- Description of Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp. nov., and Luteibacter aegosomatissinici sp. nov. isolated from the Intestines of Aegosoma sinicum Larvae
-
Hae-In Joe , Jee-Won Choi , June-Young Lee , Hojun Sung , Su-Won Jeong , Yun-Seok Jeong , Jae-Yun Lee , Jin-Woo Bae
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J. Microbiol. 2023;61(6):603-613. Published online May 5, 2023
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DOI: https://doi.org/10.1007/s12275-023-00051-7
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96
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 Abstract
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Three novel bacterial strains, 321T,
335T,
and 353T,
were isolated from the intestines of Aegosoma sinicum larvae collected
from Paju-Si, South Korea. The strains were Gram-negative, obligate aerobe and had rod-shaped cells with a single flagellum.
The three strains belonged to the genus Luteibacter in the family Rhodanobacteraceae and shared < 99.2% similarity
in their 16S rRNA gene sequence and < 83.56% similarity in thier whole genome sequence. Strains 321T,
335T,
and 353T
formed a monophyletic clade with Luteibacter yeojuensis KACC 11405T,
L. anthropi KACC 17855T,
and L. rhizovicinus
KACC 12830T,
with sequence similarities of 98.77–98.91%, 98.44–98.58%, and 97.88–98.02%, respectively. Further
genomic analyses, including the construction of the Up-to-date Bacterial Core Gene (UBCG) tree and assessment of other
genome-related indices, indicated that these strains were novel species belonging to the genus Luteibacter. All three strains
contained ubiquinone Q8 as their major isoprenoid quinone and iso-C15:0 and summed feature 9 (
C16:0 10-methyl and/or
iso-C17:1 ω9c) as their major cellular fatty acids. Phosphatidylethanolamine and diphosphatidylglycerol were the major polar
lipids in all the strains. The genomic DNA G + C contents of strains 321T,
335T,
and 353T
were 66.0, 64.5, and 64.5 mol%,
respectively. Based on multiphasic classification, strains 321T,
335T,
and 353T
were classified into the genus Luteibacter
as the type strains of novel species, for which the names Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp.
nov., and Luteibacter aegosomatissinici sp. nov. are proposed, respectively.
-
Citations
Citations to this article as recorded by  - Luteibacter sahnii sp. nov., A Novel Yellow-Colored Xanthomonadin Pigment Producing Probiotic Bacterium from Healthy Rice Seed Microbiome
Gagandeep Jaiswal, Rekha Rana, Praveen Kumar Nayak, Rekha Chouhan, Sumit G. Gandhi, Hitendra K. Patel, Prabhu B. Patil
Current Microbiology.2024;[Epub] CrossRef - Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef
- Description of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fish
-
Do-Hun Gim , So-Yeon Lee , Jeong Eun Han , Jae-Yun Lee , Seo Min Kang , Jin-Woo Bae
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J. Microbiol. 2022;60(11):1061-1069. Published online September 1, 2022
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DOI: https://doi.org/10.1007/s12275-022-2250-5
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91
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5
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6
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Abstract
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Three novel strains, (D17T, D13, and D25T) isolated from the
gut of the Korean dark sleeper (Odontobutis platycephala),
Kumgang fat minnow (Rhynchocypris kumgangensis), and
the Korean oily bitterling (Tanakia koreensis) were identified
as two novel species. Strains D17T and D13 showed the highest
similarities in 16S rRNA gene and complete genome sequences
to Deefgea rivuli WB 3.4-79T (98.0% and 97.9%, respectively,
of 16S rRNA gene sequence similarity, 77.8% and 77.7%, respectively,
of orthologous average nucleotide identity, Ortho-
ANI, and 21.9% and 21.9%, respectively, of digital DNA-DNA
hybridization, dDDH). Strain D17T showed the highest similarities
in 16S rRNA gene and complete genome sequences to
D13 (99.9% of 16S rRNA gene sequence similarity, 91.8% of
OrthoANI, and 45.1% of dDDH); therefore, strains D17T and
D13 were assigned as the same species. Strain D25T showed the
highest similarities in 16S rRNA gene and complete genome
sequences to D. chitinilytica Nsw-4T (98.2% of 16S rRNA gene
sequence similarity, 82.4% of OrthoANI, and 25.1% of dDDH).
