- Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.
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Yujin Kim , Yeon Bee Kim , Juseok Kim , Joon Yong Kim , Tae Woong Whon , Won-Hyong Chung , Eun-Ji Song , Young-Do Nam , Se Hee Lee , Seong Woon Roh
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J. Microbiol. 2022;60(7):678-688. Published online July 4, 2022
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DOI: https://doi.org/10.1007/s12275-022-1581-6
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 Abstract
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Two Gram-stain-positive, oxidase-negative, catalase-positive,
and coccus-shaped bacterial strains, designated CBA3104T
and CBA3105T, were isolated from kimchi. Strain CBA3104T
and CBA3105T grew at 10–35°C (optimum, 25°C and 30°C,
respectively), at pH 6.0–8.5 (optimum, pH 6.5), and in the
presence of 0–15% (w/v) NaCl (optimum, 5%). A phylogenetic
analysis based on 16S rRNA gene sequences revealed
that strain CBA3104T formed a distinct phylogenetic lineage
within the genus Brachybacterium whereas strain CBA3105T
was closely positioned with Brachybacterium halotolerans
MASK1Z-5T. The 16S rRNA gene sequence similarity between
strains CBA3104T and CBA3105T was 99.9%, but ANI
and dDDH values between strains CBA3104T and CBA3105T
were 93.61% and 51.5%, respectively. Strain CBA3104T showed
lower ANI and dDDH values than species delineation against
three closely related strains and type species of the genus
Brachybacterium, however, strain CBA3105T showed 96.63%
ANI value and 69.6% dDDH value with Brachybacterium
halotolerans MASK1Z-5T. Among biochemical analysis results,
strain CBA3104T could uniquely utilize bromo-succinic
acid whereas only strain CBA3105T was positive for alkaline
phosphatase and α-fucosidase among two novel strains, closely
related strains, and type species of the genus Brachybacterium.
Compared with strain CBA3105T and Brachybacterium
halotolerans JCM 34339T, strain CBA3105T was differentially
positive for acid production of D-arabinose, D-adonitol, and
potassium 5-ketogluconate and enzyme activity of β-glucuronidase.
Both strains contained menaquinone-7 as the dominant
quinone. The cell-wall peptidoglycan of two novel
strains contained meso-diaminopimelic acid. The major fatty
acids of strains CBA3104T and CBA3105T were anteiso-C15:0,
anteiso-C17:0, and iso-C16:0. The major polar lipids of both
strains were phosphatidylglycerol and diphosphatidylglycerol.
Strain CBA3104T possessed a uniquely higher abundance of
tRNA (97 tRNAs) than four Brachybacterium strains used for
comparative taxonomic analysis (54–62 tRNAs). Both the
CBA3104T and CBA3105T strain harbored various oxidoreductase,
transferase, hydrolase, and lyase as strain-specific
functional genes compared to closely related strains and Brachybacterium
type species. The results of biochemical/physiological,
chemotaxonomic, and genomic analyses demonstrated
that strains CBA3104T and CBA3105T represent a novel species
of the genus Brachybacterium and a novel subspecies of
B. halotolerans, respectively, for which the names Brachybacterium
kimchii sp. nov. and B. halotolerans subsp. kimchii
subsp. nov. are proposed. The type strains of the novel
species and the novel subspecies are CBA3104T (= KCCM
43417T = JCM 34759T) and CBA3105T (= KCCM 43418T =
JCM 34760T), respectively.
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Citations
Citations to this article as recorded by  - Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
Alexander G. Elcheninov, Kseniya S. Zayulina, Alexandra A. Klyukina, Mariia K. Kremneva, Ilya V. Kublanov, Tatiana V. Kochetkova
Microorganisms.2023; 12(1): 16. CrossRef - Validation List no. 208. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef -
Complete Genome Sequence of
Brachybacterium
sp. Strain NBEC-018, Isolated from Nematode-Infected Potatoes
Ling Chen, Yueying Wang, Nanxi Liu, Lei Zhu, Yong Min, Yimin Qiu, Yuxi Tian, Xiaoyan Liu, David Rasko
Microbiology Resource Announcements.2022;[Epub] CrossRef
- Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
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Young Joon Oh , Joon Yong Kim , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi
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J. Microbiol. 2021;59(5):460-466. Published online April 28, 2021
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DOI: https://doi.org/10.1007/s12275-021-0513-1
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74
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Abstract
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To date, all species in the genus Salicibibacter have been isolated
in Korean commercial kimchi. We aimed to describe
the taxonomic characteristics of two strains, NKC5-3T and
NKC21-4T, isolated from commercial kimchi collected from
various regions in the Republic of Korea. Cells of these strains
were rod-shaped, Gram-positive, aerobic, oxidase- and catalase-
positive, non-motile, halophilic, and alkalitolerant. Both
strains, unlike other species of the genus Salicibibacter, could
not grow without NaCl. Strains NKC5-3T and NKC21-4T
could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and
grow at pH 7.0–10.0 (optimum 8.5) and 8.0–9.0 (optimum
8.5), respectively; they showed 97.1% 16S rRNA gene sequence
similarity to each other and were most closely related
to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively).
