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- Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., isolated from Korean coastal surface seawater
- Jisoo Han, Yeonjung Lim, Mirae Kim, Jang-Cheon Cho
- J. Microbiol. 2025;63(8):e2504017. Published online August 13, 2025
- DOI: https://doi.org/10.71150/jm.2504017
- 1,323 View
- 60 Download
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Abstract
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Supplementary Material -
Two Gram-stain-negative, obligately aerobic, non-motile, short rod-shaped bacteria, designated IMCC43871T and IMCC45206T, were isolated from coastal surface seawater collected from the Yellow Sea and the South Sea of Korea, respectively. The two strains shared 99.2% 16S rRNA gene sequence similarity with each other and exhibited ≤ 98.4% similarity to three described Rubrivirga species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between IMCC43871T and IMCC45206T were 88.5% and 36.3%, respectively, confirming that they represent two distinct species. Their ANI (≤ 77.7%) and dDDH (≤ 21.4%) values relative to the type strains of the genus Rubrivirga further supported the recognition of strains IMCC43871T and IMCC45206T as two novel species within the genus. The complete genomes of IMCC43871T (4.17 Mb, 71.8% G + C content) and IMCC45206T (4.17 Mb, 72.8% G + C content) fall within the known genomic range of the genus. Cellular fatty acid, quinone, and polar lipid profiles were consistent with the chemotaxonomic features of the genus Rubrivirga, supporting their affiliation with the genus. Based on phylogenetic, genomic, and phenotypic evidence, strains IMCC43871T and IMCC45206T are proposed as two novel species, Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., respectively. The type strains are IMCC43871T (= KCTC 102072T = NBRC 116463T) and IMCC45206T (= KCTC 92925T = NBRC 116172T = CCTCC AB 2023136T).
Journal Articles
- Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
- Meora Rajeev, Jang-Cheon Cho
- J. Microbiol. 2024;62(11):985-997. Published online November 15, 2024
- DOI: https://doi.org/10.1007/s12275-024-00187-0
- 394 View
- 7 Download
- 9 Web of Science
- 8 Crossref
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Abstract
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- Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.
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Citations
Citations to this article as recorded by
- Ecological disposal of bauxite tailings and red mud: A sustainable strategy for bauxite industrial waste reuse
Xusheng Jiang, Xuehong Zhang, Xijun Liu, Hui Qiu, Mengting Lin, Guo Yu, Shouhui Zhang, Jie Liu
Resources, Conservation and Recycling.2025; 218: 108259. CrossRef - Variation of Microorganisms and Water Quality, and Their Impacts on the Production of Penaeus vannamei in Small-Scale Greenhouse Ponds
Siyu Wu, Haochang Su, Lei Su, Yucheng Cao, Guoliang Wen, Yu Xu, Bin Shen, Shanshan Wu, Yuting Su, Xiaojuan Hu
Microorganisms.2025; 13(3): 546. CrossRef - Effect of hydraulic retention time of sponge-based trickling filter for shrimp culture recirculating tank
Penpicha Satanwat, Mami Nagai, Tharin Boonprasertsakul, Akihiro Nagano, Tsutomu Okubo, Nur Adlin, Takahiro Watari, Masashi Hatamoto, Takashi Yamaguchi, Sitthakarn Sitthi, Wiboonluk Pungrasmi, Rapeepun Vanichviriyakit, Sorawit Powtongsook
Process Safety and Environmental Protection.2025; 198: 107154. CrossRef - Divergence patterns of bacterial communities between larviculture systems of two Penaeus vannamei strains with distinct culture traits
Heng Chen, Fengdie Zhang, Junqi Yu, Rudan Chen, Demin Zhang, Chen Chen, Kai Wang
Aquaculture.2025; 606: 742572. CrossRef - Influence of Polyester and Denim Microfibers on the Treatment and Formation of Aerobic Granules in Sequencing Batch Reactors
Victoria Okhade Onyedibe, Hassan Waseem, Hussain Aqeel, Steven N. Liss, Kimberley A. Gilbride, Roxana Sühring, Rania Hamza
Processes.2025; 13(7): 2272. CrossRef - Where Have You Been? Backtracking Microplastic to Its Source Using the Biomolecular Composition of the Ecocorona
Amanda L. Dawson, Utpal Bose, Sophia Escobar-Correas, Kuok Yap, David J. Craik, Cassandra L. Pegg
