- Proposal of Flavihumibacter fluvii sp. nov. as a replacement name for the effectively published but invalidated epithet Flavihumibacter fluminis Park et al. 2022
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Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho
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J. Microbiol. 2023;61(6):649-651. Published online June 12, 2023
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DOI: https://doi.org/10.1007/s12275-023-00057-1
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82
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 Abstract
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The name Flavihumibacter fluminis Park et al. 2022, which was effectively published but invalidated, is an illegitimate
homonymic epithet of Flavihumibacter fluminis Guo et al. 2023. The low 16S rRNA gene sequence similarity and genomic
relatedness between the type strains IMCC34837T
and RY-1T of the two homonymic species indicated that they are different
species. To avoid further confusion, we propose a new name Flavihumibacter fluvii sp. nov. to replace the effectively
published but invalidated homonymic epithet Flavihumibacter fluminis Park et al. 2022.
-
Citations
Citations to this article as recorded by  - Validation List no. 214. 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
- Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre
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Hyunyoung Jo , Miri S. Park , Yeonjung Lim , Ilnam Kang , Jang-Cheon Cho
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J. Microbiol. 2023;61(5):495-510. Published online May 23, 2023
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DOI: https://doi.org/10.1007/s12275-023-00054-4
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91
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9
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8
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Abstract
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Eleven bacterial strains were isolated from freshwater environments and identified as Flavobacterium based on 16S rRNA
gene sequence analyses. Complete genome sequences of the 11 strains ranged from 3.45 to 5.83 Mb with G + C contents
of 33.41–37.31%. The average nucleotide identity (ANI) values showed that strains IMCC34515T
and IMCC34518 belonged to the same species, while the other nine strains represented each separate species. The ANI values between
the strains and their closest Flavobacterium species exhibited ≤ 91.76%, indicating they represent each novel species. All
strains had similar characteristics such as being Gram-stain-negative, rod-shaped, and contained iso-C15:0 as the predominant
fatty acid, menaquinone-6 as the respiratory quinone, and phosphatidylethanolamine and aminolipids as major polar
lipids. Genomic, phylogenetic, and phenotypic characterization confirmed that the 11 strains were distinct from previously
recognized Flavobacterium species. Therefore, Flavobacterium praedii sp. nov. (IMCC34515T = KACC 22282T = NBRC 114937T),
Flavobacterium marginilacus sp. nov. (IMCC34673T = KACC 22284T = NBRC 114940T), Flavobacterium aestivum sp. nov.
(IMCC34774T = KACC 22285T = NBRC 114941T), Flavobacterium flavigenum sp. nov. (IMCC34775T = KACC22286T = NBRC 114942T),
Flavobacterium luteolum sp. nov. (IMCC34776T = KACC 22287T = NBRC 114943T), Flavobacterium gelatinilyticum sp. nov.
(IMCC34777T = KACC 22288T = NBRC 114944T), Flavobacterium aquiphilum sp.nov. (IMCC34779T = KACC 22289T = NBRC 114945T),
Flavobacterium limnophilum sp. nov. (IMCC36791T = KACC22290T = NBRC 114947T), Flavobacterium lacustre sp. nov.
(IMCC36792T = KACC 22291T = NBRC 114948T), and Flavobacterium eburneipallidum sp. nov. (IMCC36793T = KACC 22292T = NBRC 114949T)
are proposed as novel species.
-
Citations
Citations to this article as recorded by - Indoor pollution of funeral homes and potential health risk of workers: A case study in central China
Jinjun Ye, Zhengtao Ai, Lup Wai Chew
Building and Environment.2025; 272: 112677. CrossRef -
Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues
Leonor Matos, Lorrie Maccarrio, Ana Paula Chung, Diogo N. Proença, Søren Sørensen, Paula V. Morais, Romeu Francisco
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
Systematic and Applied Microbiology.2024; 47(4): 126518. CrossRef - Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
Journal of Microbiology.2024; 62(12): 1089. CrossRef - Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions
Jegadeesh Raman, Young-Joon Ko, Jeong-Seon Kim, Da-Hye Kim, Soo-Jin Kim
Journal of Microbiology and Biotechnology.2024; 34(3): 710. CrossRef - Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] 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 - Validation List no. 213. 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
- Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream
-
Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho
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J. Microbiol. 2022;60(8):806-813. Published online July 29, 2022
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DOI: https://doi.org/10.1007/s12275-022-2298-2
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84
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6
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Abstract
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Two Gram-stain-positive, aerobic, chemoheterotrophic, nonmotile,
rod-shaped, and yellow-pigmented bacterial strains,
designated IMCC34837T and IMCC34838T, were isolated from
a freshwater stream. Results of 16S rRNA gene-based phylogenetic
analyses showed that strains IMCC34837T and IMCC-
34838T shared 96.3% sequence similarity and were most closely
related to Flavihumibacter profundi Chu64-6-1T (99.6%)
and Flavihumibacter cheonanensis WS16T (96.4%), respectively.
Complete whole-genome sequences of strains IMCC-
34837T and IMCC34838T were 5.0 Mbp and 4.3 Mbp of genome
size with 44.5% and 47.9% of DNA G + C contents,
respectively. Average nucleotide identity (ANI) and digital
DNA- DNA hybridization (dDDH) values between the two
strains were 70.0% and 17.9%, repectively, revealing that they
are independent species. The two strains showed ≤ 75.2% ANI
and ≤ 19.3% dDDH values to each closely related species of the
genus Flavihumibacter, indicating that the two strains represent
each novel species. Major fatty acid constituents of
strain IMCC34837T were iso-C15:0, iso-C15:1 G and anteiso-C15:0
and those of strain IMCC34838T were iso-C15:0 and iso-C15:1
G. The predominant isoprenoid quinone detected in both
strains was menaquinone-7 (MK-7). Major polar lipids of
both strains were phosphatidylethanolamine, aminolipids,
and glycolipids. Based on the phylogenetic and phenotypic
characterization, strains IMCC34837T and IMCC34838T were
considered to represent two novel species within the genus
Flavihumibacter, for which the names Flavihumibacter fluminis
sp. nov. and Flavihumibacter rivuli sp. nov. are proposed
with IMCC34837T (= KACC 21752T = NBRC 115292T)
and IMCC34838T (= KACC 21753T = NBRC 115293T) as
the type strains, respectively.
