- Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt
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Hye Seon Song , Juseok Kim , Yeon Bee Kim , Se Hee Lee , Tae Woong Whon , Seong Woon Roh
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J. Microbiol. 2022;60(9):899-904. Published online July 14, 2022
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DOI: https://doi.org/10.1007/s12275-022-2137-5
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Two novel halophilic archaeal strains, CBA1133T and CBA-
1134, were isolated from solar salt in South Korea. The 16S
rRNA gene sequences of the isolates were identical to each
other and were closely related to the genera Natronomonas
(92.3–93.5%), Salinirubellus (92.2%), Halomarina (91.3–
92.0%), and Haloglomus (91.4%). The isolated strains were
coccoid, Gram-stain-negative, aerobic, oxidase-positive, and
catalase-negative. Growth occurred under temperatures of
25–50°C (optimum, 45°C), NaCl levels of 10–30% (optimum,
15%), pH levels of 6.0–8.5 (optimum, 7.0), and MgCl2 concentrations
of 0–500 mM (optimum, 100 mM). Digital DNADNA
hybridization values between the strains and related
genera ranged from 18.3% to 22.7%. The major polar lipids
of the strains were phosphatidyl glycerol, phosphatidyl glycerol
phosphate methyl ester, and phosphatidyl glycerol sulfate.
Genomic, phenotypic, physiological, and biochemical
analyses of the isolates revealed that they represent a novel
genus and species in the family Halobacteriaceae. The type
strain is CBA1133T (= KACC 22148T = JCM 34265T), for which
the name Sala cibi gen. nov., sp. nov. is proposed.
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Citations
Citations to this article as recorded by  - Phylogenomic and comparative analyses on protein sequences from Halobacteria to identify taxon-specific molecular markers which demarcate different Halobacteriaceae and Haloarculaceae genera
Radhey S. Gupta, Bashudev Rudra, Josh Tony, Sarah Bello
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Dominance and diversity of archaea in food-grade salts: insights for histamine degradation in salt-fermented foods
Jing Hou, Ya-Ling Mao, Na Li, Xiao-Yan Yang, Chidiebele Nwankwo, Heng-Lin Cui
International Journal of Food Science and Technology.2024; 59(12): 9490. CrossRef - Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef - Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat
Yao Hu, Xue Ma, Shun Tan, Xin-Xin Li, Mu Cheng, Jing Hou, Heng-Lin Cui
Antonie van Leeuwenhoek.2024;[Epub] CrossRef - Assessing the impact of heavy metals on bacterial diversity in coastal regions of Southeastern India
Chandra Veluchamy, Avinash Sharma, Kalaivani Thiagarajan
Environmental Monitoring and Assessment.2024;[Epub] CrossRef - Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively
Umakant Bhoopati Deshmukh, Aharon Oren
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Halorarius litoreus gen. nov., sp. nov., Halorarius halobius sp. nov., Haloglomus halophilum sp. nov., Haloglomus salinum sp. nov., and Natronomonas marina sp. nov., extremely halophilic archaea isolated from tidal flat and marine solar salt
Ya-Ping Sun, Bei-Bei Wang, Zhang-Ping Wu, Xi-Wen Zheng, Jing Hou, Heng-Lin Cui
Frontiers in Marine Science.2023;[Epub] CrossRef - Naming new taxa of prokaryotes in the 21st century
Aharon Oren
Canadian Journal of Microbiology.2023; 69(4): 151. CrossRef
- Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp
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Juseok Kim , Joon Yong Kim , Hye Seon Song , In-Tae Cha , Seong Woon Roh , Se Hee Lee
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J. Microbiol. 2019;57(6):444-449. Published online May 27, 2019
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DOI: https://doi.org/10.1007/s12275-019-8704-8
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A Gram-stain-negative and facultatively aerobic bacterium,
designated as strain CBA4604T, was isolated from a traditional
Korean salted and fermented shrimp food (saeu-jeot).