Environmental Science & Technology.2025; 59(41): 22227. CrossRef - Effects of butyric acid on the inhibition of Vibrio parahaemolyticus and its impacts on growth performance, intestinal microbiota, and water microbiota in Litopenaeus vannamei
Minghan Yin, Zhangyi Zheng, Ruiyan Xing, Lefei Jiao, Moussa Gouife, Tinghong Ming, Fei Kong, Shuang Qiu, Jiajie Xu
Aquaculture Reports.2025; 45: 103078. CrossRef - Evaluating the potential of Rhodopseudomonas faecalis PA2 as a probiotic and biofloc supplement for Nile tilapia (Oreochromis niloticus)
Wipavee Thaimuangphol, Ranumas Sukkum, Zhongliang Wang, Chewapat Saejung
Aquaculture Reports.2025; 45: 103201. CrossRef
- Ecological disposal of bauxite tailings and red mud: A sustainable strategy for bauxite industrial waste reuse
- 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
- J. Microbiol. 2024;62(9):739-748. Published online July 18, 2024
- DOI: https://doi.org/10.1007/s12275-024-00158-5
- 546 View
- 9 Download
- 5 Web of Science
- 5 Crossref
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Abstract
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- Two Gram-stain-negative, aerobic, motile by means of flagella, short rod-shaped bacterial strains, designated IMCC43200(T) and IMCC45268(T), were isolated from coastal seawater samples collected from the South Sea of Korea. Strains IMCC43200(T) and IMCC45268(T) shared 98.6% 16S rRNA gene sequence similarity and were closely related to Congregibacter litoralis KT71(T) (98.8% and 98.7%, respectively). Complete whole-genome sequences of IMCC43200(T) and IMCC45268(T) were 3.93 and 3.86 Mb in size with DNA G + C contents of 54.8% and 54.2%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 74.5% and 23.4%, respectively, revealing that they are independent species. The two strains showed ANI values of ≤ 75.8% and dDDH values of ≤ 23.0% to the type and only species of the genus Congregibacter (C. litoralis), indicating that each strain represents a novel species. Both strains contained summed feature 3 (comprising C(16:1) ω6c and/or C(16:1) ω7c) and summed feature 8 (comprising C(18:1) ω6c and/or C(18:1) ω7c) as major fatty acid constituents. The predominant isoprenoid quinone detected in both strains was ubiquinone-8 (Q-8). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and aminolipids. Based on the phylogenetic, genomic, and phenotypic characterization, strains IMCC43200(T) and IMCC45268(T) were considered to represent two novel species within the genus Congregibacter, for which the names Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. are proposed with IMCC43200(T) (= KCTC 8133(T) = NBRC 116295(T) = CCTCC AB 2023139(T)) and IMCC45268(T) (= KCTC 92921(T) = NBRC 116135(T)) as the type strains, respectively.
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Citations
Citations to this article as recorded by- Validation List no. 223. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef - Phycobium rhodophyticola gen. nov., sp. nov. and Aliiphycobium algicola gen. nov., sp. nov., isolated from the phycosphere of marine red algae
Jeong Min Kim, Woonhee Baek, Byeong Jun Choi, Hülya Bayburt, Jae Kyeong Lee, Sung Chul Lee, Che Ok Jeon
Journal of Microbiology.2025; 63(6): e2503014. CrossRef - Notification of changes in taxonomic opinion previously published outside the IJSEM. List of Changes in Taxonomic Opinion no. 42
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef - Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., isolated from Korean coastal surface seawater
Jisoo Han, Yeonjung Lim, Mirae Kim, Jang-Cheon Cho
Journal of Microbiology.2025; 63(8): e2504017. 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
- Validation List no. 223. Valid publication of new names and new combinations effectively published outside the IJSEM
Letter
- 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
- J. Microbiol. 2023;61(6):649-651. Published online June 12, 2023
- DOI: https://doi.org/10.1007/s12275-023-00057-1
- 317 View
- 0 Download
- 1 Web of Science
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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.