-
Citations
Citations to this article as recorded by - Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Raúl Riesco, Martha E. Trujillo
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
Journal of Microbiology.2024; 62(12): 1089. 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 - Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef - Validation List no. 211. 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 - Proposal of Flavihumibacter fluvii sp. nov. as a replacement name for the effectively published but invalidated epithet Flavihumibacter fluminis Park et al. 2022
Miri S. Park, Hyeonuk Sa, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(6): 649. CrossRef
- Metaviromics coupled with phage-host identification to open the viral ‘black box’
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Kira Moon , Jang-Cheon Cho
-
J. Microbiol. 2021;59(3):311-323. Published online February 23, 2021
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DOI: https://doi.org/10.1007/s12275-021-1016-9
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70
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9
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9
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Abstract
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Viruses are found in almost all biomes on Earth, with bacteriophages
(phages) accounting for the majority of viral particles
in most ecosystems. Phages have been isolated from
natural environments using the plaque assay and liquid medium-
based dilution culturing. However, phage cultivation is
restricted by the current limitations in the number of culturable
bacterial strains. Unlike prokaryotes, which possess
universally conserved 16S rRNA genes, phages lack universal
marker genes for viral taxonomy, thus restricting cultureindependent
analyses of viral diversity. To circumvent these
limitations, shotgun viral metagenome sequencing (i.e., metaviromics)
has been developed to enable the extensive sequencing
of a variety of viral particles present in the environment
and is now widely used. Using metaviromics, numerous
studies on viral communities have been conducted in oceans,
lakes, rivers, and soils, resulting in many novel phage sequences.
Furthermore, auxiliary metabolic genes such as ammonic
monooxygenase C and β-lactamase have been discovered
in viral contigs assembled from viral metagenomes.
Current attempts to identify putative bacterial hosts of viral
metagenome sequences based on sequence homology have
been limited due to viral sequence variations. Therefore, culture-
independent approaches have been developed to predict
bacterial hosts using single-cell genomics and fluorescentlabeling.
This review focuses on recent viral metagenome
studies conducted in natural environments, especially in aquatic
ecosystems, and their contributions to phage ecology.
Here, we concluded that although metaviromics is a key tool
for the study of viral ecology, this approach must be supplemented
with phage-host identification, which in turn requires
the cultivation of phage-bacteria systems.
-
Citations
Citations to this article as recorded by - Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
Joanna Warwick-Dugdale, Funing Tian, Michelle L. Michelsen, Dylan R. Cronin, Karen Moore, Audrey Farbos, Lauren Chittick, Ashley Bell, Ahmed A. Zayed, Holger H. Buchholz, Luis M. Bolanos, Rachel J. Parsons, Michael J. Allen, Matthew B. Sullivan, Ben Tempe
Nature Communications.2024;[Epub] CrossRef - Tools and methodology to in silico phage discovery in freshwater environments
Carlos Willian Dias Dantas, David Tavares Martins, Wylerson Guimarães Nogueira, Oscar Victor Cardenas Alegria, Rommel Thiago Jucá Ramos
Frontiers in Microbiology.2024;[Epub] CrossRef - A Pseudomonas Lysogenic Bacteriophage Crossing the Antarctic and Arctic, Representing a New Genus of Autographiviridae
Zhenyu Liu, Wenhui Jiang, Cholsong Kim, Xiaoya Peng, Cong Fan, Yingliang Wu, Zhixiong Xie, Fang Peng
International Journal of Molecular Sciences.2023; 24(8): 7662. CrossRef - Evaluation of the ABL NGS assay for HIV-1 drug resistance testing
Thomas Lhossein, Karine Sylvain, Véronique Descamps, Virginie Morel, Baptiste Demey, Etienne Brochot
Heliyon.2023; 9(11): e22210. CrossRef - Human virome: Implications in cancer
Rafael Tamayo-Trujillo, Patricia Guevara-Ramírez, Santiago Cadena-Ullauri, Elius Paz-Cruz, Viviana A. Ruiz-Pozo, Ana Karina Zambrano
Heliyon.2023; 9(3): e14086. CrossRef - Metaviromics analysis of marine biofilm reveals a glycoside hydrolase endolysin with high specificity towards Acinetobacter baumannii
Georgios E. Premetis, Nikolaos D. Georgakis, Angeliki Stathi, Nikolaos E. Labrou
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.2023; 1871(4): 140918. CrossRef - Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining
Kang Du, Feng Yang, Jun-Tao Zhang, Rong-Cheng Yu, Ziqing Deng, Wei-Fang Li, Yuxing Chen, Qiong Li, Cong-Zhao Zhou
Microbiome.2022;[Epub] CrossRef - Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing
Harilanto Felana Andrianjakarivony, Yvan Bettarel, Fabrice Armougom, Christelle Desnues
Viruses.2022; 15(1): 76. CrossRef - Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef
- [Editorial]Omics-based microbiome analysis in microbial ecology: from sequences to information
-
Jang-Cheon Cho
-
J. Microbiol. 2021;59(3):229-232.
-
DOI: https://doi.org/10.1007/s12275-021-0698-3
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68
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6
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5
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Abstract
-
Microbial ecology is the study of microorganisms present in
nature. It particularly focuses on microbial interactions with
any biota and with surrounding environments. Microbial
ecology is entering its golden age with innovative multi-omics
methods
triggered by next-generation sequencing technologies.
However, the extraction of ecologically relevant information
from ever-increasing omics data remains one of
the most challenging tasks in microbial ecology. This special
issue includes 11 review articles that provide an overview of
the state of the art of omics-based approaches in the field of
microbial ecology, with particular emphasis on the interpretation
of omics data, environmental pollution tracking,
interactions in microbiomes, and viral ecology.
