- High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
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Suhyun Kim , Miri S. Park , Jaeho Song , Ilnam Kang , Jang-Cheon Cho
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J. Microbiol. 2020;58(11):893-905. Published online October 30, 2020
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DOI: https://doi.org/10.1007/s12275-020-0452-2
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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  - The silent partners: A perspective on the overlooked and essential roles of archaea in the rhizosphere
Hassan Etesami
Rhizosphere.2026; 38: 101341. CrossRef - Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing
Eglantina Lopez-Echartea, Nicholas Dusek, Mallory Misialek, Mohammad Al Mahmud-Un-Nabi, Riley Williamson, Komal Marathe, Barney A. Geddes
Microbiology
.2025;[Epub] CrossRef - Tunable lysis of functionalized nanocultures for efficient microbial and nucleic acid recovery
Shanna-Leigh Davidson, Lisa M. Stabryla, Shakira M. Martínez Vásquez, Jennifer Dootz, Monique E. Hunter, Tagbo H.R. Niepa
Chemical Engineering Journal.2025; 523: 168770. CrossRef - High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules
Hugo Sallet, Marion Calvo, Matteo Titus, Nicolas Jacquemin, Karin Lederballe Meibom, Rizlan Bernier-Latmani
ISME Communications.2025;[Epub] CrossRef - Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order
Maria-Cecilia Chiriac, Paul Layoun, Clafy Fernandes, Tiberiu Szőke-Nagy, Vojtech Kasalicky, Yusuke Okazaki, Jason N. Woodhouse, Hans-Peter Grossart, Kasia Piwosz, Petr Znachor, Bettina Sonntag, Cristiana Callieri, Sandi Orlić, Ruben Sommaruga, Cécile Lepè
Microbiome.2025;[Epub] CrossRef - 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
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Shan-Hui Li , Jaeho Song , Ilnam Kang , Juchan Hwang , Jang-Cheon Cho
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J. Microbiol. 2020;58(6):463-471. Published online May 27, 2020
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DOI: https://doi.org/10.1007/s12275-020-0206-1
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1,019
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Abstract
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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 - Microbiome Single Cell Atlases Generated with a Commercial Instrument
Xiangpeng Li, Linfeng Xu, Benjamin Demaree, Cecilia Noecker, Jordan E. Bisanz, Daniel W. Weisgerber, Cyrus Modavi, Peter J. Turnbaugh, Adam R. Abate
Advanced Science.2025;[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 - 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
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J. Microbiol. 2019;57(11):982-990. Published online October 28, 2019
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DOI: https://doi.org/10.1007/s12275-019-9378-y
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1,150
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Abstract
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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
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Yang Liu, Kai Liao, Yang Zhang, Qi Hu, Xiaoxue He, Fengjun Xie, Lin Zhang, Zhongming Huo, Jilin Xu
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Bin Li, Hamid R. Baniasadi, Jue Liang, Margaret A. Phillips, Anthony J. Michael
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Olga Nedashkovskaya, Sergey Baldaev, Alexander Ivaschenko, Evgenia Bystritskaya, Natalia Zhukova, Viacheslav Eremeev, Andrey Kukhlevskiy, Valeria Kurilenko, Marina Isaeva
Life.2025; 15(3): 331. 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
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J. Microbiol. 2019;57(8):676-687. Published online June 14, 2019
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DOI: https://doi.org/10.1007/s12275-019-9001-2
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Abstract
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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
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PeerJ.2026; 14: e21390. CrossRef - Culture-supported ecophysiology of the SAR116 clade demonstrates metabolic and spatial niche partitioning
Jordan T Coelho, Lauren Teubner, Michael W Henson, V Celeste Lanclos, Conner Y Kojima, J Cameron Thrash
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Environmental Microbiology Reports.2025;[Epub] CrossRef - Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322
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Journal of Microbiology.2024; 62(4): 297. CrossRef - Effect of Light Regime on Candidatus Puniceispirillum marinum IMCC1322 in Nutrient-Replete Conditions
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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
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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
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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
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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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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).
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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
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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
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Marine Genomics.2022; 61: 100916. CrossRef - The Alteration of Intestinal Microbiota Profile and Immune Response in Epinephelus coioides during Pathogen Infection
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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
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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
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DOI: https://doi.org/10.1007/s12275-019-8712-8
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1,015
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3
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3
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Abstract
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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.