The genome of strain NKC5-3T was nearly 4.6 Mb in
size, with 4,456 protein-coding sequences (CDSs), whereas
NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs.
OrthoANI values between the novel strains and S. kimchii
NKC1-1T were far lower than the species demarcation threshold.
NKC5-3T and NKC21-4T clustered together to form
branches that were distinct from the other Salicibibacter species.
The major fatty acids in these strains were anteiso-C15:0
and anteiso-C17:0, and the predominant menaquinone was
menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol
(DPG), phosphatidylglycerol (PG), and
five unidentified phospholipids (PL), and those of NKC21-4T
included DPG, PG, seven unidentified PLs, and an unidentified
lipid. Both isolates had DPG, which is the first case in
the genus Salicibibacter. The genomic G + C content of strains
NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively.
Based on phenotypic, genomic, phylogenetic, and chemotaxonomic
analyses, strains NKC5-3T (= KACC 22040T
= DSM 111417T) and NKC21-4T (= KACC 22041T = DSM
111418T) represent two novel species of the genus Salicibibacter,
for which the names Salicibibacter cibarius sp. nov.
and Salicibibacter cibi sp. nov. are proposed.
-
Citations
Citations to this article as recorded by - Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef
- Omics in gut microbiome analysis
-
Tae Woong Whon , Na-Ri Shin , Joon Yong Kim , Seong Woon Roh
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J. Microbiol. 2021;59(3):292-297. Published online February 23, 2021
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DOI: https://doi.org/10.1007/s12275-021-1004-0
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62
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38
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Abstract
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Our understanding of the interactions between microbial communities
and their niche in the host gut has improved owing
to recent advances in environmental microbial genomics.
Integration of metagenomic and metataxonomic sequencing
data with other omics data to study the gut microbiome
has become increasingly common, but downstream analysis
after data integration and interpretation of complex omics
data remain challenging. Here, we review studies that have
explored the gut microbiome signature using omics approaches,
including metagenomics, metataxonomics, metatranscriptomics,
and metabolomics. We further discuss recent
analytics programs to analyze and integrate multi-omics datasets
and further utilization of omics data with other advanced
techniques, such as adaptive immune receptor repertoire sequencing,
microbial culturomics, and machine learning, to
evaluate important microbiome characteristics in the gut.
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- Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food
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Young Joon Oh , Joon Yong Kim , Hee Eun Jo , Hyo Kyeong Park , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi
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J. Microbiol. 2020;58(5):387-394. Published online April 11, 2020
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DOI: https://doi.org/10.1007/s12275-020-9507-7
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Abstract
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Two bacterial strains designated NKC220-2T and NKC851-2
were isolated from commercial kimchi from different areas
in Korea. The strains were Gram-positive, aerobic, oxidaseand
catalase-positive, rod-shaped, spore-forming, non-motile,
and halophilic bacteria. Both strains grew without NaCl,
unlike type species in the genus Lentibacillus. The optimal
pH for growth was 8.0, higher than that of the type species
in the genus Lentibacillus, although growth was observed at
pH 5.5–9.0. 16S rRNA gene sequence-based phylogenetic analysis
indicated that the two strains (99.3–99.9% similarity)
are grouped within the genus Lentibacillus and most closely
related to Lentibacillus juripiscarius IS40-3T (97.4–97.6% similarity)
isolated from fish sauce in Thailand. OrthoANI value
between two novel strains and Lentibacillus lipolyticus SSKP1-
9T (79.5–79.6% similarity) was far lower than the species demarcation
threshold. Comparative genomic analysis displayed
differences between the two strains as well as among other
strains belonging to Lentibacillus. Furthermore, each isolate
had strain-specific groups of orthologous genes based on pangenome
analysis. Genomic G + C contents of strains NKC-
220-2T and NKC851-2 were 41.9 and 42.2 mol%, respectively.