-
Citations
Citations to this article as recorded by - Advancing early warning and surveillance for zoonotic diseases under climate change: Interdisciplinary systematic perspectives
Chen-Xi Wang, Le-Shan Xiu, Qin-Qin Hu, Tung-Chun Lee, Jia Liu, Leilei Shi, Xiao-Nong Zhou, Xiao-Kui Guo, Liyuan Hou, Kun Yin
Advances in Climate Change Research.2023; 14(6): 814. CrossRef - Mercury methylation in boreal aquatic ecosystems under oxic conditions and climate change: a review
Juanjo Rodríguez
Frontiers in Marine Science.2023;[Epub] CrossRef - Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review
Gabriel Dorado, Sergio Gálvez, Teresa E. Rosales, Víctor F. Vásquez, Pilar Hernández
Biomolecules.2021; 11(8): 1111. CrossRef - Microbial diversity analysis of two full-scale seawater desalination treatment trains provides insights into detrimental biofilm formation
Mircea Podar, Amanda L. May, Weiliang Bai, Kellie Peyton, Dawn M. Klingeman, Cynthia M. Swift, Devan A.F. Linson, Jacques Mathieu, Daniel Siljeström, Ignacio Beneyto, Lauren B. Stadler, Yosef Pinhas, Frank E. Löffler, Pedro J.J. Alvarez, Manish Kumar
Journal of Membrane Science Letters.2021; 1(1): 100001. CrossRef - Removal of PCR inhibitors from soil DNA by chemical flocculation
Michael D Braid, Laura M Daniels, Christopher L Kitts
Journal of Microbiological Methods.2003; 52(3): 389. CrossRef
- [PROTOCOL] High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
-
Suhyun Kim , Miri S. Park , Jaeho Song , Ilnam Kang , Jang-Cheon Cho
-
J. Microbiol. 2020;58(11):893-905. Published online October 30, 2020
-
DOI: https://doi.org/10.1007/s12275-020-0452-2
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78
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11
Web of Science
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12
Crossref
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Abstract
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Multi-omics approaches, including metagenomics and single-
cell amplified genomics, have revolutionized our understanding
of the hidden diversity and function of microbes
in nature. Even in the omics age, cultivation is an essential
discipline in microbial ecology since microbial cultures are
necessary to assess the validity of an in silico prediction about
the microbial metabolism and to isolate viruses infecting bacteria
and archaea. However, the ecophysiological characteristics
of predominant freshwater bacterial lineages remain
largely unknown due to the scarcity of cultured representatives.
In an ongoing effort to cultivate the uncultured majority
of freshwater bacteria, the most abundant freshwater
Actinobacteria acI clade has recently been cultivated from
Lake Soyang through catalase-supplemented high-throughput
cultivation based on dilution-to-extinction. This method
involves physical isolation of target microbes from mixed populations,
culture media simulating natural habitats, and removal
of toxic compounds. In this protocol, we describe detailed
procedures for isolating freshwater oligotrophic microbes,
as well as the essence of the dilution-to-extinction culturing.
As a case study employing the catalase-supplemented
dilution-to-extinction protocol, we also report a cultivation
trial using a water sample collected from Lake Soyang. Of the
480 cultivation wells inoculated with a single lake-water sample,
75 new acI strains belonging to 8 acI tribes (acI-A1, A2,
A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each
representative strain per subclade could be revived from glycerol
stocks. These cultivation results demonstrate that the
protocol described in this study is efficient in isolating freshwater
bacterioplankton harboring streamlined genomes.
-
Citations
Citations to this article as recorded by - Frontiers of lake microbial ecology opened up by new technologies.
Yusuke OKAZAKI
Japanese Journal of Limnology (Rikusuigaku Zasshi).2024; 85(1): 1. CrossRef - Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria
Minjia Zheng, Linran Wen, Cailing He, Xinlan Chen, Laiting Si, Hao Li, Yiting Liang, Wei Zheng, Feng Guo
Nature Communications.2024;[Epub] CrossRef - Adaptive genetic traits in pelagic freshwater microbes
Maria‐Cecilia Chiriac, Markus Haber, Michaela M. Salcher
Environmental Microbiology.2023; 25(3): 606. CrossRef - Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability
Xavier Rey-Velasco, Ona Deulofeu-Capo, Isabel Sanz-Sáez, Clara Cardelús, Isabel Ferrera, Josep M. Gasol, Olga Sánchez, Vincent J. Denef
Microbiology Spectrum.2023;[Epub] CrossRef - Two-Dimensional Cell Separation: a High-Throughput Approach to Enhance the Culturability of Bacterial Cells from Environmental Samples
Krishna K. Yadav, Yogesh Nimonkar, Bhagyashri J. Poddar, Lochana Kovale, Isita Sagar, Yogesh Shouche, Hemant J. Purohit, Anshuman A. Khardenavis, Stefan J. Green, Om Prakash, Kristen M. DeAngelis
Microbiology Spectrum.2022;[Epub] CrossRef - Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications—a review
Hoda Hosseini, Hareb M. Al‐Jabri, Navid R. Moheimani, Simil A. Siddiqui, Imen Saadaoui
Journal of Basic Microbiology.2022; 62(9): 1030. CrossRef - Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis
Tereza Smrhova, Kunal Jani, Petr Pajer, Gabriela Kapinusova, Tomas Vylita, Jachym Suman, Michal Strejcek, Ondrej Uhlik
Environmental Microbiome.2022;[Epub] CrossRef - Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended descrip
Dong-Wook Hyun, Euon Jung Tak, Pil Soo Kim, Jin-Woo Bae
Journal of Microbiology.2021; 59(2): 132. CrossRef - Metaviromics coupled with phage-host identification to open the viral ‘black box’
Kira Moon, Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 311. CrossRef - Heme auxotrophy in abundant aquatic microbial lineages
Suhyun Kim, Ilnam Kang, Jin-Won Lee, Che Ok Jeon, Stephen J. Giovannoni, Jang-Cheon Cho
Proceedings of the National Academy of Sciences.2021;[Epub] CrossRef - Recent trend, biases and limitations of cultivation-based diversity studies of microbes
Om Prakash, Mrinalini Parmar, Manali Vaijanapurkar, Vinay Rale, Yogesh S Shouche
FEMS Microbiology Letters.2021;[Epub] CrossRef - Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period
Suhyun Kim, Md. Rashedul Islam, Ilnam Kang, Jang-Cheon Cho
Frontiers in Microbiology.2021;[Epub] CrossRef
- Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater
-
Shan-Hui Li , Jaeho Song , Ilnam Kang , Juchan Hwang , Jang-Cheon Cho
-
J. Microbiol. 2020;58(6):463-471. Published online May 27, 2020
-
DOI: https://doi.org/10.1007/s12275-020-0206-1
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76
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7
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6
Crossref
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Abstract
-
A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated,
and chemoheterotrophic bacterium, designated
IMCC3088T, was isolated from coastal seawater of the Yellow
Sea. The 16S rRNA gene sequence analysis indicated that
this strain belonged to the family Halieaceae which shared
the highest sequence similarities with Luminiphilus syltensis
NOR5-1BT (94.5%) and Halioglobus pacificus S1-72T (94.5%),
followed by 92.3–94.3% sequence similarities with other species
within the aforementioned family. Phylogenetic analyses
demonstrated that strain IMCC3088T was robustly clustered
with Luminiphilus syltensis NOR5-1BT within the family
Halieaceae. However, average amino acid identity (AAI), percentages
of conserved proteins (POCP), average nucleotide
identity (ANI), and alignment fraction (AF) between strain
IMCC3088T and Luminiphilus syltensis NOR5-1BT were 54.5%,
47.7%, 68.0%, and 16.5%, respectively, suggesting that they
belonged to different genera. Whole-genome sequencing of
strain IMCC3088T revealed a 3.1 Mbp genome size with a
DNA G + C content of 51.7 mol%. The genome encoded diverse
metabolic pathways including sulfur oxidation, phenol
degradation, and proteorhodopsin phototrophy. Mono-unsaturated
fatty acids were found to be the predominant cellular
fatty acid components in the strain. Phosphatidylethanolamine,
phosphatidylglycerol, and diphosphatidylglycerol
were the primarily identified polar lipids, and ubiquinone-8
was identified as a major respiratory quinone. The taxonomic
data collected herein suggested that strain IMCC3088T represented
a novel genus and species of the family Halieaceae,
for which the name Aequoribacter fuscus gen. nov., sp. nov.