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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
- Validation List no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM
Journal Articles
- 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
- Hyunyoung Jo , Miri S. Park , Yeonjung Lim , Ilnam Kang , Jang-Cheon Cho
- J. Microbiol. 2023;61(5):495-510. Published online May 23, 2023
- DOI: https://doi.org/10.1007/s12275-023-00054-4
- 454 View
- 0 Download
- 9 Web of Science
- 9 Crossref
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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.
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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 - Comparative genomics and evolutionary insights into zeaxanthin biosynthesis in two novel Flavobacterium species
Ye Zhuo, Chun-Zhi Jin, Chang-Soo Lee, Kee-Sun Shin, Hyung-Gwan Lee
BMC 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
- Indoor pollution of funeral homes and potential health risk of workers: A case study in central China
- Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream
- Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho
- J. Microbiol. 2022;60(8):806-813. Published online July 29, 2022
- DOI: https://doi.org/10.1007/s12275-022-2298-2
- 404 View
- 2 Download
- 5 Web of Science
- 6 Crossref
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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.
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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
- Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Review
- Metaviromics coupled with phage-host identification to open the viral ‘black box’
- Kira Moon , Jang-Cheon Cho
- J. Microbiol. 2021;59(3):311-323. Published online February 23, 2021
- DOI: https://doi.org/10.1007/s12275-021-1016-9
- 355 View
- 0 Download
- 11 Web of Science
- 10 Crossref
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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.
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Citations
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Ha-eun Cho, Min Jin Kim, Jongmun Choi, Yong-Hak Sohn, Jae Joon Lee, Kyung Sun Park, Sun Young Cho, Ki-Ho Park, Young Jin Kim
Microorganisms.2025; 13(6): 1338. CrossRef - Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
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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
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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
- Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections
Journal Article
- [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
- 345 View
- 1 Download
- 14 Web of Science
- 15 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.
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Citations
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Review
- 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
- 354 View
- 0 Download
- 7 Web of Science
- 7 Crossref
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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).
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Journal of Microbiology.2024; 62(9): 739. CrossRef - Diversity, abundance, and expression of proteorhodopsin genes in the northern South China Sea
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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
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Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment
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Journal Articles
- 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
- 331 View
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- 5 Web of Science
- 6 Crossref
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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).
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Zhengbo Zhou, Jiayi Cao, Minnan Wu, Wen Yang, Lin Zhang, Xiaojun Yan, Jilin Xu
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Dalila Crucitti, Michele Sonnessa, Francesco Carimi, Tiziano Caruso, Davide Pacifico
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Olga Nedashkovskaya, Sergey Baldaev, Alexander Ivaschenko, Evgenia Bystritskaya, Natalia Zhukova, Viacheslav Eremeev, Andrey Kukhlevskiy, Valeria Kurilenko, Marina Isaeva
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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
- Bacillus sp. enhances the interspecific competitiveness of its host Cyclotella atomus
- 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
- 338 View
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- 14 Web of Science
- 13 Crossref
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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.
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Jordan T Coelho, Lauren Teubner, Michael W Henson, V Celeste Lanclos, Conner Y Kojima, J Cameron Thrash
The ISME Journal.2025;[Epub] CrossRef - 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 - Effect of Light Regime on Candidatus Puniceispirillum marinum IMCC1322 in Nutrient-Replete Conditions
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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
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- 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
- DOI: https://doi.org/10.1007/s12275-019-9150-3
- 342 View
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Abstract
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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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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
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Joan Tang Xiao Joe, Yung-Che Tseng, Jen-Leih Wu, Ming-Wei Lu
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Aharon Oren, George Garrity
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- Complete genome sequence of Sulfitobacter pontiacus WPMT18310, a dimethylsulfoniopropionate (DMSP) degradation bacterium isolated from the Mariana Trench
- Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean
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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
- 339 View
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- 2 Web of Science
- 2 Crossref
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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
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- Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River
- Yochan Joung , Hye-Jin Jang , Jaeho Song , Jang-Cheon Cho
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- DOI: https://doi.org/10.1007/s12275-019-8436-9
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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).