The strains contained meso-diaminopimelic acid in their
cell walls, and the major menaquinone was menaquinone-7.
Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified
glycolipid, aminophospholipid, and phospholipid were
the major polar lipid components of both strains. The major
cellular fatty acids of the strains were anteiso-C15:0 and anteiso-
C17:0. Based on phenotypic, genomic, phylogenetic, and
chemotaxonomic features, strains NKC220-2T and NKC851-2
represent novel species of the genus Lentibacillus, for which
the name Lentibacillus cibarius sp. nov. is proposed. The type
strain is NKC220-2T (= KACC 21232T = JCM 33390T).
-
Citations
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International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis
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Marina Ghislaine Abré, Clémentine Amenan Kouakou-Kouamé, Florent Kouadio N’guessan, Corinne Teyssier, Didier Montet
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Yun Wang, Gang-Qiang Jiang, Hong-Ping Lin, Peng Sun, Hong-Yan Zhang, Dong-Mei Lu, Li-Yun Wang, Chang-Jin Kim, Shu-Kun Tang
Archives of Microbiology.2021; 203(2): 621. CrossRef - Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. 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 - List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef
- Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
-
Young Joon Oh , Joon Yong Kim , Hyo Kyeong Park , Ja-Young Jang , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi
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J. Microbiol. 2019;57(11):997-1002. Published online October 28, 2019
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DOI: https://doi.org/10.1007/s12275-019-9421-z
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Abstract
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A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic
bacterium–designated as strain NKC3-5T–was isolated
from kimchi that was collected from the Geumsan area
in the Republic of Korea. Cells of isolated strain NKC3-5T
were 0.5–0.7μm wide and 1.4–2.8 μm long. The strain
NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum
10%), pH 6.5–10.0 (optimum pH 9.0), and 25–40°C (optimum
35°C). The cells were able to reduce nitrate under aerobic
conditions, which is the first report in the genus Salicibibacter.
The genome size and genomic G + C content of
strain NKC3-5T were 3,754,174 bp and 45.9 mol%, respectively;
it contained 3,630 coding sequences, 16S rRNA genes
(six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic
analysis based on 16S rRNA showed that strain NKC-
3-5T clustered with bacterium Salicibibacter kimchii NKC1-1T,
with a similarity of 96.2–97.6%, but formed a distinct branch
with other published species of the family Bacillaceae. In addition,
OrthoANI value between strain NKC3-5T and Salicibibacter
kimchii NKC1-1T was far lower than the species demarcation
threshold. Using functional genome annotation,
the result found that carbohydrate, amino acid, and vitamin
metabolism related genes were highly distributed in the genome
of strain NKC3-5T. Comparative genomic analysis revealed
that strain NKC3-5T had 716 pan-genome orthologous
groups (POGs), dominated with carbohydrate metabolism.
Phylogenomic analysis based on the concatenated core
POGs revealed that strain NKC3-5T was closely related to
Salicibibacter kimchii. The predominant polar lipids were
phosphatidylglycerol and two unidentified lipids. Anteiso-
C15:0, iso-C17:0, anteiso-C17:0, and iso-C15:0 were the major cellular
fatty acids, and menaquinone-7 was the major isoprenoid
quinone present in strain NKC3-5T. Cell wall peptidoglycan
analysis of strain NKC3-5T showed that meso-diaminopimelic
acid was the diagnostic diamino acid. The phenotypic,
genomic, phylogenetic, and chemotaxonomic properties
reveal that the strain represents a novel species of
the genus Salicibibacter, for which the name Salicibibacter
halophilus sp. nov. is proposed, with the type strain NKC3-5T
(= KACC 21230T = JCM 33437T).
-
Citations
Citations to this article as recorded by - Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. CrossRef - The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
Genes.2021; 12(11): 1756. CrossRef - List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef
- Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp
-
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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6
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6
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Abstract
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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).