is proposed with the type strain (= KACC 15529T = NBRC
108213T).
-
Citations
Citations to this article as recorded by - 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 - Diversity, abundance, and expression of proteorhodopsin genes in the northern South China Sea
Shanhui Li, Lingzi Yin, Li Duan, Jialing Li, Pandeng Wang, Shaoming Gao, Wendong Xian, Wenjun Li
Environmental Research.2024; 259: 119514. CrossRef - Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov.
Pravin Kumar, Ashish Verma, Pooja Yadav, Joyasree Das, Lalit Kumar, Srinivasan Krishnamurthi
Science of The Total Environment.2024; 933: 172995. CrossRef - Metabolic Versatility of the FamilyHalieaceaeRevealed by the Genomics of Novel Cultured Isolates
Shan-Hui Li, Ilnam Kang, Jang-Cheon Cho, Eva C. Sonnenschein
Microbiology Spectrum.2023;[Epub] CrossRef -
Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment
Shan Jiang, Feng-Bai Lian, You-Yang Sun, Xiao-Kui Zhang, Zong-Jun Du
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef - 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
- Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta
-
Jaeho Song , Yeonjung Lim , Hye-Jin Jang , Yochan Joung , Ilnam Kang , Seong-Joo Hong , Choul-Gyun Lee , Jang-Cheon Cho
-
J. Microbiol. 2019;57(11):982-990. Published online October 28, 2019
-
DOI: https://doi.org/10.1007/s12275-019-9378-y
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75
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4
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4
Crossref
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Abstract
-
Microalgae and bacteria are known to be closely associated in
diverse environments. To isolate dominant bacterial species
associated with a green alga, Dunaliella tertiolecta, a photoreactor
culture of the microalga was investigated using culture-
based and culture-independent approaches. The bacterial
community structure of the algal culture showed that
the most abundant bacterial species under the culture conditions
was related to the genus Winogradskyella. The closely
related amplicon sequences, showing ≥ 99.5% 16S rRNA gene
sequence similarity to one of the isolates, designated IMCC-
33238T, constituted > 49% of the bacterial community and
was therefore regarded as the most dominant species in the
algal culture. Strain IMCC33238T was characterized by Gramstaining-
negative and orange-colored rods. Phylogenetic analyses
of the 16S rRNA genes as well as whole genome sequences
revealed that strain IMCC33238T belonged to Winogradskyella
and shared more than 97.2% 16S rRNA gene sequence
similarity with Winogradskyella species. The strain
contained iso-C15:1 G, iso-C15:0, iso-C15:0 3-OH, and summed
feature 3 (C16:1 ω6c and/or C16:1 ω7c) as major fatty acids and
MK-6 as the predominant quinone. The polar lipids found
in strain IMCC33238T were phosphatidylethanolamine, two
unidentified aminolipids, and three unidentified lipids. The
genome of strain IMCC33238T was 3.37 Mbp in size with
33.9 mol% G + C content and proteorhodopsin. Many genes
encoding folate and vitamin production are considered to play
an important role in the bacteria-algae interaction. On the
basis of phylogenetic and phenotypic characteristics, strain
IMCC33238T represents a novel species in the genus Winogradskyella,
for which the name Winogradskyella algicola sp.
nov. is proposed. The type strain is IMCC33238T (= KACC
21192T = NBRC 113704T).
-
Citations
Citations to this article as recorded by - Bacillus sp. enhances the interspecific competitiveness of its host Cyclotella atomus
Zhengbo Zhou, Jiayi Cao, Minnan Wu, Wen Yang, Lin Zhang, Xiaojun Yan, Jilin Xu
Aquaculture.2025; 595: 741577. CrossRef -
Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment
Yu-Yan Yue, Yu-Qi Ye, Zi-Yang Zhou, Meng-Di Zhang, Ya-Wei Jia, Zong-Jun Du
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(7): 4043. CrossRef - Taxonomic study of nine new Winogradskyella species occurring in the shallow waters of Helgoland Roads, North Sea. Proposal of Winogradskyella schleiferi sp. nov., Winogradskyella costae sp. nov., Winogradskyella helgolandensis sp. nov., Winogradskyella v
Carlota Alejandre-Colomo, Tomeu Viver, Mercedes Urdiain, Ben Francis, Jens Harder, Peter Kämpfer, Rudolf Amann, Ramon Rosselló-Móra
Systematic and Applied Microbiology.2020; 43(6): 126128. CrossRef
- Isolation, cultivation, and genome analysis of proteorhodopsincontaining SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322
-
Junhak Lee , Kae Kyoung Kwon , Seung-Il Lim , Jaeho Song , Ah Reum Choi , Sung-Hyun Yang , Kwang-Hwan Jung , Jung-Hyun Lee , Sung Gyun Kang , Hyun-Myung Oh , Jang-Cheon Cho
-
J. Microbiol. 2019;57(8):676-687. Published online June 14, 2019
-
DOI: https://doi.org/10.1007/s12275-019-9001-2
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82
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12
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11
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Abstract
-
Strain IMCC1322 was isolated from a surface water sample
from the East Sea of Korea. Based on 16S rRNA analysis,
IMCC1322 was found to belong to the OCS28 sub-clade of
SAR116. The cells appeared as short vibrioids in logarithmicphase
culture, and elongated spirals during incubation with
mitomycin or in aged culture. Growth characteristics of strain
IMCC1322 were further evaluated based on genomic information;
proteorhodopsin (PR), carbon monoxide dehydrogenase,
and dimethylsulfoniopropionate (DMSP)-utilizing
enzymes. IMCC1322 PR was characterized as a functional
retinylidene protein that acts as a light-driven proton pump
in the cytoplasmic membrane. However, the PR-dependent
phototrophic potential of strain IMCC1322 was only observed
under CO-inhibited and nutrient-limited culture conditions.
