling Zhang, Shigang Zheng, Dan Rao, Ze Chun, Ruoxi Zhao
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef - Validation List no. 206. 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 .2022;[Epub] CrossRef - Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil
Jayoung Paek, Lu Bai, Yeseul Shin, Hongik Kim, Joong-Ki Kook, Young-Hyo Chang
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
- Microbiodiversity Landscape Present in the Mine-Tailings of the “Sierra de Huautla” Biosphere Reserve, Mexico
- Mixed starter of Lactococcus lactis and Leuconostoc citreum for extending kimchi shelf-life
- Mi-Ju Kim , Hae-Won Lee , Mo-Eun Lee , Seong Woon Roh , Tae-Woon Kim
- J. Microbiol. 2019;57(6):479-484. Published online May 27, 2019
- DOI: https://doi.org/10.1007/s12275-019-9048-0
- 333 View
- 0 Download
- 29 Web of Science
- 26 Crossref
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Abstract
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- To develop a starter culture system for improving the shelflife and quality of kimchi, we prepared a mixed starter composed of Lactococcus lactis and Leuconostoc citreum. Two strains, L. lactis WiKim0098 and Leu. citreum WiKim0096, showed high antimicrobial activity and mannitol productivity, respectively. These lactic acid bacteria (LAB) were introduced as a starter into kimchi following cultivation in foodgrade liquid medium. Two kimchi samples, with and without starter, were fermented for 12 days at 10°C. Compared to the control kimchi without starter, a lower initial pH and higher number of LAB were observed in kimchi with starter at 0 day. However, the starter in kimchi prolonged the period taken by kimchi to reach to pH 4.2 by approximately 1.5-fold compared to that in the control kimchi. To estimate the effect of the starter on the flavor of kimchi, metabolite changes were evaluated by gas chromatography/mass spectrometry. In starter fermented kimchi, the levels of mannitol and amino acid, which are associated with the flavor of kimchi, were increased following fermentation. The amount of mannitol was confirmed by high-performance liquid chromatography analysis, showing concentrations of 3.4 and 5.1 mg/ml for the control and starter fermented kimchi, respectively. Thus, mixed starter inoculated with L. lactis WiKim0098 and Leu. citreum WiKim0096 may extend the shelf-life of kimchi and improve its sensory characteristics.
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Citations
Citations to this article as recorded by- Effects of storage temperature on the diversity of white colony-forming yeast and correlations between bacterial and yeast communities in salted kimchi cabbage
Chan-Il Bae, Yoon-Soo Gwak, Su-Jeong Eom, Shinyoung Lee, Mi-Ju Kim
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Siti Hajar-Azhari, Fateen Aqlima Haniem Ab Jabar, Zul Ilham, Muhamad Hafiz Abd Rahim, Nurul Aqilah Mohd Zaini, Wan Abd Al Qadr Imad Wan-Mohtar
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Hye Jin Yu, Sung Hee Park, Eun Hae Kim, Yun-Jeong Choi, Sung Gi Min
Journal of Food Science and Technology.2023; 60(10): 2695. CrossRef - Effects of the addition of starches with different amylose contents on kimchi microbiota and metabolites
Seong-Eun Park, Kwang-Moon Cho, Sun Jae Kwon, Eun-Ju Kim, Seung-Ho Seo, Duyun Jeong, Hyun-Jung Chung, Hong-Seok Son
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Elvina Parlindungan, Oliver A. H. Jones
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Food Research International.2022; 155: 111059. CrossRef - Effects of mixed inoculation of Leuconostoc citreum and Lactobacillus plantarum on suansun (Sour bamboo shoot) fermentation
Honghao Lu, Cuiji Huang, Kena Yu, Zhaoming Liu
Food Bioscience.2022; 47: 101688. CrossRef - Comparison of fermentation characteristics of kimchi made with fresh and stored spring kimchi cabbage
Sung-gi Min, Mi-Ju Kim, Jun-young Jeon, Hae-Yeong Kim, Eung Soo Han
Food Science and Biotechnology.2022; 31(2): 221. CrossRef - Influence of Salinity on the Microbial Community Composition and Metabolite Profile in Kimchi
Mi-Ai Lee, Yun-Jeong Choi, Hyojung Lee, Sojeong Hwang, Hye Jin Lee, Sung Jin Park, Young Bae Chung, Ye-Rang Yun, Sung-Hee Park, Sunggi Min, Lee-Seung Kwon, Hye-Young Seo
Fermentation.2021; 7(4): 308. CrossRef - Suitability Analysis of 17 Probiotic Type Strains of Lactic Acid Bacteria as Starter for Kimchi Fermentation
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Foods.2021; 10(6): 1435. CrossRef - Development of Edible Medium for Kimchi Starter, and Application of
Kimchi Fermentation Control
Chang Hee Jeong, Hye In Ko, Tae Woon Kim
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Annals of Microbiology.2020;[Epub] CrossRef - Improvement in the Quality of Kimchi by Fermentation with Leuconostoc mesenteroides ATCC 8293 as Starter Culture
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Journal of the Science of Food and Agriculture.2019; 99(14): 6474. CrossRef
- Effects of storage temperature on the diversity of white colony-forming yeast and correlations between bacterial and yeast communities in salted kimchi cabbage
- Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp
- Juseok Kim , Joon Yong Kim , Hye Seon Song , In-Tae Cha , Seong Woon Roh , Se Hee Lee
- J. Microbiol. 2019;57(6):444-449. Published online May 27, 2019
- DOI: https://doi.org/10.1007/s12275-019-8704-8
- 351 View
- 0 Download
- 6 Web of Science
- 6 Crossref
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Abstract
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- A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA- 4604T was observed at 10–40°C (optimum, 37°C), pH 6.0–10.0 (optimum, pH 7.0), and in the presence of 0–8.0% (w/v) NaCl (optimum, 0–2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA- 4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).