-
Citations
Citations to this article as recorded by - Bacteroides faecium sp. nov. isolated from human faeces
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
-
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
-
J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018
-
DOI: https://doi.org/10.1007/s12275-019-8487-y
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92
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21
Web of Science
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22
Crossref
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Abstract
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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.
-
Citations
Citations to this article as recorded by - Effects of total microbiota-containing backslop from 450-day-fermented kimchi on microbe and metabolite dynamics
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
- Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi
-
Ja-Young Jang , Young Joon Oh , Seul Ki Lim , Hyo Kyeong Park , Changsu Lee , Joon Yong Kim , Mi-Ai Lee , Hak-Jong Choi
-
J. Microbiol. 2018;56(12):880-885. Published online October 25, 2018
-
DOI: https://doi.org/10.1007/s12275-018-8518-0
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94
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11
Web of Science
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12
Crossref
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Abstract
-
A moderately halophilic and alkalitolerant bacterial strain
NKC1-1T was isolated from commercial kimchi in Korea.
Strain NKC1-1T was Gram-stain-positive, aerobic, rod-shaped,
non-motile, and contained diaminopimelic acid-type murein.
Cell growth was observed in a medium containing 0–25%
(w/v) NaCl (optimal at 10% [w/v]), at 20–40°C (optimal at
37°C) and pH 6.5–10.0 (optimal at pH 9.0). The major isoprenoid
quinone of the isolate was menaquinone-7, and the
major polar lipids were phosphatidylglycerol and unidentified
phospholipids. Cell membrane of the strain contained
iso-C17:0 and anteiso-C15:0 as the major fatty acids. Its DNA
G + C content was 45.2 mol%. Phylogenetic analysis indicated
the strain to be most closely related to Geomicrobium halophilum
with 92.7–92.9% 16S rRNA gene sequence similarity.
Based on polyphasic taxonomic evaluation with phenotypic,
phylogenetic, and chemotaxonomic analyses, the strain represents
a novel species in a new genus, for which the name
Salicibibacter kimchii gen. nov., sp. nov. is proposed (= CECT
9537T; KCCM 43276T).
-
Citations
Citations to this article as recorded by - A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families
Yangjie Li, Dechao Zhang, Dexin Bo, Donghai Peng, Ming Sun, Jinshui Zheng
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives
Sharareh Harirchi, Taner Sar, Mohaddaseh Ramezani, Habibu Aliyu, Zahra Etemadifar, Seyed Ali Nojoumi, Fatemeh Yazdian, Mukesh Kumar Awasthi, Mohammad J. Taherzadeh
Microorganisms.2022; 10(12): 2355. CrossRef - Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. CrossRef - The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
Genes.2021; 12(11): 1756. CrossRef - Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection
Seung Woo Ahn, Se Hee Lee, Uh Jin Kim, Hee-Chang Jang, Hak-Jong Choi, Hyon E. Choy, Seung Ji Kang, Seong Woon Roh
Gut Pathogens.2021;[Epub] CrossRef - Haloplanus rubicundus sp. nov., an extremely halophilic archaeon isolated from solar salt
Yeon Bee Kim, Joon Yong Kim, Hye Seon Song, Se Hee Lee, Na-Ri Shin, Jin-Woo Bae, Jinjong Myoung, Ki-Eun Lee, In-Tae Cha, Jin-Kyu Rhee, Seong Woon Roh
Systematic and Applied Microbiology.2020; 43(3): 126085. CrossRef - Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses
Min Young Jung, Changsu Lee, Myung-Ji Seo, Seong Woon Roh, Se Hee Lee
BMC Microbiology.2020;[Epub] CrossRef - Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food
Young Joon Oh, Joon Yong Kim, Hee Eun Jo, Hyo Kyeong Park, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2020; 58(5): 387. CrossRef - Effects of an auxin-producing symbiotic bacterium on cell growth of the microalga Haematococcus pluvialis: Elevation of cell density and prolongation of exponential stage
Changsu Lee, Min Seo Jeon, Joon Yong Kim, Se Hee Lee, Dae Geun Kim, Seong Woon Roh, Yoon-E Choi
Algal Research.2019; 41: 101547. CrossRef - Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
Young Joon Oh, Joon Yong Kim, Hyo Kyeong Park, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2019; 57(11): 997. CrossRef - List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef - Propionibacterium freudenreichii CIRM-BIA 129 Osmoadaptation Coupled to Acid-Adaptation Increases Its Viability During Freeze-Drying
