Journal of Microbiology

Ilnam Kang

10 Articles

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

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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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Validation List no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre: 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

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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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Structure and Metabolic Potential of Microbial Communities in High-altitude Lake Enriched with Dissolved Organic Carbon
Anna Kallistova, Alexander Savvichev, Stepan Toshchakov, Nina Tutubalina, Igor Rusanov, Kristina Petrova, Vitaly Kadnikov, Alexey Beletsky, Elena Zakharova, Nikolai Ravin, Nikolai Pimenov
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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
Flavobacterium adiutor sp. nov., a newly identified freshwater bacterium potentially supporting Microcystis growth via oxidative stress reduction
Ve Van Le, So-Ra Ko, Yuna Shin, Kyunghyun Kim, Sang-Ah Lee, Chi-Yong Ahn
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
Systematic and Applied Microbiology.2024; 47(4): 126518. CrossRef
Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
Journal of Microbiology.2024; 62(12): 1089. CrossRef
Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions
Jegadeesh Raman, Young-Joon Ko, Jeong-Seon Kim, Da-Hye Kim, Soo-Jin Kim
Journal of Microbiology and Biotechnology.2024; 34(3): 710. CrossRef
Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream: Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2022;60(8):806-813. Published online July 29, 2022; DOI: https://doi.org/10.1007/s12275-022-2298-2

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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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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

High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang: Suhyun Kim , Miri S. Park , Jaeho Song , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2020;58(11):893-905. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0452-2

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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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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
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Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater: Shan-Hui Li , Jaeho Song , Ilnam Kang , Juchan Hwang , Jang-Cheon Cho; J. Microbiol. 2020;58(6):463-471. Published online May 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0206-1

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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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Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
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Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta: Jaeho Song , Yeonjung Lim , Hye-Jin Jang , Yochan Joung , Ilnam Kang , Seong-Joo Hong , Choul-Gyun Lee , Jang-Cheon Cho; J. Microbiol. 2019;57(11):982-990. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9378-y

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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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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

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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 3.9􍾘Mbp 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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Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean: Jaeho Song , Ilnam Kang , Yochan Joung , Susumu Yoshizawa , Ryo Kaneko , Kenshiro Oshima , Masahira Hattori , Koji Hamasaki , Soochan Kim , Kangseok Lee , Jang-Cheon Cho; J. Microbiol. 2019;57(5):413-422. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8712-8

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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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Grimontia marina sp. nov., a Marine Bacterium Isolated from the Yellow Sea: Ahyoung Choi , Kyung-Mi Kim , Ilnam Kang , Seok-Hyun Youn , Young-Sang Suh , Yoon Lee , Jang-Cheon Cho; J. Microbiol. 2012;50(1):170-174. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1615-6

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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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Evaluation of the Sensitivity and Specificity of Primer Pairs and the Efficiency of RNA Extraction Procedures to Improve Noroviral Detection from Oysters by Nested Reverse Transcription-Polymerase Chain Reaction: Cheonghoon Lee , Sooryun Cheong , Hee-Jung Lee , Miye Kwon , Ilnam Kang , Eun-Gyoung Oh , Hong-Sik Yu , Soon-Bum Shin , Sang-Jong Kim; J. Microbiol. 2010;48(5):586-593. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0047-4

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Noroviruses (NoV) are the key cause of acute epidemic gastroenteritis, and oysters harvested from NoVpolluted sea areas are considered as the significant vectors of viral transmission. To improve NoV detection from oyster using nested reverse transcription-polymerase chain reaction (RT-PCR), we evaluated the sensitivity and specificity of previously published primer pairs and the efficiency of different RNA extraction procedures. Among the primer pairs used for RT-PCR, the sensitivity of GIF1/GIR1-GIF2/GIR1 and GIIF1/GIIR1-GIIF2/GIIR1 was higher than that of other primer pairs used in nested RT-PCR for the detection of NoV genogroup I (NoV GI) and NoV GII from both NoV-positive stool suspension and NoVseeded oyster concentrates, respectively; the resulting products showed neither unspecific bands in the positive samples nor false-positive bands in the negative controls. The extraction of NoV RNA from oyster samples using a QIAamp? Viral RNA Mini kit with a QIAshredderTM Homogenizer pretreatment afforded more efficient recovery (mean recovery for NoV GI and GII, 6.4%) and the procedure was less time consuming (<30 min) than most other RNA extraction procedures. The results of RNA extraction procedure and primer pairs evaluated by nested RT-PCR assay in this study can be useful for monitoring NoV contamination in oysters, which is an indicator of possible public health risks.

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