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Citations
Citations to this article as recorded by- Bacteroides faecium sp. nov. isolated from human faeces
Juseok Kim, Hye Seon Song, Joon Yong Kim, Tae Woong Whon, Won-Hyong Chung, Young-Do Nam, Yoon-E Choi, Seong Woon Roh
International Journal of Systematic and Evolutionary Microbiology.2023;[Epub] CrossRef - ODFM, an omics data resource from microorganisms associated with fermented foods
Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
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Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa
Anusha Rai, Smita N, Suresh G, Shabbir A, Deepshikha G, Sasikala Ch, Ramana Ch.V
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1720. CrossRef - Pectin Degradation is an Important Determinant for Alfalfa Silage Fermentation through the Rescheduling of the Bacterial Community
Bing Wang, Zhiqiang Sun, Zhu Yu
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- Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables
- Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh
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- 388 View
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- 23 Web of Science
- 22 Crossref
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Abstract
PDF
-
White colony-forming yeasts (WCFYs) often appear in fermented
foods, depending on the storage method. Despite
the ongoing research on fermented foods, the community
and genome features of WCFYs have not been well studied.
In this study, the community structures of WCFYs on fermented
vegetables (kimchi) prepared with various raw materials
were investigated using deep sequencing. Only eight
operational taxonomic units (OTUs) were detected, indicating
that the community structure of WCFYs on kimchi is very
simple. The five most abundant OTUs represented Pichia
kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora
uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables. -
Citations
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Mi-Ju Kim, Sung-gi Min, So Won Shin, Jiyong Shin, Hae-Yeong Kim
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Dmitry Mamaev, Renata Zvyagilskaya
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- Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea
- Eui-Sang Cho , In-Tae Cha , Hak-Jong Choi , Seong Woon Roh , Young-Do Nam , Sung Man Seo , Myung-Ji Seo
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- 316 View
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- 6 Web of Science
- 6 Crossref
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Abstract
PDF
- A yellow pigmented bacterium designated strain MBLN094T within the family Flavobacteriaceae was isolated from a halophyte Salicornia europaea on the coast of the Yellow Sea. This strain was a Gram-stain negative, aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain MBLN094T was found to be related to the genus Zunongwangia, exhibiting 16S rRNA gene sequence similarity values of 97.0, 96.8, 96.4, and 96.3% to Zunongwangia mangrovi P2E16T, Z. profunda SM-A87T, Z. atlantica 22II14-10F7T, and Z. endophytica CPA58T, respectively. Strain MBLN094T grew at 20‒37°C (optimum, 25‒ 30°C), at pH 6.0‒10.0 (optimum, 7.0‒8.0), and with 0.5‒15.0% (w/v) NaCl (optimum, 2.0‒5.0%). Menaquinone MK-6 was the sole respiratory quinone. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, and four unidentified lipids. Major fatty acids were iso-C17:0 3-OH, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and iso-C15:0. The genomic DNA G + C content was 37.4 mol%. Based on these polyphasic taxonomic data, strain MBLN094T is considered to represent a novel species of the genus Zunongwangia, for which the name Zunongwangia flava sp. nov. is proposed. The type strain is MBLN094T (= KCTC 62279T = JCM 32262T).
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Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment
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International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef - Validation List no. 206. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
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International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef - Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory
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Journal of Microbiology.2020; 58(5): 357. CrossRef - Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta
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Research Support, Non-U.S. Gov'ts
- Directed analysis of cyanobacterial membrane phosphoproteome using stained phosphoproteins and titanium-enriched phosphopeptides§
- Dong-Gi Lee , Joseph Kwon , Chi-Yong Eom , Young-Moon Kang , Seong Woon Roh , Kyung-Bok Lee , Jong-Soon Choi
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Abstract
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- Gel-free shotgun phosphoproteomics of unicellular cyanobacterium Synechocystis sp. PCC 6803 has not been reported up to now. The purpose of this study is to develop directed membrane phosphoproteomic method in Synechocystis sp. Total Synechocystis membrane proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and phosphoprotein-stained gel bands were selectively subjected to in-gel trypsin digestion. The phosphorylation sites of the resulting peptides were determined by assigning the neutral loss of [M-H3PO4] to Ser, Thr, and Tyr residues using nano-liquid chromatography 7 Tesla Fourier transform mass spectrometry. As an initial application, 111 proteins and 33 phosphoproteins were identified containing 11 integral membrane proteins. Identified four unknown phosphoproteins with transmembrane helices were suggested to be involved in membrane migration or transporters based on BLASTP search annotations. The overall distribution of hydrophobic amino acids in pTyr was lower in frequency than that of pSer or pThr. Positively charged amino acids were abundantly revealed in the surrounding amino acids centered on pTyr. A directed shotgun membrane phosphoproteomic strategy provided insight into understanding the fundamental regulatory processes underlying Ser, Thr, and Tyr phosphorylation in multi-layered membranous cyanobacteria.