Floriane Gaucher, Koffigan Kponouglo, Houem Rabah, Sylvie Bonnassie, Jordane Ossemond, Sandrine Pottier, Julien Jardin, Valérie Briard-Bion, Pierre Marchand, Philippe Blanc, Romain Jeantet, Gwénaël Jan
Frontiers in Microbiology.2019;[Epub] CrossRef
- Acinetobacter apis sp. nov., Isolated from the Intestinal Tract of a Honey Bee, Apis mellifera
-
Pil Soo Kim , Na-Ri Shin , Joon Yong Kim , Ji-Hyun Yun , Dong-Wook Hyun , Jin-Woo Bae
-
J. Microbiol. 2014;52(8):639-645. Published online August 1, 2014
-
DOI: https://doi.org/10.1007/s12275-014-4078-0
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87
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39
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Abstract
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A novel Gram-negative, obligate aerobic, non-motile, and both coccobacillus- and bacillus-shaped bacterium, designated strain HYN18T, was isolated from the intestinal tract of a honey bee (Apis mellifera). The isolate was oxidasenegative
and catalase-positive. Strain HYN18T showed optimum growth at 25°C, pH 6–7, and in the presence of 1% (w/v) NaCl in trypticase soy broth medium. The isolate was
negative for hydrolyses of starch, casein, gelatin and urea, indole production from tryptone and hemolysis on sheep blood agar. A phylogenetic analysis based on the 16S rRNA gene and rpoB gene sequence showed that strain HYN18T was most closely related to Acinetobacter nectaris SAP 763.2T and A. boissieri SAP 284.1T with 98.3% and 98.1% similarity (16S rRNA gene), respectively, and 84.4% similarity with Acinetobacter nectaris SAP 763.2T (rpoB gene). The major cellular fatty acids were summed features 3 (comprising C16:1ω7c/C16:1ω6c), C12:0 and C16:0. The main isoprenoid quinone was ubiquinone-9 (Q-9). The polar lipids of strain
HYN18T were phosphatidylethanolamine, three unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 40.6 mol%. DNADNA hybridization experiments indicated less than 33 ± 10% relatedness to the closest phylogenetic species, Acinetobacter nectaris SAP 763.2T. Thus, the phenotypic, phylogenetic and genotypic analyses indicate that strain HYN18T is a novel species within the genus Acinetobacter, for which the name Acinetobacter apis is proposed. The type strain is HYN18T (=KACC 16906T =JCM 18575T).
-
Citations
Citations to this article as recorded by - Tiny but mighty? Overview of a decade of research on nectar bacteria
Sergio Quevedo‐Caraballo, Clara de Vega, Bart Lievens, Tadashi Fukami, Sergio Álvarez‐Pérez
New Phytologist.2025; 245(5): 1897. CrossRef -
Genome evolution following an ecological shift in nectar-dwelling
Acinetobacter
Vivianna A. Sanchez, Tanya Renner, Lydia J. Baker, Tory A. Hendry, Michael J. Imperiale
mSphere.2025;[Epub] CrossRef - Exploring the Multifaceted Genus Acinetobacter: the Facts, the Concerns and the Oppoptunities the Dualistic Geuns Acinetobacter
Tsvetana Muleshkova, Inga Bazukyan, Konstantinos Papadimitriou, Velitchka Gotcheva, Angel Angelov, Svetoslav G. Dimov
Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef - The Latitudinal Biotic Interaction Hypothesis revisited: contrasting latitudinal richness gradients in actively vs. passively accumulated interaction partners of honey bees
Alyssa R. Cirtwill, Tomas Roslin, Pablo Peña-Aguilera, Agathe Agboto, William Bercê, Svetlana N. Bondarchuk, Robert Brodschneider, Behzad Heidari, Camara Kaizirege, Justine Muhoro Nyaga, Ojonugwa Ekpah, Gonzalo Ossa Gomez, Claudia Paz, Christian Pirk, Ami
BMC Ecology and Evolution.2025;[Epub] CrossRef - DNA in honey could describe the changes in flower visits and microbe encounters of honey bees over decades
Alyssa R. Cirtwill, Helena Wirta
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FEMS Microbiology Ecology.2024;[Epub] CrossRef - Bumble bee microbiota shows temporal succession and increase of lactic acid bacteria when exposed to outdoor environments
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Microbial Ecology.2023; 86(1): 377. CrossRef - Molecular identification of major bacteria in honey and the effect of microwave treatment on its microbial quality and antibacterial activity
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AIMS Agriculture and Food.2022; 7(3): 594. CrossRef - Collection Time, Location, and Mosquito Species Have Distinct Impacts on the Mosquito Microbiota
Daniel W. Pérez-Ramos, Martina M. Ramos, Kyle C. Payne, Bryan V. Giordano, Eric P. Caragata