A DMSP-enhanced growth response was observed in addition
to cultures grown on C1 compounds like methanol, formate,
and methane sulfonate. Strain IMCC1322 cultivation
analysis revealed biogeochemical processes characteristic of
the SAR116 group, a dominant member of the microbial community
in euphotic regions of the ocean. The polyphasic taxonomy
of strain IMCC1322 is given as Candidatus Puniceispirillum
marinum, and was confirmed by chemotaxonomic
tests, in addition to 16S rRNA phylogeny and cultivation
analyses.
-
Citations
Citations to this article as recorded by - Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322
Ji Hyen Lee, Hyun-Myung Oh
Journal of Microbiology.2024; 62(4): 297. CrossRef - Identification of Structural and Morphogenesis Genes of Sulfitobacter Phage ΦGT1 and Placement within the Evolutionary History of the Podoviruses
Stephen C. Hardies, Byung Cheol Cho, Gwang Il Jang, Zhiqing Wang, Chung Yeon Hwang
Viruses.2023; 15(7): 1475. CrossRef - Seasonal niche differentiation among closely related marine bacteria
Adrià Auladell, Albert Barberán, Ramiro Logares, Esther Garcés, Josep M Gasol, Isabel Ferrera
The ISME Journal.2022; 16(1): 178. CrossRef - Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period
Suhyun Kim, Md. Rashedul Islam, Ilnam Kang, Jang-Cheon Cho
Frontiers in Microbiology.2021;[Epub] CrossRef - Towards culturing the microbe of your choice
J. Cameron Thrash
Environmental Microbiology Reports.2021; 13(1): 36. CrossRef - Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics
Atsushi Kobiyama, Jonaira Rashid, Md. Shaheed Reza, Yuri Ikeda, Yuichiro Yamada, Toshiaki Kudo, Nanami Mizusawa, Saki Yanagisawa, Daisuke Ikeda, Shigeru Sato, Takehiko Ogata, Kazuho Ikeo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Sat
Scientific Reports.2021;[Epub] CrossRef - Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater
Shan-Hui Li, Jaeho Song, Ilnam Kang, Juchan Hwang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(6): 463. CrossRef - Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea
Paul A. Steiner, Javier Geijo, Eduard Fadeev, Aleix Obiol, Eva Sintes, Thomas Rattei, Gerhard J. Herndl
Frontiers in Microbiology.2020;[Epub] CrossRef - High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
Suhyun Kim, Miri S. Park, Jaeho Song, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(11): 893. CrossRef - Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy
Konstantinos T. Konstantinidis, Ramon Rosselló‐Móra, Rudolf Amann
Environmental Microbiology.2020; 22(3): 819. CrossRef - Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation
Michael W. Henson, V. Celeste Lanclos, David M. Pitre, Jessica Lee Weckhorst, Anna M. Lucchesi, Chuankai Cheng, Ben Temperton, J. Cameron Thrash, Robert M. Kelly
Applied and Environmental Microbiology.2020;[Epub] CrossRef
- Sulfitobacter profundi sp. nov., isolated from deep seawater
-
Jaeho Song , Hye-Jin Jang , Yochan Joung , Ilnam Kang , Jang-Cheon Cho
-
J. Microbiol. 2019;57(8):661-667. Published online April 22, 2019
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DOI: https://doi.org/10.1007/s12275-019-9150-3
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77
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11
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13
Crossref
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Abstract
-
A Gram-stain-negative, rod-shaped, obligately aerobic, chemoheterotrophic
bacterium which is motile by means of a
single polar flagellum, designated SAORIC-263T, was isolated
from deep seawater of the Pacific Ocean. Phylogenetic
analyses based on 16S rRNA gene sequences and genomebased
phylogeny revealed that strain SAORIC-263T belonged
to the genus Sulfitobacter and shared 96.1–99.9% 16S rRNA
gene sequence similarities with Sulfitobacter species. Wholegenome
sequencing of strain SAORIC-263T revealed a genome
size of 3.9Mbp and DNA G+C content of 61.3 mol%.
The SAORIC-263T genome shared an average nucleotide identity
and digital DNA-DNA hybridization of 79.1–88.5% and
18.9–35.0%, respectively, with other Sulfitobacter genomes.
The SAORIC-263T genome contained the genes related to
benzoate degradation, which are frequently found in deep-sea
metagenome. The strain contained summed feature 8 (C18:1
ω7c), C18:1 ω7c 11-methyl, and C16:0 as the predominant cellular
fatty acids as well as ubiquinone-10 (Q-10) as the major
respiratory quinone. The major polar lipids of the strain
were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol,
phosphatidylcholine, and aminolipid.
On the basis of taxonomic data obtained in this study, it is
suggested that strain SAORIC-263T represents a novel species
of the genus Sulfitobacter, for which the name Sulfitobacter
profundi sp. nov. is proposed. The type strain is SAORIC-263T
(= KACC 21183T = NBRC 113428T).