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- Global Profiling of Protein Phosphorylation, Acetylation, and β-Hydroxybutyrylation in Nannochloropsis oceanica
- Citrimicrobium luteum gen. nov., sp. nov., Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Gut of a Sea Cucumber Stichopus japonicus
- Hong-Joo Jung , In-Tae Cha , Kyung June Yim , Hye Seon Song , Kichul Cho , Daekyung Kim , Hae-Won Lee , Jae Kook Lee , Myung-Ji Seo , Seong Woon Roh , Sung-Jae Lee
- J. Microbiol. 2014;52(10):819-824. Published online August 27, 2014
- DOI: https://doi.org/10.1007/s12275-014-4136-7
- 310 View
- 0 Download
- 1 Crossref
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Abstract
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- A Gram-stain negative, yellow-pigmented, motile, pleomorphic bacterium, designated strain CBA4602T, was isolated from the gut of the sea cucumber Stichopus japonicus, which was collected from Jeju Island in the Republic of Korea. In a phylogenetic analysis based on the 16S rRNA gene, strain CBA4602T belonged to the order Sphingomonadales in the class Alphaproteobacteria. The 16S rRNA gene sequence similarity between strain CBA4602T and ‘Citromicrobium bathyomarinum’ JF-1, the most closely related strain having nonvalidly published name, was 98.4%, followed by 95.2–96.7% identities with sequence of the other closest strains in the genus Erythrobacter. Strain CBA4602T had bacteriochlorophyll a and carotenoids. Strain CBA4602T grew in 0–10% (w/v) NaCl, at 10–42°C and pH 6.0–8.0, with optimal growth in 1–2% NaCl, at 30–37°C and pH 7.0. Strain CBA4602T was positive for catalase and oxidase activities and was able to hydrolyse gelatine and Tween 20 and 40, but not starch, Tween 80 or L-tyrosine. The G+C content of genomic DNA from strain CBA4602T was 68.0 mol% and Q-10 was the major detected isoprenoid quinone. The polar lipids were three unidentified phospholipids, three unidentified glycolipids, and two unidentified lipids. The dominant fatty acids were anteiso-C15:0, C16:0, anteiso-C17:0 and C18:0. As considering the current taxonomic status of the genus ‘Citromicrobium’ and polyphasic taxonomic analyses, strain CBA4602T represents a novel genus and species. The name Citrimicrobium luteum is proposed for the type strain CBA4602T (=KACC 17668T =JCM 19530T).
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Citations
Citations to this article as recorded by- Association of aerobic anoxygenic phototrophs and zebra mussels, Dreissena polymorpha, within the littoral zone of Lake Winnipeg
Steven Brady Kuzyk, Kaitlyn Wiens, Xiao Ma, Vladimir Yurkov
Journal of Great Lakes Research.2021; 47(3): 567. CrossRef
- Association of aerobic anoxygenic phototrophs and zebra mussels, Dreissena polymorpha, within the littoral zone of Lake Winnipeg
- Rhodopirellula rosea sp. nov., a Novel Bacterium Isolated from an Ark Clam Scapharca broughtonii
- Seong Woon Roh , Hae-Won Lee , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Na-Lae Lim , Daekyung Kim , Jin-Woo Bae
- J. Microbiol. 2013;51(3):301-304. Published online June 28, 2013
- DOI: https://doi.org/10.1007/s12275-013-3210-x
- 213 View
- 0 Download
- 16 Scopus
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Abstract
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- A novel Gram-negative, motile, and ovoid-shaped strain, LHWP3T, which belonged to the family Planctomycetaceae in the phylum Planctomycetes, was isolated from a dead ark clam Scapharca broughtonii collected during a mass mortality event on the south coast of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the isolate was most closely related to the type strain of Rhodopirellula baltica, with a shared 16S rRNA gene sequence similarity of 94.8%. The isolate grew optimally at 30°C in 4–6% (w/v) NaCl, and at pH 7. The major isoprenoid quinone was menaquinone-6 (MK-6). The dominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified polar lipids. The predominant cellular fatty acids were C16:0, C18:1 ω9c, and C18:0. The genomic DNA G+C content of strain LHWP3T was 53.0 mol%. Based on polyphasic taxonomic analyses, strain LHWP3T should be classified as a novel species in the genus Rhodopirellula in the family Planctomycetaceae, for which the name Rhodopirellula rosea sp. nov. is proposed. The type strain is LHWP3T (=KACC 15560T =JCM 17759T).