Phylogenetic analysis based on 16S rRNA gene sequences
showed that strain CBA4604T formed a clearly distinct phyletic
lineage from closely related species within the genus
Paracoccus. Strain CBA4604T was the most closely related to
P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity)
and other type strains (≤ 97.0%). The genome comprised a
chromosome and two plasmids of 3,299,166 bp with 66.5%
G+C content. The DNA-DNA relatedness values between
strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM
8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and
16.7%, respectively. Cells of the strain were short rod-shaped
and oxidase- and catalase-positive. The growth of strain CBA-
4604T was observed at 10–40°C (optimum, 37°C), pH 6.0–10.0
(optimum, pH 7.0), and in the presence of 0–8.0% (w/v) NaCl
(optimum, 0–2.0%). Strain CBA4604T contained ubiquinone
10 as the sole isoprenoid quinone and summed feature 8 (C18:1
ω7c/C18:1 ω6c) and C18:0 as the major cellular fatty acids. The
polar lipids consisted of phosphatidylcholine, phosphatidylglycerol,
diphosphatidylglycerol, phospholipid, an unidentified
aminolipid, an unidentified glycolipid, and three unidentified
lipids. Based on its phylogenetic, genomic, phenotypic,
and chemotaxonomic features, we concluded that strain CBA-
4604T represents a novel species in the genus Paracoccus and
we propose the name Paracoccus jeotgali sp. nov. The type
strain is CBA4604T (= KACC 19579T = JCM 32510T).
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Citations
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Juseok Kim, Hye Seon Song, Joon Yong Kim, Tae Woong Whon, Won-Hyong Chung, Young-Do Nam, Yoon-E Choi, Seong Woon Roh
International Journal of Systematic and Evolutionary Microbiology.2023;[Epub] CrossRef - ODFM, an omics data resource from microorganisms associated with fermented foods
Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
Scientific Data.2021;[Epub] CrossRef - Flaviflexus ciconiae sp. nov., isolated from the faeces of the oriental stork, Ciconia boyciana
Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2020; 70(10): 5439. CrossRef -
Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa
Anusha Rai, Smita N, Suresh G, Shabbir A, Deepshikha G, Sasikala Ch, Ramana Ch.V
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(3): 1720. CrossRef - Pectin Degradation is an Important Determinant for Alfalfa Silage Fermentation through the Rescheduling of the Bacterial Community
Bing Wang, Zhiqiang Sun, Zhu Yu
Microorganisms.2020; 8(4): 488. CrossRef - Iodobacter ciconiae sp. nov., a bacterium isolated from feces of oriental stork, Ciconia boyciana
Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2019; 69(9): 2948. CrossRef
- Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables
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Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh
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J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018
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DOI: https://doi.org/10.1007/s12275-019-8487-y
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White colony-forming yeasts (WCFYs) often appear in fermented
foods, depending on the storage method. Despite
the ongoing research on fermented foods, the community
and genome features of WCFYs have not been well studied.
In this study, the community structures of WCFYs on fermented
vegetables (kimchi) prepared with various raw materials
were investigated using deep sequencing. Only eight
operational taxonomic units (OTUs) were detected, indicating
that the community structure of WCFYs on kimchi is very
simple. The five most abundant OTUs represented Pichia
kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora
uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs
were isolated from the surface of the food samples. Whole
genomes of the five major yeast strains were sequenced and
annotated. The total genome length for the strains ranged
from 8.97 Mbp to 21.32 Mbp. This is the first study to report
genome sequences of the two yeasts Pichia kluyveri and Candida
sake. Genome analysis indicated that each yeast strain
had core metabolic pathways such as oxidative phosphorylation;
purine metabolism; glycolysis/gluconeogenesis; aminoacyl-
tRNA biosynthesis; citrate cycle; but strain specific
pathways were also found. In addition, no toxin or antimicrobial
resistance genes were identified. Our study provides
genome information for five WCFY strains that may highlight
their potential beneficial or harmful metabolic effects
in fermented vegetables.