-
Citations
Citations to this article as recorded by - Complete genome sequence of Sulfitobacter pontiacus WPMT18310, a dimethylsulfoniopropionate (DMSP) degradation bacterium isolated from the Mariana Trench
Zeping He, Lian Yuan, Haoran Li, Lihua Peng, Xiao Liang, Jin-Long Yang
Marine Genomics.2025; 79: 101151. CrossRef - Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation
Xiaokun Xu, Mengdan He, Qingjie Xue, Xiuzhen Li, Ang Liu
BMC Genomics.2024;[Epub] CrossRef - Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium
Mirae Kim, Jaeho Song, Seung Yeol Shin, Kazuhiro Kogure, Ilnam Kang, Jang-Cheon Cho
Frontiers in Marine Science.2024;[Epub] CrossRef - Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation
Isabel Sanz-Sáez, Pablo Sánchez, Guillem Salazar, Shinichi Sunagawa, Colomban de Vargas, Chris Bowler, Matthew B Sullivan, Patrick Wincker, Eric Karsenti, Carlos Pedrós-Alió, Susana Agustí, Takashi Gojobori, Carlos M Duarte, Josep M Gasol, Olga Sánchez, S
ISME Communications.2023;[Epub] CrossRef - Comparative Genomic Analysis of Cold-Water Coral-Derived Sulfitobacter faviae: Insights into Their Habitat Adaptation and Metabolism
Shituan Lin, Yunxue Guo, Zixian Huang, Kaihao Tang, Xiaoxue Wang
Marine Drugs.2023; 21(5): 309. CrossRef - Genomics of prokaryotic extremophiles to unfold the mystery of survival in extreme environments
Richa Salwan, Vivek Sharma
Microbiological Research.2022; 264: 127156. CrossRef - Metagenomic and Recombination Analyses of Antimicrobial Resistance Genes from Recreational Waters of Black Sea Coastal Areas and Other Marine Environments Unveil Extensive Evidence for Their both Intrageneric and Intergeneric Transmission across Genetical
Ekaterine Gabashvili, Saba Kobakhidze, Tamar Chkhikvishvili, Leila Tabatadze, Rusudan Tsiklauri, Ketevan Dadiani, Stylianos Koulouris, Mamuka Kotetishvili
Marine Genomics.2022; 61: 100916. CrossRef - The Alteration of Intestinal Microbiota Profile and Immune Response in Epinephelus coioides during Pathogen Infection
Joan Tang Xiao Joe, Yung-Che Tseng, Jen-Leih Wu, Ming-Wei Lu
Life.2021; 11(2): 99. CrossRef - Complete Genome of Marine Microalgae Associated Algicidal Bacterium Sulfitobacter pseudonitzschiae H46 with Quorum Sensing System
Tianyi Hu, Shuai Wang, Yishi Shan, Yanchao Zhang, Yunjin Zhu, Li Zheng
Current Microbiology.2021; 78(10): 3741. CrossRef - Beyond Archaea: The Table Salt Bacteriome
Leila Satari, Alba Guillén, Adriel Latorre-Pérez, Manuel Porcar
Frontiers in Microbiology.2021;[Epub] CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(7): 4043. CrossRef - Complete Genome Sequence ofSulfitobacterPhage ϕGT1, Isolated from a Tidal Flat
Chung Y. Hwang, Yirang Cho, Gwang I. Jang, Byung C. Cho, Stephen C. Hardies, Simon Roux
Microbiology Resource Announcements.2020;[Epub] CrossRef - A comparison of bacterial communities from OMZ sediments in the Arabian Sea and the Bay of Bengal reveals major differences in nitrogen turnover and carbon recycling potential
Jovitha Lincy, Cathrine Sumathi Manohar
Marine Biology Research.2020; 16(8-9): 656. CrossRef
- Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean
-
Jaeho Song , Ilnam Kang , Yochan Joung , Susumu Yoshizawa , Ryo Kaneko , Kenshiro Oshima , Masahira Hattori , Koji Hamasaki , Soochan Kim , Kangseok Lee , Jang-Cheon Cho
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J. Microbiol. 2019;57(5):413-422. Published online February 26, 2019
-
DOI: https://doi.org/10.1007/s12275-019-8712-8
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76
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2
Web of Science
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2
Crossref
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Abstract
-
Although culture-independent studies have shown the presence
of Verrucomicrobia in the deep sea, verrucomicrobial
strains from deep-sea environments have been rarely cultured
and characterized. Recently, Rubritalea profundi SAORIC-
165T, a psychrophilic bacterium of the phylum Verrucomicrobia,
was isolated from a depth of 2,000 m in the northwestern
Pacific Ocean. In this study, the genome sequence
of R. profundi SAORIC-165T, the first deep-sea verrucomicrobial
isolate, is reported with description of the genome
properties and comparison to surface-borne Rubritalea genomes.
The draft genome consisted of four contigs with an
entire size of 4,167,407 bp and G+C content of 47.5%. The
SAORIC-165T genome was predicted to have 3,844 proteincoding
genes and 45 non-coding RNA genes. The genome
contained a repertoire of metabolic pathways, including the
Embden-Meyerhof-Parnas pathway, pentose phosphate pathway,
tricarboxylic acid cycle, assimilatory sulfate reduction,
and biosynthesis of nicotinate/nicotinamide, pantothenate/
coenzyme A, folate, and lycopene. The comparative genomic
analyses with two surface-derived Rubritalea genomes showed
that the SAORIC-165T genome was enriched in genes involved
in transposition of mobile elements, signal transduction, and
carbohydrate metabolism, some of which might be related to
bacterial enhancement of ecological fitness in the deep-sea
environment. Amplicon sequencing of 16S rRNA genes from
the water column revealed that R. profundi-related phylotypes
were relatively abundant at 2,000 m and preferred a
particle-associated life style in the deep sea. These findings
suggest that R. profundi represents a genetically unique and
ecologically relevant verrucomicrobial group well adapted
to the deep-sea environment.