- Paenibacillus marinisediminis sp. nov., a Bacterium Isolated from Marine Sediment
- Hae-Won Lee , Seong Woon Roh , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Joon Yong Kim , Dong-Wook Hyun , Daekyung Kim , Jin-Woo Bae
- J. Microbiol. 2013;51(3):312-317. Published online June 28, 2013
- DOI: https://doi.org/10.1007/s12275-013-3198-2
- 199 View
- 0 Download
- 13 Scopus
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Abstract
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- A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35T was most closely related to Paenibacillus taiwanensis G-soil-2-3T (97.2% similarity). The optimal growth conditions for strain LHW35T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C15:0 and C16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified aminohospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35T (=KACC 16317T =JCM 17886T).
- Ruminococcus faecis sp. nov., Isolated from Human Faeces
- Min-Soo Kim , Seong Woon Roh , Jin-Woo Bae
- J. Microbiol. 2011;49(3):487-491. Published online June 30, 2011
- DOI: https://doi.org/10.1007/s12275-011-0505-7
- 219 View
- 0 Download
- 14 Crossref
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Abstract
PDF
- Bacterial strain Eg2T, an anaerobic, Gram-positive, non-motile, and non-spore-forming coccus, was isolated from human faeces. The optimal temperature for its growth was 37°C. Oxidase activity was negative, but catalase activity was positive. The strain was able to hydrolyze esculin and to produce acids from the fermentation of several substrates, including glucose. Lactic and acetic acids were the main products of glucose fermentation. The major fatty acids present in this strain were C16:0, C14:0, and C18:1 cis11 DMA. The G+C content was 43.4 mol%. Based on the 16S rRNA gene sequence, strain Eg2T was closely related to species of the genus Ruminococcus (96.3% similarity to R. torques and 96.2% similarity to R. lactaris), and its taxonomic position was placed within the Clostridium cluster XIVa. Based on phenotypic, chemotaxonomic, genotypic, and phylogenetic evidence, we propose that this novel strain be assigned to the genus Ruminococcus and be named Ruminococcus faecis sp. nov. The type strain is Eg2T (=KCTC 5757T =JCM 15917T).
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Feng‐Qi Liu, Zhuo‐Yu An, Li‐Juan Cui, Meng‐Yu Xiao, Ye‐Jun Wu, Wei Li, Bang‐Shuo Zhang, Li Yu, Jia Feng, Zhuo‐Gang Liu, Ru Feng, Zhong‐Xing Jiang, Rui‐Bin Huang, Hong‐Mei Jing, Jin‐Hai Ren, Xiao‐Yu Zhu, Yun‐Feng Cheng, Yu‐Hua Li, He‐Bing Zhou, Da Gao, Yi
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Valeria Alvarado, Shu-Chien Hsu, Zhuoying Wu, Huichuan Zhuang, Po-Heng Lee, Jeremy S. Guest
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- NOTE] Oceanobacillus kimchii sp. nov. Isolated from a Traditional Korean Fermented Food
- Tae Woong Whon , Mi-Ja Jung , Seong Woon Roh , Young-Do Nam , Eun-Jin Park , Kee-Sun Shin , Jin-Woo Bae
- J. Microbiol. 2010;48(6):862-866. Published online January 9, 2011
- DOI: https://doi.org/10.1007/s12275-010-0214-7
- 336 View
- 0 Download
- 31 Crossref
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Abstract
PDF
- A moderate halophile, strain X50T, was isolated from mustard kimchi, a traditional Korean fermented food. The organism grew under conditions ranging from 0-15.0% (w/v) NaCl (optimum: 3.0%), pH 7.0-10.0 (optimum: pH 9.0) and 15-45°C (optimum: 37°C). The morphological, physiological, and biochemical features and the 16S rRNA gene sequences of strain X50T were characterized. Colonies of the isolate were creamcolored and the cells were rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X50T belongs to the genus Oceanobacillus and is closely related phylogenetically to the type strain O. iheyensis HTE831T (98.9%) and O. oncorhynchi subsp. oncorhynchi R-2T (97.0%). The cellular fatty acid profiles predominately included anteiso-C15:0 and iso-C15:0. The G+C content of the genomic DNA of the isolate was 37.9 mol% and the major isoprenoid quinone was MK-7. Analysis of the 16S rRNA gene sequences, DNA-DNA relatedness and physiological and biochemical tests indicated genotypic and phenotypic differences among strain X50T and reference species in the genus Oceanobacillus. Therefore, strain X50T was proposed as a novel species and named Oceanobacillus kimchii. The type strain of the new species is X50T (=JCM 16803T =KACC 14914T =DSM 23341T).