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Citations
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Dongjun Kim, Seong-Eun Park, Juhan Pak, Joon Yong Kim, Tae Woong Whon, Kwang-Moon Cho, Suryang Kwak, Hong-Seok Son, Seong Woon Roh
Food Chemistry.2025; 468: 142420. CrossRef - Effects of storage temperature on the diversity of white colony-forming yeast and correlations between bacterial and yeast communities in salted kimchi cabbage
Chan-Il Bae, Yoon-Soo Gwak, Su-Jeong Eom, Shinyoung Lee, Mi-Ju Kim
Food Science and Biotechnology.2025; 34(4): 1001. CrossRef - Effects of white colony-forming yeast on microbial communities and metabolites in kimchi
Yoon-Soo Gwak, Shinyoung Lee, Chan-Il Bae, Su-Jeong Eom, Mi-Ju Kim
Food Chemistry.2025; 465: 142059. CrossRef - D-Limonene Inhibits Pichia kluyveri Y-11519 in Sichuan Pickles by Disrupting Metabolism
Chaoyi Zeng, Yue Sun, Haoran Lin, Ziyu Li, Qing Zhang, Ting Cai, Wenliang Xiang, Jie Tang, Patchanee Yasurin
Molecules.2024; 29(15): 3561. CrossRef - Genomic analysis of Kazachstania aerobia and Kazachstania servazzii reveals duplication of genes related to acetate ester production
Mandy Man-Hsi Lin, Michelle E. Walker, Vladimir Jiranek, Krista M. Sumby
Microbial Genomics
.2023;[Epub] CrossRef - Fabrication of Gold Nanoparticles and Cinnamaldehyde-Functionalized Paper-Based Films and Their Antimicrobial Activities against White Film-Forming Yeasts
Seong Youl Lee, Eun Hae Kim, Tae-Woon Kim, Young-Bae Chung, Ji-Hee Yang, Sung Hee Park, Mi-Ai Lee, Sung Gi Min
ACS Omega.2023; 8(9): 8256. CrossRef - Combined effect of a neonicotinoid insecticide and a fungicide on honeybee gut epithelium and microbiota, adult survival, colony strength and foraging preferences
Riccardo Favaro, Paula Melisa Garrido, Daniele Bruno, Chiara Braglia, Daniele Alberoni, Loredana Baffoni, Gianluca Tettamanti, Martin Pablo Porrini, Diana Di Gioia, Sergio Angeli
Science of The Total Environment.2023; 905: 167277. CrossRef - The potential correlation between microbial communities and flavors in fermented bamboo shoots
Shubo Li, Minghao Sun, Yufeng Tian, Cuiwen Jian, Beibei Lv, Yunxia Bai, Xiaoling Liu, Yuan Guo
Food Bioscience.2023; 56: 103066. CrossRef - Profiling the composition and metabolic functions of microbial community in pellicle-forming radish paocai
Ting Mi, Yao Jin, Yulan Che, Jun Huang, Rongqing Zhou, Chongde Wu
International Journal of Food Microbiology.2023; 388: 110087. CrossRef - Long-term population dynamics of viable microbes in a closed ecosystem of fermented vegetables
Joon Yong Kim, Seong-Eun Park, Eun-Ju Kim, Seung-Ho Seo, Tae Woong Whon, Kwang-Moon Cho, Sun Jae Kwon, Seong Woon Roh, Hong-Seok Son
Food Research International.2022; 154: 111044. CrossRef - Safety assessment of white colony-forming yeasts in kimchi
Chang Hee Jeong, Joon Yong Kim, Young Joon Oh, Hye In Ko, Seong Woon Roh, Sung Wook Hong, Hyuk Cheol Kwon, Sung Gu Han, Tae Woon Kim
Food Microbiology.2022; 106: 104057. CrossRef - Safety Assessment of White Colony-Forming Yeasts in Kimchi
Chang Hee Jeong, Joon Yong Kim, Young Joon Oh, Hye In Ko, Seong Woon Roh, Sung Wook Hong, Hyuk Cheol Kwon, Sung Gu Han, Tae-Woon Kim
SSRN Electronic Journal .2022;[Epub] CrossRef - Real-time PCR assays for the quantitative detection of Kazachstania servazzii and Candida sake related to undesirable white colony on kimchi
Mi-Ju Kim, Sung-gi Min, So Won Shin, Jiyong Shin, Hae-Yeong Kim
Food Control.2021; 125: 107984. CrossRef -
Yarrowia lipolytica: a multitalented yeast species of ecological significance
Dmitry Mamaev, Renata Zvyagilskaya
FEMS Yeast Research.2021;[Epub] CrossRef - ODFM, an omics data resource from microorganisms associated with fermented foods
Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
Scientific Data.2021;[Epub] CrossRef - Growth Inhibitory Effect of Garlic Powder and Cinnamon Extract on White Colony-Forming Yeast in Kimchi