-
Citations
Citations to this article as recorded by - Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium
Mirae Kim, Jaeho Song, Seung Yeol Shin, Kazuhiro Kogure, Ilnam Kang, Jang-Cheon Cho
Frontiers in Marine Science.2024;[Epub] CrossRef - Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents
Joel Slinger, James W. Wynne, Mark B. Adams
Frontiers in Animal Science.2021;[Epub] CrossRef
- Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River
-
Yochan Joung , Hye-Jin Jang , Jaeho Song , Jang-Cheon Cho
-
J. Microbiol. 2019;57(5):343-349. Published online February 5, 2019
-
DOI: https://doi.org/10.1007/s12275-019-8436-9
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67
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9
Web of Science
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10
Crossref
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Abstract
-
A non-motile, yellow-pigmented bacterial strain, designated
IMCC34762T, was isolated from a freshwater sample collected
from Lake Cheongpyeong in Korea. Phylogenetic analysis
based on 16S rRNA gene sequences showed that strain IMCC-
34762T formed a lineage within the genus Flavobacterium
and was most closely related to F. pectinovorum DSM 6368T
(98.3% sequence similarity), followed by F. piscis CCUG
60099T (98.3%), F. branchiicola 59B-3-09T (98.2%), and F.
saccharophilum DSM 1811T (98.2%). The average nucleotide
identity and the genome-to-genome distance between strain
IMCC34762T and the closely related strains were 61–62%
and 26–27%, respectively, indicating that IMCC34762T is a
novel species of the genus Flavobacterium. The major fatty
acids (> 5%) of strain IMCC34762T were summed feature 3
(C16:1 ω6c and/or C16:1 ω7c, 17.3%), iso-C15:0 (15.0%), iso-C15:0
G (9.0%), C15:0 ω6c (7.4%), iso-C15:0 (7.4%), and iso-C16:0 (5.3%).
The major respiratory quinone and polyamine were MK-6 and
sym-homospermidine, respectively. The major polar lipids
were phosphatidylethanolamine, an unidentified aminophospholipid,
and an unidentified lipid. The DNA G+C content
of strain IMCC34762T was 34.4 mol%. Based on the taxonomic
data presented in this study, strain IMCC34762T represents
a novel species within the genus Flavobacterium, for which
the name Flavobacterium aquariorum, sp. nov. is proposed.
The type strain is IMCC34762T (= KACC 19725T = NBRC
113425T).
-
Citations
Citations to this article as recorded by - Flavobacterium algoriphilum sp. nov., Flavobacterium arabinosi sp. nov., Flavobacterium cryoconiti sp. nov., Flavobacterium galactosi sp. nov., Flavobacterium melibiosi sp. nov., and Flavobacterium algoris sp. nov., six novel cold-adapted bacteria isolate
Lei-Lei Yang, Yu-Hua Xin, Qing Liu
BMC Microbiology.2025;[Epub] CrossRef -
Flavobacterium anseongense sp. nov. and Flavobacterium wongokense sp. nov., isolated from freshwater and freshwater soil in South Korea
Jung-Hun Jo, Soon-Youl Lee, Se-Yoon Chun, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef - Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
Seomin Kang, Jae-Yun Lee, Jeong Eun Han, Yun-Seok Jeong, Do-Hun Gim, Jin-Woo Bae
Journal of Microbiology.2022; 60(9): 890. CrossRef - Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiont
Izzet Burcin Saticioglu
Archives of Microbiology.2021; 203(9): 5783. CrossRef - Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout
Muhammed Duman, Hilal Ay, Soner Altun, Nevzat Sahin, Izzet Burcin Saticioglu
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef - Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Muhammed Duman, Nevzat Sahin
Systematic and Applied Microbiology.2021; 44(2): 126186. CrossRef - Flavobacterium bernardetii sp. nov., a possible emerging pathogen of farmed rainbow trout (Oncorhynchus mykiss) in cold water
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nevzat Sahin, Muhammed Duman
Aquaculture.2021; 540: 736717. CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(7): 4043. CrossRef -
Rhodoferax lacus sp. nov., isolated from a large freshwater lake
Miri Park, Jaeho Song, Gi Gyun Nam, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology
.2019; 69(10): 3135. CrossRef
- Pedobacter aquicola sp. nov., isolated from freshwater
-
Yochan Joung , Hye-jin Jang , Miri Park , Jaeho Song , Jang-Cheon Cho
-
J. Microbiol. 2018;56(7):478-484. Published online June 14, 2018
-
DOI: https://doi.org/10.1007/s12275-018-7499-3
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71
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11
Crossref
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Abstract
-
A non-motile, pink-pigmented bacterial strain designated
IMCC25679T, was isolated from freshwater Lake Chungju of
Korea. Phylogenetic trees based on 16S rRNA gene sequences
showed that the strain IMCC25679T formed a lineage within
the genus Pedobacter. The strain IMCC25679T was closely
related to Pedobacter daechungensis Dae 13T (96.4% sequence
similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter
lentus DS-40T (94.3%). The major fatty acids of IMCC-
25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising
C16:1 ω6c and/or C16:1 ω7c). The major respiratory quinone
was MK-7. The major polar lipids were phosphatidylethanolamine
(PE), an unidentified sphingolipid (SL), an
unidentified aminolipid (AL) and three unidentified polar
lipids (PL). The DNA G + C content of IMCC25679T was 32.2
mol%. Based on the evidence presented in this study, the
strain IMCC25679T represents a novel species within the genus
Pedobacter, with the proposed name Pedobacter aquicola,
sp. nov. The type strain is IMCC25679T (= KACC 19486T
= NBRC113131T).