Frontiers in Tropical Diseases.2022;[Epub] CrossRef - Potential effects of nectar microbes on pollinator health
Valerie N. Martin, Robert N. Schaeffer, Tadashi Fukami
Philosophical Transactions of the Royal Society B: Biological Sciences.2022;[Epub] CrossRef - Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee
Helena Kristiina Wirta, Mohammad Bahram, Kirsten Miller, Tomas Roslin, Eero Vesterinen, Wolfgang Blenau
PLOS ONE.2022; 17(7): e0268250. CrossRef - The distinctive roles played by the superoxide dismutases of the extremophile Acinetobacter sp. Ver3
Bruno Alejandro Steimbrüch, Mariana Gabriela Sartorio, Néstor Cortez, Daniela Albanesi, María-Natalia Lisa, Guillermo Daniel Repizo
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Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
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- Dyella jejuensis sp. nov., Isolated from Soil of Hallasan Mountain in Jeju Island
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Min-Soo Kim , Dong-Wook Hyun , Joon Yong Kim , Soyeon Kim , Jin-Woo Bae , Eun-Jin Park
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J. Microbiol. 2014;52(5):373-377. Published online May 9, 2014
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DOI: https://doi.org/10.1007/s12275-014-3670-7
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Abstract
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A novel bacterium, designated JP1T, was isolated from soil of Hallasan Mountain in Jeju Island. The isolate was a Gram- negative, aerobic, motile and rod-shaped (0.2–0.4 × 1.2–2.0 μm) bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain JP1T was closely related to Dyella koreensis with 97.6% similarity. Growth of strain JP1T occurred at 10–37°C, pH 5–7 and 0–1% (w/v) NaCl. The genomic DNA G+C content of strain JP1T was 62.1 mol%. The major fatty acids were iso-C16:0, iso-C17:1 ω9c, and iso- C15:0. The predominant quinone was ubiquinone-8. The major polar lipids of strain JP1T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, uniden-tified aminolipids and unidentified aminophospholipids. The DNA-DNA relatedness values between strain JP1T and pre-viously reported Dyella species were <10%. Based on pheno-typic, genotypic, and phylogenetic distinctness, strain JP1T represents a novel species in the genus Dyella, for which the name Dyella jejuensis sp. nov. is proposed. The type strain is JP1T (=KACC 17701T =JCM 19615T).
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Citations
Citations to this article as recorded by - Effects of different cultivation media on root bacterial community characteristics of greenhouse tomatoes
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Frontiers in Microbiology.2023;[Epub] CrossRef - Soil pH and aridity influence distributions of branched tetraether lipids in grassland soils along an aridity transect
Jingjing Guo, Tian Ma, Nana Liu, Xinying Zhang, Huifeng Hu, Wenhong Ma, Zhiheng Wang, Xiaojuan Feng, Francien Peterse
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Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China
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Dyella halodurans sp. nov., isolated from lower subtropical forest soil
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International Journal of Systematic and Evolutionary Microbiology.2017; 67(3): 736. CrossRef -
Dyella lipolytica sp. nov., a lipolytic bacterium isolated from lower subtropical forest soil
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- Paenibacillus marinisediminis sp. nov., a Bacterium Isolated from Marine Sediment
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Hae-Won Lee , Seong Woon Roh , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Joon Yong Kim , Dong-Wook Hyun , Daekyung Kim , Jin-Woo Bae
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J. Microbiol. 2013;51(3):312-317. Published online June 28, 2013
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DOI: https://doi.org/10.1007/s12275-013-3198-2
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57
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Abstract
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A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35T was most closely related to Paenibacillus taiwanensis G-soil-2-3T (97.2% similarity). The optimal growth conditions for strain LHW35T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C15:0 and C16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified aminohospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35T (=KACC 16317T =JCM 17886T).
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