- 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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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).
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Citations
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Genes.2021; 12(11): 1756. CrossRef - Lentibacillus saliphilus. sp. nov., a moderately halophilic bacterium isolated from a saltern in Korea
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
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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
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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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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).
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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
- Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi
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Ja-Young Jang , Young Joon Oh , Seul Ki Lim , Hyo Kyeong Park , Changsu Lee , Joon Yong Kim , Mi-Ai Lee , Hak-Jong Choi
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J. Microbiol. 2018;56(12):880-885. Published online October 25, 2018
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DOI: https://doi.org/10.1007/s12275-018-8518-0
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1,286
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Abstract
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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).
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J. Microbiol. 2017;55(12):933-938. Published online December 7, 2017
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DOI: https://doi.org/10.1007/s12275-017-7386-3
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1,038
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A Gram-stain-positive, halophilic, rod-shaped, non-motile,
spore forming bacterium, strain NKC1-2T, was isolated from
kimchi, a Korean fermented food. Comparative analysis based
on 16S rRNA gene sequence demonstrated that the isolated
strain was a species of the genus Virgibacillus. Strain NKC1-
2T exhibited high level of 16S rRNA gene sequence similarity
with the type strains of Virgibacillus xinjiangensis SL6-1T
(96.9%), V. sediminis YIM kkny3T (96.8%), and V. salarius
SA-Vb1T (96.7%). The isolate grew at pH 6.5–10.0 (optimum,
pH 8.5–9.0), 0.0–25.0% (w/v) NaCl (optimum, 10–15% NaCl),
and 15–50°C (optimum, 37°C). The major menaquinone in
the strain was menaquinone-7, and the main peptidoglycan
of the strain was meso-diaminopimelic acid. The predominant
fatty acids of the strain were iso-C14:0, anteisio-C15:0, iso-
C15:0, and iso-C16:0 (other components were < 10.0%). The
polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol.
The genomic DNA G + C content of NKC1-2T
was 42.5 mol%. On the basis of these findings, strain NKC1-
2T is proposed as a novel species in the genus Virgibacillus,
for which the name Virgibacillus kimchii sp. nov. is proposed
(=KACC 19404T =JCM 32284T). The type strain of Virgibacillus
kimchii is NKC1-2T.
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Journal of Microbiology.2021; 59(5): 460. CrossRef - Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
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