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Citations
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- NOTE] Halomonas jeotgali sp. nov., a New Moderate Halophilic Bacterium Isolated from a Traditional Fermented Seafood
- Min-Soo Kim , Seong Woon Roh , Jin-Woo Bae
- J. Microbiol. 2010;48(3):404-410. Published online June 23, 2010
- DOI: https://doi.org/10.1007/s12275-010-0032-y
- 190 View
- 0 Download
- 24 Crossref
-
Abstract
PDF
- A moderate halophilic, Gram-negative, non-motile, rod-shape, and aerobe designated as strain HwaT was isolated from traditional fermented Korean seafood, which presented as a single cell or paired cells. Optimal growth occurred at 25°C in 10% (w/v) salts at pH 7.0-8.0; however, growth occurred in a temperature range of 10-32°C, a salts concentration of 5-25% (w/v) and pH 5.0-10.0. Tests for oxidase and catalase were positive. The cells produced poly-β-hydroxybutyric acid, but not exopolysaccharide. Based on the 16S rRNA gene sequence, not only was there low similarity between strain HwaT and all other species (94.1% similarity with H. subglaciescola DSM 4683T, 94.0% similarity with H. sulfidaeris Esulfide1T, 93.6% similarity with H. cerina SP4T and 93.0% similarity with H. halodurans DSM 5160T), but the phylogenetic analysis revealed that the isolate may be classified as a novel species belonging to the genus Halomonas in the class Gammaproteobacteria. The predominant fatty acids of strain HwaT were C18:1 ω7c, C16:0, C12:0 3-OH and C16:1 ω7c/C15:0 iso 2-OH. The DNA G+C content was calculated as 61.7 mol%. Based on phenotypic, genotypic, and phylogenetic characteristics, it is proposed that the strain designated as HwaT be assigned to the genus Halomonas as Halomonas jeotgali sp. nov. (=KCTC 22487T =JCM 15645T).
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Citations
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Shohei Katsuya, Yoshikazu Kawata, Masayuki Sugimoto, Taku Nishimura, Jun Tsubota
Bioscience, Biotechnology, and Biochemistry.2024; 88(9): 1073. CrossRef - Sporosarcina jeotgali sp. nov., Sporosarcina oncorhynchi sp. nov., and Sporosarcina trichiuri sp. nov., Isolated from Jeotgal, a Traditional Korean Fermented Seafood
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- Phenotypic Characterization and Genomic Analysis of the Shigella sonnei Bacteriophage SP18
- Kyoung-Ho Kim , Ho-Won Chang , Young-Do Nam , Seong Woon Roh , Jin-Woo Bae
- J. Microbiol. 2010;48(2):213-222. Published online May 1, 2010
- DOI: https://doi.org/10.1007/s12275-010-0055-4
- 225 View
- 0 Download
- 12 Crossref
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Abstract
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- A novel bacteriophage that infects Shigella sonnei was isolated from the Gap River in Korea, and its phenotypic and genomic characteristics were investigated. The virus, called SP18, showed morphology characteristic of the family Myoviridae, and phylogenetic analysis of major capsid gene (gp23) sequences classified it as a T4-like phage. Based on host spectrum analysis, it is lytic to S. sonnei, but not to Shigella flexneri, Shigella boydii or members of the genera Escherichia and Salmonella. Pyrosequencing of the SP18 bacteriophage genome revealed a 170-kb length sequence. In total, 286 ORFs and 3 tRNA genes were identified, and 259 ORFs showed similarity (BLASTP e-value<0.001) to genes of other bacteriophages. The results from comparative genomic analysis indicated that the enterophage JS98, isolated from human stool, is the closest relative of SP18. Based on phylogenetic analysis of gp23 protein-coding sequences, dot plot comparison and BLASTP analysis of genomes, SP18 and JS98 appear to be closely related to T4-even phages. However, several insertions, deletions, and duplications indicate differences between SP18 and JS98. Comparison of duplicated gp24 genes and the soc gene showed that duplication events are responsible for the differentiation and evolution of T4-like bacteriophages.
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- Application of Quantitative Real-Time PCR for Enumeration of Total Bacterial, Archaeal, and Yeast Populations in Kimchi
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- 198 View
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- 37 Scopus
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Abstract
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- Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45×106 which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.
- Halorubrum cibi sp. nov., an Extremely Halophilic Archaeon from Salt-Fermented Seafood
- Seong Woon Roh , Jin-Woo Bae
- J. Microbiol. 2009;47(2):162-166. Published online May 2, 2009
- DOI: https://doi.org/10.1007/s12275-009-0016-y
- 267 View
- 0 Download
- 22 Crossref
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Abstract
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- Strain B31T is a Gram-staining-negative, motile, and extremely halophilic archaeon that was isolated from salt-fermented seafood. Its morphology, physiology, biochemical features, and 16S rRNA gene sequence were determined. Phylogenetic analysis of its 16S rRNA gene sequence and composition of its major polar lipids placed this archaeon in the genus Halorubrum of the family Halobacteriaceae. Strain B31T showed 97.3, 97.2, and 96.9% 16S rRNA similarity to the type strains of Halorubrum alkaliphilum, Hrr. tibetense, and Hrr. vacuolatum, respectively. Its major polar lipids were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulfated diglycosyl diether (S-DGD). Genomic DNA from strain B31T has a 61.7 mol% G+C content. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified genotypic and phenotypic differences between strain B31T and other Halorubrum species. The type strain of the novel species is B31T (=JCM 15757T =DSM 19504T).