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Citations
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Lei-Lei Yang, Yu-Hua Xin, Qing Liu
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Izzet Burcin Saticioglu
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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
- 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
- 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
- 359 View
- 0 Download
- 11 Crossref
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Abstract
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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).
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Citations
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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
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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
- Genome-Based Classification of Pedobacter albus sp. nov. and Pedobacter flavus sp. nov. Isolated from Soil
Research Support, Non-U.S. Gov'ts
- 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
- 180 View
- 0 Download
- 10 Crossref
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Abstract
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- 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).
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Citations
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Enterovibrio paralichthyis sp. nov., isolated from the gut of an olive flounder Paralichthys olivaceus
Young-Ok Kim, In-Suk Park, Dong-Gyun Kim, Sooyeon Park, Sung Hoon Han, Jung-Hoon Yoon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef - Veronia nyctiphanis gen. nov., sp. nov., Isolated from the Stomach of the Euphausiid Nyctiphanes simplex (Hansen, 1911) in the Gulf of California, and Reclassification of Enterovibrio pacificus as Veronia pacifica comb. nov.
Bruno Gomez-Gil, Adrián González-Castillo, Mario J. Aguilar-Méndez, Alejandro López-Cortés, Jaime Gómez-Gutiérrez, Ana Roque, Elke Lang, Julissa Enciso-Ibarra
Current Microbiology.2021; 78(10): 3782. CrossRef -
Grimontia sedimenti sp. nov., isolated from benthic sediments near coral reefs south of Kuwait
Huda Mahmoud, Liny Jose, Susan Eapen
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef - Heterologous expression of a cryptic gene cluster from Grimontia marina affords a novel tricyclic peptide grimoviridin
Kohta Unno, Issara Kaweewan, Hiroyuki Nakagawa, Shinya Kodani
Applied Microbiology and Biotechnology.2020; 104(12): 5293. CrossRef - Corallibacterium pacifica gen. nov., sp. nov., a Novel Bacterium of the Family Vibrionaceae Isolated from Hard Coral
Sachithra Amarin Hettiarachchi, Su-Jin Lee, Youngdeuk Lee, Young-Kyung Kwon, Kae Kyoung Kwon, Sung-Hyun Yang, Eunyoung Jo, Do-Hyung Kang, Chulhong Oh
Current Microbiology.2018; 75(7): 835. CrossRef - Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater
Zhaobin Huang, Chunming Dong, Zongze Shao
International Journal of Systematic and Evolutionary Microbiology.2016; 66(8): 3050. CrossRef - Grimontia celer sp. nov., from sea water
María J. Pujalte, Teresa Lucena, Lidia Rodrigo-Torres, Alexandra La Mura, María A. Ruvira, David R. Arahal
International Journal of Systematic and Evolutionary Microbiology.2016; 66(8): 2906. CrossRef - Grimontia indica AK16T, sp. nov., Isolated from a Seawater Sample Reports the Presence of Pathogenic Genes Similar to Vibrio Genus
Aditya Singh, Bhumika Vaidya, Indu Khatri, T. N. R. Srinivas, Srikrishna Subramanian, Suresh Korpole, Anil Kumar Pinnaka, Axel Cloeckaert
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Enterovibrio paralichthyis sp. nov., isolated from the gut of an olive flounder Paralichthys olivaceus
- 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
- 300 View
- 0 Download
- 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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Zhengfeng Yang, Zhendi Huang, Qian Wu, Xianghua Tang, Zunxi Huang
International Journal of Molecular Sciences.2023; 24(10): 8532. CrossRef - Five decades of terrestrial and freshwater research at Ny-Ålesund, Svalbard
Å.Ø. Pedersen, P. Convey, K.K. Newsham, J.B. Mosbacher, E. Fuglei, V. Ravolainen, B.B. Hansen, T.C. Jensen, A. Augusti, E.M. Biersma, E.J. Cooper, S.J. Coulson, G.W. Gabrielsen, J.C. Gallet, U. Karsten, S.M. Kristiansen, M.M. Svenning, A.T. Tveit, M. Uchi