Mi-Ju Kim, Seong-Eun Kang, Chang Hee Jeong, Sung-Gi Min, Sung Wook Hong, Seong Woon Roh, Deok-Young Jhon, Tae-Woon Kim
Foods.2021; 10(3): 645. CrossRef - Halotolerant Yeasts: Biodiversity and Potential Application
O.D. Ianieva
Mikrobiolohichnyi Zhurnal.2020; 82(5): 65. CrossRef - Impact of fermentation conditions on the diversity of white colony-forming yeast and analysis of metabolite changes by white colony-forming yeast in kimchi
Mi-Ju Kim, Hae-Won Lee, Joon Yong Kim, Seong Eun Kang, Seong Woon Roh, Sung Wook Hong, Seung Ran Yoo, Tae-Woon Kim
Food Research International.2020; 136: 109315. CrossRef - Non-tandem repeat polymorphisms at microsatellite loci in wine yeast species
María Laura Raymond Eder, Alberto Luis Rosa
Molecular Genetics and Genomics.2020; 295(3): 685. CrossRef - Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches
Se Hee Lee, Tae Woong Whon, Seong Woon Roh, Che Ok Jeon
Applied Microbiology and Biotechnology.2020; 104(18): 7731. CrossRef - Draft Genome Sequences of Two Isolates of the Yeast Kazachstania servazzii Recovered from Soil in Ireland
Lynne Faherty, Clifton Lewis, Matt McElheron, Niall Garvey, Róisín Duggan, Ben Shovlin, Tadhg Ó Cróinín, Kevin P. Byrne, Caoimhe E. O’Brien, Kenneth H. Wolfe, Geraldine Butler, Antonis Rokas
Microbiology Resource Announcements.2019;[Epub] CrossRef - Effect of lactic acid bacteria on phenyllactic acid production in kimchi
Sera Jung, Hyelyeon Hwang, Jong-Hee Lee
Food Control.2019; 106: 106701. CrossRef
- Citrimicrobium luteum gen. nov., sp. nov., Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Gut of a Sea Cucumber Stichopus japonicus
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Hong-Joo Jung , In-Tae Cha , Kyung June Yim , Hye Seon Song , Kichul Cho , Daekyung Kim , Hae-Won Lee , Jae Kook Lee , Myung-Ji Seo , Seong Woon Roh , Sung-Jae Lee
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J. Microbiol. 2014;52(10):819-824. Published online August 27, 2014
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DOI: https://doi.org/10.1007/s12275-014-4136-7
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A Gram-stain negative, yellow-pigmented, motile, pleomorphic
bacterium, designated strain CBA4602T, was isolated
from the gut of the sea cucumber Stichopus japonicus, which
was collected from Jeju Island in the Republic of Korea. In
a phylogenetic analysis based on the 16S rRNA gene, strain
CBA4602T belonged to the order Sphingomonadales in the
class Alphaproteobacteria. The 16S rRNA gene sequence similarity
between strain CBA4602T and ‘Citromicrobium bathyomarinum’
JF-1, the most closely related strain having nonvalidly
published name, was 98.4%, followed by 95.2–96.7%
identities with sequence of the other closest strains in the
genus Erythrobacter. Strain CBA4602T had bacteriochlorophyll
a and carotenoids. Strain CBA4602T grew in 0–10%
(w/v) NaCl, at 10–42°C and pH 6.0–8.0, with optimal growth
in 1–2% NaCl, at 30–37°C and pH 7.0. Strain CBA4602T
was positive for catalase and oxidase activities and was able
to hydrolyse gelatine and Tween 20 and 40, but not starch,
Tween 80 or L-tyrosine. The G+C content of genomic DNA
from strain CBA4602T was 68.0 mol% and Q-10 was the major
detected isoprenoid quinone. The polar lipids were three
unidentified phospholipids, three unidentified glycolipids,
and two unidentified lipids. The dominant fatty acids were
anteiso-C15:0, C16:0, anteiso-C17:0 and C18:0. As considering
the current taxonomic status of the genus ‘Citromicrobium’
and polyphasic taxonomic analyses, strain CBA4602T represents
a novel genus and species. The name Citrimicrobium
luteum is proposed for the type strain CBA4602T (=KACC
17668T =JCM 19530T).
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Citations
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Steven Brady Kuzyk, Kaitlyn Wiens, Xiao Ma, Vladimir Yurkov
Journal of Great Lakes Research.2021; 47(3): 567. CrossRef
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