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Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes
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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(9): 2129. CrossRef
- Tissue-like multicellular development triggered by mechanical compression in archaea
- Henriciella marina gen. nov., sp. nov., a Novel Member of the Family Hyphomonadaceae Isolated from the East Sea
- Zhe-Xue Quan , Dan-Ning Zeng , Yi-Ping Xiao , Seong Woon Roh , Young-Do Nam , Ho-Won Chang , Jung-Hoon Yoon , Hee-Mock Oh , Jin-Woo Bae
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- DOI: https://doi.org/10.1007/s12275-008-0290-0
- 282 View
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- 15 Crossref
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Abstract
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- A bacterial strain, designated Iso4T, was isolated from the East Sea of Korea and was subjected to a polyphasic taxonomy study including phenotypic and chemotaxonomic characteristics as well as 16S rRNA gene sequence analysis. Cells of the strain were Gram-negative, motile, non-budding, non-stalked, and strictly aerobic. Strain Iso4T grew optimally at 20°C in the presence of 1~2% (w/v) NaCl and at pH 6.9~7.6. The major respiratory quinone was Q-10 and the major cellular fatty acids were C18:1 ω7c (53.5%), C17:1 ω5c (11.7%), C17:1 ω6c (8.1%), C16:0 (7.8%), C17:0 (4.8%), C15:0 (2.9%), and C16:1 ω5c (2.2%). The DNA G+C content of strain Iso4T was 56.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Iso4T formed a monophyletic clade in the family Hyphomonadaceae, supported by high bootstrap value and was most closely related to the genus Hyphomonas (92~94%), a member of marine bacteria in the family. The phenotypic, genotypic, and chemotaxonomic evidences also suggest strain Iso4T represents a novel genus and species in the family Hyphomonadaceae, for which the name Henriciella gen. nov., sp. nov. is proposed. The type strain is Iso4T (=KCTC 12513T =DSM 19595T =JCM 15116T).
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Citations
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David R. Arahal, Hans-Jürgen Busse, Carolee T. Bull, Henrik Christensen, Maria Chuvochina, Svetlana N. Dedysh, Pierre-Edouard Fournier, Konstantinos T. Konstantinidis, Charles T. Parker, Ramon Rosselló-Móra, Antonio Ventosa, Markus Göker
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- Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People
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- DOI: https://doi.org/10.1007/s12275-008-0199-7
- 294 View
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- 66 Crossref
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Abstract
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- The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).
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- NOTE] Aliihoeflea aestuarii gen. nov., sp. nov., a Novel Bacterium Isolated from Tidal Flat Sediment
- Seong Woon Roh , Kyoung-Ho Kim , Young-Do Nam , Ho-Won Chang , Min-Soo Kim , Kee-Sun Shin , Jung-Hoon Yoon , Hee-Mock Oh , Jin-Woo Bae
- J. Microbiol. 2008;46(5):594-598. Published online October 31, 2008
- DOI: https://doi.org/10.1007/s12275-008-0196-x
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Abstract
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- A novel Gram-negative and rod-shaped bacterium, designated N8T, was isolated from tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences showed that N8T strain is associated with the family Phyllobacteriaceae: two uncultured clones (98.4 and 99.8% 16S rRNA gene sequence similarity) and the genus Mesorhizobium (≤97.0%). The novel strain formed a separate clade with uncultured clones in the phylogenetic tree based on 16S rRNA gene sequences. Cellular fatty acid profiles predominately comprised C18:1 ω7c and C19:0 cyclo ω8c. The major isoprenoid quinone is ubiquinone-10 and genomic DNA G+C content is 53.4 mol%. The polyphasic taxonomic study indicates that the novel strain N8T represents a novel species of the new genus in the family Phyllobacteriaceae, named Aliihoeflea aestuarii. The type strain is N8T (= KCTC 22052T= JCM 15118T= DSM 19536T).
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Abstract
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- A novel bacterium B9T was isolated from tidal flat sediment. Its morphology, physiology, biochemical features, and 16S rRNA gene sequence were characterized. Colonies of this strain are yellow and the cells are Gram-negative, rod-shaped, and do not require NaCl for growth. The 16S rRNA gene sequence similarity indicated that strain B9T is associated with the genus Lysobacter (≤ 97.2%), Xanthomonas (≤ 96.8%), Pseudomonas (≤ 96.7%), and Luteimonas (≤ 96.0%). However, within the phylogenetic tree, this novel strain shares a branching point with the species Luteimonas composti CC-YY255T (96.0%). The DNA-DNA hybridization experiments showed a DNA-DNA homology of 23.0% between strain B9T and Luteimonas mephitis B1953/27.1T. The G+C content of genomic DNA of the type strain is 64.7 mol% (SD, 1.1). The predominant fatty acids are iso-C11:0, iso-C15:0, iso-C16:0, iso-C17:0, iso-C17:1 ω9c, and iso-C11:0 3-OH. Combined analysis of the 16S rRNA gene sequences, fatty acid profile, and results from physiological and biochemical tests indicated that there is genotypic and phenotypic differentiation of the isolate from other Luteimonas species. For these reasons, strain B9T was proposed as a novel species, named Luteimonas aestuarii. The type strain of the new species is B9T (= KCTC 22048T, DSM 19680T).