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Hossein Ahangari, Parivar Yazdani, Vida Ebrahimi, Saiedeh Razi Soofiyani, Robab Azargun, Vahideh Tarhriz, Shirin Eyvazi
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Xiu-Lan Chen, Yan Wang, Peng Wang, Yu-Zhong Zhang
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MUHAMMAD ASYRAF ABD LATIP, SITI AISYAH ALIAS, SMYKLA JERZY, FARIDAH YUSOF, MOHD AZRUL NAIM MOHAMAD, NOOR FAIZUL HADRY NORDIN
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Kattia Núñez-Montero, Damián Quezada-Solís, Zeinab Khalil, Robert Capon, Fernando Andreote, Leticia Barrientos
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Junaid Furhan
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An-Zhang Li, Xi-Bin Han, Ming-Xia Zhang, Yang Zhou, Meng Chen, Qing Yao, Hong-Hui Zhu
Frontiers in Microbiology.2019;[Epub] CrossRef - Analysis of the bacterial community from high alkaline (pH > 13) drainage water at a brown mud disposal site near Žiar nad Hronom (Banská Bystrica region, Slovakia) using 454 pyrosequencing
Jana Kisková, Zuzana Stramová, Peter Javorský, Jana Sedláková-Kaduková, Peter Pristaš
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Ceren Daskaya-Dikmen, Funda Karbancioglu-Guler, Beraat Ozcelik
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Soumya Chatterjee, Sourav K. Mukhopadhyay, Samiran S. Gauri, Satyahari Dey
International Immunopharmacology.2018; 60: 84. CrossRef - Advances in Antarctic Research for Antimicrobial Discovery: A Comprehensive Narrative Review of Bacteria from Antarctic Environments as Potential Sources of Novel Antibiotic Compounds Against Human Pathogens and Microorganisms of Industrial Importance
Kattia Núñez-Montero, Leticia Barrientos
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Emanuele Bosi, Marco Fondi, Valerio Orlandini, Elena Perrin, Isabel Maida, Donatella de Pascale, Maria Luisa Tutino, Ermenegilda Parrilli, Angelina Lo Giudice, Alain Filloux, Renato Fani
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Se Jong Han, Heeyong Park, Sunghui Kim, Dockyu Kim, Ha Ju Park, Joung Han Yim
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Dockyu Kim, Miyoun Yoo, Eungbin Kim, Soon Gyu Hong
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Yongqin Liu, John C. Priscu, Tandong Yao, Trista J. Vick-Majors, Alexander B. Michaud, Nianzhi Jiao, Juzhi Hou, Lide Tian, Anyi Hu, Zhong-Qiang Chen
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Cristian De Gobba, Gorazd Tompa, Jeanette Otte
Food Chemistry.2014; 165: 205. CrossRef - Isolation and physiological characterization of psychrophilic denitrifying bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway)
Andy Canion, Om Prakash, Stefan J. Green, Linda Jahnke, Marcel M. M. Kuypers, Joel E. Kostka
Environmental Microbiology.2013; 15(5): 1606. CrossRef - Enzymes from the gut bacteria of Atlantic cod, Gadus morhua and their influence on intestinal enzyme activity
C.C. LAZADO, C.M.A. CAIPANG, V. KIRON
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Polar Biology.2012; 35(9): 1433. CrossRef - Analysis and comparison of the microflora isolated from fresco surface and from surrounding air environment through molecular and biodegradative assays
Domenico Pangallo, Lucia Kraková, Katarína Chovanová, Alexandra Šimonovičová, Filomena De Leo, Clara Urzì
World Journal of Microbiology and Biotechnology.2012; 28(5): 2015. CrossRef
- Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst
- Antarcticimonas flava gen. nov., sp. nov., Isolated from Antarctic Coastal Seawater
- Seung-Jo Yang , Hyun-Myung Oh , Sangyun Chung , Jang-Cheon Cho
- J. Microbiol. 2009;47(5):517-523. Published online October 24, 2009
- DOI: https://doi.org/10.1007/s12275-009-0225-4
- 166 View
- 0 Download
- 9 Scopus
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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.
Introductory Journal Article
- [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
- 312 View
- 4 Download
- 6 Web of Science
- 5 Crossref
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Abstract
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-
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. -
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Gabriel Dorado, Sergio Gálvez, Teresa E. Rosales, Víctor F. Vásquez, Pilar Hernández
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