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Citations
Citations to this article as recorded by - Lycium barbarum glycopeptide alleviates diabetic retinopathy by modulating the gut microbiota and metabolites
Yiwen Ou, Yinhua Huang, Zekai Cui, Shangli Ji, Xu Yang, Rangsheng Mei, Zhexiong Yu, Kwok-Fai So, Jiansu Chen, Shibo Tang, Jacey Hongjie Ma
Neural Regeneration Research.2026; 21(11): 5462. 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 - 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
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Yochan Joung , Hye-Jin Jang , Jaeho Song , Jang-Cheon Cho
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J. Microbiol. 2019;57(5):343-349. Published online February 5, 2019
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DOI: https://doi.org/10.1007/s12275-019-8436-9
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1,001
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10
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11
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Abstract
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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 - Unveiling the hidden threat: heavy metal accumulation in crops and soil microbial dynamics in a teaching experimental farmland
Xue Gu, Xuegang Yu, Qing Li, Yanjun Mao, Zhiwei Zhou, Huan Hu, Rui Huang, Jiayu Zhou, Yuanyi Sun, Yancheng Li, Aijiang Yang
Plant and Soil.2025; 517(2): 1211. 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
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J. Microbiol. 2018;56(7):478-484. Published online June 14, 2018
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DOI: https://doi.org/10.1007/s12275-018-7499-3
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1,078
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12
Crossref
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Abstract
PDF
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A non-motile, pink-pigmented bacterial strain designated
IMCC25679T, was isolated from freshwater Lake Chungju of
Korea. Phylogenetic trees based on 16S rRNA gene sequences
showed that the strain IMCC25679T formed a lineage within
the genus Pedobacter. The strain IMCC25679T was closely
related to Pedobacter daechungensis Dae 13T (96.4% sequence
similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter
lentus DS-40T (94.3%). The major fatty acids of IMCC-
25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising
C16:1 ω6c and/or C16:1 ω7c). The major respiratory quinone
was MK-7. The major polar lipids were phosphatidylethanolamine
(PE), an unidentified sphingolipid (SL), an
unidentified aminolipid (AL) and three unidentified polar
lipids (PL). The DNA G + C content of IMCC25679T was 32.2
mol%. Based on the evidence presented in this study, the
strain IMCC25679T represents a novel species within the genus
Pedobacter, with the proposed name Pedobacter aquicola,
sp. nov. The type strain is IMCC25679T (= KACC 19486T
= NBRC113131T).
-
Citations
Citations to this article as recorded by - Duganella paludis sp. nov. and Pedobacter jaeyakensis sp. nov., isolated from the wetland fresh water
Yu Jeong Lee, Hae Jin Kim, Won Jeong Hwang, Byung Hee Chun
Antonie van Leeuwenhoek.2026;[Epub] CrossRef - 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
- Isolation and Characterization of the Smallest Bacteriophage P4 Derivatives Packaged into P4-Size Head in Bacteriophage P2-P4 System
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Kyoung-Jin Kim , Jaeho Song
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J. Microbiol. 2006;44(5):530-536.
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DOI: https://doi.org/2444 [pii]
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Abstract
PDF
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Bacteriophage P4, a satellite phage of coliphage P2, is a very useful experimental tool for the study of viral capsid assembly and cos-cleavage. For an in vitro cos-cleavage reaction study of the P2-P4 system, new shortened and selectable markers containing P4 derivative plasmids were designed as a substrate molecules. They were constructed by swapping the non-essential segment of P4 DNA for either the kanamycin resistance (kmr) gene or the ampicillin resistance (apr) gene. The size of the genomes of the resulting markers were 82% (P4 ash8 delRI:: kmr) and 79% (P4 ash8 delRI:: apr) of the wild type P4 genome. To determine the lower limit of genome size that could be packaged into the small P4-size head, these shortened P4 plasmids were converted to phage particles with infection of the helper phage P2. The conversion of plasmid P4 derivatives to bacteriophage particles was verified by the heat stability test and the burst size determination experiment. CsCl buoyant equilibrium density gradient experiments confirmed not only the genome size of the viable phage form of shortened P4 derivatives, but also their packaging into the small P4-size head. P4 ash8 delRI:: apr turned out to be the smallest P4 genome that can be packaged into P4-sized head.
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