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- Characterization of the Depth-Related Changes in the Microbial Communities in Lake Hovsgol Sediment by 16S rRNA Gene-Based Approaches
- Young-Do Nam , Youlboong Sung , Ho-Won Chang , Seong Woon Roh , Kyoung-Ho Kim , Sung-Keun Rhee , Jung-Chan Kim , Joo-Yong Kim , Jung-Hoon Yoon , Jin-Woo Bae
- J. Microbiol. 2008;46(2):125-136. Published online June 11, 2008
- DOI: https://doi.org/10.1007/s12275-007-0189-1
- 191 View
- 0 Download
- 28 Scopus
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Abstract
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- The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial <br>communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39~42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta- and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria <br>(some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly deteced by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the <br>archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing <br>depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.
- Arthrobacter soli sp. nov., a Novel Bacterium Isolated from Wastewater Reservoir Sediment
- Seong Woon Roh , Youlboong Sung , Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Jung-Hoon Yoon , Che Ok Jeon , Hee-Mock Oh , Jin-Woo Bae
- J. Microbiol. 2008;46(1):40-44.
- DOI: https://doi.org/10.1007/s12275-007-0239-8
- 269 View
- 0 Download
- 73 Crossref
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Abstract
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- A novel Gram-positive bacterium, designated SYB2T, was isolated from wastewater reservoir sediment, and a polyphasic taxonomic study was conducted based on its morphological, physiological, and biochemical features, as well as the analysis of its 16S rRNA gene sequence. During the phylogenetic analysis of the strain SYB2T, results of a 16S rRNA gene sequence analysis placed this bacterium in the genus Arthrobacter within the family Micrococcaceae. SYB2T and Arthrobacter protophormiae ATCC 19271T, the most closely related species, both exhibited a 16S rRNA gene sequence similarity of 98.99%. The genomic DNA G+C content of the novel strain was found to be 62.0 mol%. The predominant fatty acid composition was anteiso-C15:0, anteiso-C17:0, iso-C16:0, and iso-C15:0. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness, as well as physiological and biochemical tests, showed genotypic and phenotypic differences between strain SYB2T and other Arthrobacter species. The type strain of the novel species was identified as SYB2T (= KCTC 19291T= DSM 19449T).
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Gillisia
Seong Woon Roh, Myunglip Lee, Hae-Won Lee, Kyung June Yim, Soo Yeon Heo, Kil-Nam Kim, Changmann Yoon, Young-Do Nam, Joon Yong Kim, Dong-Wook Hyun, Jin-Woo Bae, Joon Bum Jeong, Heewan Kang, Daekyung Kim
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_10): 3640. CrossRef - Rhodopirellula rosea sp. nov., a novel bacterium isolated from an ark clam Scapharca broughtonii
Seong Woon Roh, Hae-Won Lee, Kyung June Yim, Na-Ri Shin, Jina Lee, Tae Woong Whon, Na-Lae Lim, Daekyung Kim, Jin-Woo Bae
Journal of Microbiology.2013; 51(3): 301. CrossRef -
Paenibacillus oceanisediminis sp. nov. isolated from marine sediment
Jina Lee, Na-Ri Shin, Mi-Ja Jung, Seong Woon Roh, Min-Soo Kim, Jung-Sook Lee, Keun Chul Lee, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_2): 428. CrossRef -
Ferrimonas
pelagia sp. nov., isolated from seawater
Kyung June Yim, Myunglip Lee, Hae-Won Lee, Kil-Nam Kim, Hye-Mi Yang, Mi-Ju Kim, Dong-Wook Hyun, Jin-Woo Bae, Young-Do Nam, Changmann Yoon, Moo-Sang Kim, Seong Woon Roh, Daekyung Kim
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_9): 3175. CrossRef -
Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus
Kistimonas
Jina Lee, Na-Ri Shin, Hae-Won Lee, Seong Woon Roh, Min-Soo Kim, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_12): 2865. CrossRef -
Tropicimonas sediminicola sp. nov., isolated from marine sediment
Na-Ri Shin, Seong Woon Roh, Min-Soo Kim, Bora Yun, Tae Woong Whon, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_10): 2424. CrossRef -
Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food
Jandi Kim, Mi-Ja Jung, Seong Woon Roh, Young-Do Nam, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(12): 2851. CrossRef -
Microbacterium mitrae sp. nov., isolated from salted turban shell
Yun-Ji Kim, Seong Woon Roh, Mi-Ja Jung, Min-Soo Kim, Eun-Jin Park, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(2): 399. CrossRef -
Dietzia alimentaria sp. nov., isolated from a traditional Korean food
Jandi Kim, Seong Woon Roh, Jung-Hye Choi, Mi-Ja Jung, Young-Do Nam, Min-Soo Kim, Eun-Jin Park, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(9): 2254. CrossRef -
Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil
Lars Ganzert, Felizitas Bajerski, Kai Mangelsdorf, André Lipski, Dirk Wagner
International Journal of Systematic and Evolutionary Microbiology .2011; 61(4): 979. CrossRef - Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Eun-Jin Park, Jin-Woo Bae
The ISME Journal.2010; 4(1): 1. CrossRef -
Kocuria koreensis sp. nov., isolated from fermented seafood
Eun-Jin Park, Seong Woon Roh, Min-Soo Kim, Mi-Ja Jung, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(1): 140. CrossRef - Arthrobacter antarcticus sp. nov., isolated from an Antarctic marine sediment
Pavan Kumar Pindi, Ruth Manorama, Zareena Begum, S. Shivaji
International Journal of Systematic and Evolutionary Microbiology.2010; 60(10): 2263. CrossRef - Oceanobacillus kimchii sp. nov. Isolated from a traditional Korean fermented food
Tae Woong Whon, Mi-Ja Jung, Seong Woon Roh, Young-Do Nam, Eun-Jin Park, Kee-Sun Shin, Jin-Woo Bae
The Journal of Microbiology.2010; 48(6): 862. CrossRef -
Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood
Eun-Jin Park, Min-Soo Kim, Seong Woon Roh, Mi-Ja Jung, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(4): 914. CrossRef - Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus
Seong Woon Roh, Myung-Lip Lee, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2010; 60(5): 1187. CrossRef -
Agromyces atrinae sp. nov., isolated from fermented seafood
Eun-Jin Park, Min-Soo Kim, Mi-Ja Jung, Seong Woon Roh, Ho-Won Chang, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(5): 1056. CrossRef - Arthrobacter halodurans sp. nov., a new halotolerant bacterium isolated from sea water
Yi-Guang Chen, Shu-Kun Tang, Yu-Qin Zhang, Zhao-Yang Li, Lang-Bo Yi, Yong-Xia Wang, Wen-Jun Li, Xiao-Long Cui
Antonie van Leeuwenhoek.2009; 96(1): 63. CrossRef - Paracoccus aestuarii sp. nov., isolated from tidal flat sediment
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-S. Kim, K.-S. Shin, J.-H. Yoon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(4): 790. CrossRef - Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, Y. Sung, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(9): 2359. CrossRef - Nocardioides basaltis sp. nov., isolated from black beach sand
K.-H. Kim, S. W. Roh, H.-W. Chang, Y.-D. Nam, J.-H. Yoon, C. O. Jeon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(1): 42. CrossRef - Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(2): 421. CrossRef - Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment
S. W. Roh, K.-H. Kim, Y.-D. Nam, H.-W. Chang, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(6): 1359. CrossRef - Halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood
Seong Woon Roh, Jin-Woo Bae
The Journal of Microbiology.2009; 47(2): 162. CrossRef - Nitratireductor basaltis sp. nov., isolated from black beach sand
K.-H. Kim, S. W. Roh, H.-W. Chang, Y.-D. Nam, J.-H. Yoon, C. O. Jeon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(1): 135. CrossRef - Phylogenetic Characterization of Two Novel Commensal Bacteria Involved with Innate Immune Homeostasis inDrosophila melanogaster
Seong Woon Roh, Young-Do Nam, Ho-Won Chang, Kyoung-Ho Kim, Min-Soo Kim, Ji-Hwan Ryu, Sung-Hee Kim, Won-Jae Lee, Jin-Woo Bae
Applied and Environmental Microbiology.2008; 74(20): 6171. CrossRef - Marinobacter goseongensis sp. nov., from seawater
S. W. Roh, Z.-X. Quan, Y.-D. Nam, H.-W. Chang, K.-H. Kim, S.-K. Rhee, H.-M. Oh, C. O. Jeon, J.-H. Yoon, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(12): 2866. CrossRef - Genomics of biological wastewater treatment
Roland J. Siezen, Marco Galardini
Microbial Biotechnology.2008; 1(5): 333. CrossRef - List of new names and new combinations previously effectively, but not validly, published
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(9): 1993. CrossRef - Luteimonas aestuarii sp. nov., isolated from tidal flat sediment
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Min-Soo Kim, Jung-Hoon Yoon, Hee-Mock Oh, Jin-Woo Bae
The Journal of Microbiology.2008; 46(5): 525. CrossRef - Marinomonas basaltis sp. nov., a marine bacterium isolated from black sand
H.-W. Chang, S. W. Roh, K.-H. Kim, Y.-D. Nam, J.-H. Yoon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(12): 2743. CrossRef - Aliihoeflea aestuarii gen. nov., sp. nov., a novel bacterium isolated from tidal flat sediment
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Min-Soo Kim, Kee-Sun Shin, Jung-Hoon Yoon, Hee-Mock Oh, Jin-Woo Bae
The Journal of Microbiology.2008; 46(5): 594. CrossRef
- Dependence of the Adaptation of the Strain Glutamicibacter sp. SMB32 to a High Salinity Environment Depending on Growth Stage and Temperature
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