-
Citations
Citations to this article as recorded by - Genome-Based Classification of Pedobacter albus sp. nov. and Pedobacter flavus sp. nov. Isolated from Soil
Nhan Le Thi Tuyet, Jaisoo Kim
Diversity.2024; 16(5): 292. CrossRef - Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil
Haejin Woo, Geeta Chhetri, Inhyup Kim, Yoonseop So, Sunho Park, Yonghee Jung, Taegun Seo
Antonie van Leeuwenhoek.2024;[Epub] CrossRef - Screening of potential microbial markers for lung cancer using metagenomic sequencing
Qiang Chen, Kai Hou, Mingze Tang, Shuo Ying, Xiaoyun Zhao, Guanhua Li, Jianhui Pan, Xiaomin He, Han Xia, Yuechuan Li, Zheng Lou, Li Zhang
Cancer Medicine.2023; 12(6): 7127. CrossRef - Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water
Le Tran Tien Chau, Yong-Seok Kim, Chang-Jun Cha
Antonie van Leeuwenhoek.2022; 115(3): 445. CrossRef -
Pedobacter riviphilus sp. nov., isolated from stream sediment
Hong Sik Im, Yochan Joung, Sang-Seob Lee
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef - Complete Genome Sequence of Pedobacter sp. PAMC26386 and Their Low Temperature Application in Arabinose-containing Polysaccharides Degradation
Cya-Yong Cho, So-Ra Han, Tae-Jin Oh
Current Microbiology.2021; 78(3): 944. CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(7): 4043. CrossRef - Pedobacter indicus sp. nov., isolated from deep-sea sediment
Xiao-yan He, Na Li, Xiu-lan Chen, Yu-zhong Zhang, Xi-ying Zhang, Xiao-yan Song
Antonie van Leeuwenhoek.2020; 113(3): 357. CrossRef -
Leeia aquatica sp. nov., isolated from freshwater
Jaeho Song, Yochan Joung, Shan-Hui Li, Juchan Hwang, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(11): 5848. CrossRef -
Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake
Jaeho Song, Yochan Joung, Shan-Hui Li, Juchan Hwang, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(12): 6126. CrossRef -
Rhodoferax lacus sp. nov., isolated from a large freshwater lake
Miri Park, Jaeho Song, Gi Gyun Nam, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology
.2019; 69(10): 3135. CrossRef
- NOTE] Grimontia marina sp. nov., a Marine Bacterium Isolated from the Yellow Sea
-
Ahyoung Choi , Kyung-Mi Kim , Ilnam Kang , Seok-Hyun Youn , Young-Sang Suh , Yoon Lee , Jang-Cheon Cho
-
J. Microbiol. 2012;50(1):170-174. Published online February 27, 2012
-
DOI: https://doi.org/10.1007/s12275-012-1615-6
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41
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11
Scopus
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Abstract
-
A novel species belonging to the genus Grimontia is described
in this study. A Gram-negative, chemoheterotrophic, obligately
aerobic, catalase- and oxidase-positive, motile by a
single polar flagellum, and rod-shaped bacterium, designated
IMCC5001T, was isolated from surface seawater of
the Yellow Sea. Strain IMCC5001T grew optimally at 30°C
in the presence of 3.5% NaCl. Phylogenetic analysis based
on 16S rRNA gene sequences showed that the isolate was
related most closely to Grimontia hollisae with a sequence
similarity of 95.8%, and formed a robust phyletic lineage
with Grimontia hollisae. Differential physiological characteristics
between the new strain and Grimontia hollisae
KCCM 41680T and chemotaxonomic characterization including
determination of DNA G+C content, fatty acid methyl
esters, quinone composition, and polar lipid profiles justified
the assignment of strain IMCC5001T to the genus Grimontia
as a novel species. In conclusion, strain IMCC5001T represents
a new species, for which the name Grimontia marina sp.
nov. is proposed, with the type strain IMCC5001T (=KCTC
22666T =NBRC 105794T).
- Diversity of Cold-Active Protease-Producing Bacteria from Arctic Terrestrial and Marine Environments Revealed by Enrichment Culture
-
Eun Hye Kim , Kyeung Hee Cho , Yung Mi Lee , Joung Han Yim , Hong Kum Lee , Jang-Cheon Cho , Soon Gyu Hong
-
J. Microbiol. 2010;48(4):426-432. Published online August 20, 2010
-
DOI: https://doi.org/10.1007/s12275-010-0015-z
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62
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22
Crossref
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Abstract
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A new approach for enrichment culture was applied to obtain cold-active protease-producing bacteria for marine and terrestrial samples from Svalbard, Norway. The method was developed for the enrichment of bacteria by long-term incubation at low temperatures in semi-solid agar medium containing meat pieces as the main source of carbon and energy. ZoBell and 0.1× nutrient broth were added for marine and terrestrial microorganisms, respectively, to supply basal elements for growth. One to three types of colonies were observed from each enrichment culture, indicating that specific bacterial species were enriched during the experimental conditions. Among 89 bacterial isolates, protease activity was observed from 48 isolates in the screening media containing skim milk. Good growth was observed at 4°C and 10°C while none of the isolates could grow at 37°C. At low temperatures, enzyme activity was equal to or higher than activity at higher temperatures. Bacterial isolates were included in the genera Pseudoalteromonas (33 isolates), Arthrobacter (24 isolates), Pseudomonas (16 isolates), Psychrobacter (6 isolates), Sphingobacterium (6 isolates), Flavobacterium (2 isolates), Sporosarcina (1 isolate), and Stenotrophomonas (1 isolate). Protease activity was observed from Pseudoalteromonas (33 isolates), Pseudomonas (10 isolates), Arthrobacter (4 isolates), and Flavobacterium (1 isolate).
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Citations
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- Antarcticimonas flava gen. nov., sp. nov., Isolated from Antarctic Coastal Seawater
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Seung-Jo Yang , Hyun-Myung Oh , Sangyun Chung , Jang-Cheon Cho
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J. Microbiol. 2009;47(5):517-523. Published online October 24, 2009
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DOI: https://doi.org/10.1007/s12275-009-0225-4
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Abstract
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A marine bacterium, designated IMCC3175T, was isolated from a seawater sample collected off the Antarctic coast. The strain was Gram-negative, obligately aerobic, carotenoid pigment-containing, and rod-shaped bacterium that divided by binary fission. As determined by 16S rRNA gene sequence comparisons, the most
closely related genera were Formosa (92.9~93.3%), Bizionia (91.6~93.2%), Gaetbulibacter (91.5~92.8%), Sediminibacter (92.7%), Yeosuana (92.6%), Subsaximicrobium (92.1~92.2%), and Gillisia (89.5~92.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a monophyletic clade together with the genera Sediminibacter and Subsaximicrobium but represented an independent phyletic line in this clade of the family Flavobacteriaceae. The DNA G+C content of the strain was 37.3 mol%. The
major respiratory quinone was MK-6 and the predominant cellular fatty acids were C16:1 ω7c and/or iso-C15:0 2-OH (12.8%), anteiso-C15:0 (9.4%), and iso-C16:1 (9.4%). Low 16S rRNA gene sequence similarity, formation of a distinct phylogenetic branch, and several phenotypic characteristics, including a narrow range of temperature and salinity for growth, differentiated strain IMCC3175T from other related genera in the family Flavobacteriaceae. Therefore the name Antarcticimonas flava gen. nov., sp. nov. is proposed, with strain IMCC3175T (=KCCM 42713T =NBRC 103398T) as the type strain.
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