Strains D17T and D13 were Gram-stain-negative, facultative
anaerobes, rod-shaped, non-motile, and non-flagellated. Strain
D25T was Gram-stain-negative, facultative anaerobe, rodshaped,
and motile by a single polar flagellum. These strains
had C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) as
the major cellular fatty acids and possessed Q-8 as a major
respiratory ubiquinone. All three strains contained phosphatidylethanolamine
and phosphatidylglycerol as the major polar
lipids. Based on polyphasic taxonomic data, strains D17T, D13,
and D25T represent two novel species of the genus Deefgea.
We propose the name Deefgea piscis sp. nov. for strains D17T
(= KCTC 82958T = JCM 34941T) and D13 (= KCTC 92368),
and Deefgea tanakiae sp. nov. for strain D25T (= KCTC 82959T
= JCM 34942T).
-
Citations
Citations to this article as recorded by - Systematic Literature Review Identifying Core Genera in the Gut Microbiome of Rainbow Trout (Oncorhynchus mykiss) and Species‐level Microbial Community Analysis Using Long‐Read Amplicon Sequencing
Mio Takeuchi, Kazuhiro Sugahara
Aquaculture, Fish and Fisheries.2025;[Epub] CrossRef -
Fecal metagenomic and metabolomic analyses reveal non-invasive biomarkers of
Flavobacterium psychrophilum
infection in ayu (
Plecoglossus altivelis
)
Mio Takeuchi, Erina Fujiwara-Nagata, Kyohei Kuroda, Kenji Sakata, Takashi Narihiro, Jun Kikuchi, Katherine McMahon
mSphere.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 - An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef - Validation List no. 212. 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 - Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef
- Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
-
Seomin Kang , Jae-Yun Lee , Jeong Eun Han , Yun-Seok Jeong , Do-Hun Gim , Jin-Woo Bae
-
J. Microbiol. 2022;60(9):890-898. Published online June 22, 2022
-
DOI: https://doi.org/10.1007/s12275-022-2075-2
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98
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9
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9
Crossref
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Abstract
-
Two novel bacterial strains, KSM-R2A25T and KSM-R2A30T,
were isolated from intestines of Cyclina sinensis (corb shell)
and Channa argus (northern snakehead), respectively. Both
specimens were collected in Korea. The strains were Gramstain-
negative, non-motile, and strictly aerobic. According
to phylogenetic analyses based on 16S rRNA gene sequences,
strains belonged to the genus Flavobacterium within the family
Flavobacteriaceae. 16S rRNA gene sequences of strains KSMR2A25T
and KSM-R2A30T were closely related to Flavobacterium
cucumis DSM 18830T and Flavobacterium aquaticum
JC164T with sequence similarities of 97.77% and 98.54%, respectively.
Further genomic analyses including reconstruction
of the UBCG tree and overall genome-related indices suggested
them as novel species of the genus Flavobacterium.
Both strains contained menaquinone with six isoprene units
(MK-6) as a major isoprenoid quinone and iso-C15:1 G, iso-
C15:0, and iso-C16:0 as major cellular fatty acids. The major polar
lipid in both strains was phosphatidylethanolamine. The
genomic G + C contents of strains KSM-R2A25T and KSMR2A30T
were 31.7 and 31.9%, respectively. Based on the polyphasic
taxonomic study presented here, strains KSM-R2A25T
and KSM-R2A30T represent novel species of the genus Flavobacterium,
for which the names Flavobacterium cyclinae sp.
nov and Flavobacterium channae sp. nov are proposed. The
type strains of F. cyclinae sp. nov and F. channae sp. nov
are KSM-R2A25T (= KCTC 82978T = JCM 34997T) and KSMR2A30T
(= KCTC 82979T = JCM 34998T), respectively.
-
Citations
Citations to this article as recorded by - Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[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 - The first report of submandibular lymph node infection with Flavobacterium ceti in a horse and its complete genome sequence
Seung-Ho Ryu, Beomsoon Jang, Byung-Sun Kim, Kun Taek Park
Microbial Pathogenesis.2024; 197: 107096. CrossRef - Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. 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 - An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef - Transcriptomic insights into the immune response of the intestine to Aeromonas veronii infection in northern snakehead (Channa argus)
Peng Sun, Di Zhang, Na Li, Xiao-Fei Li, Yi-Han Ma, Hui Li, Ye Tian, Tao Wang, Shahrood Ahmed Siddiquid, Wu-wen Sun, Lei Zhang, Xiao-Feng Shan, Chun-Feng Wang, Ai-Dong Qian, Dong-Xing Zhang
Ecotoxicology and Environmental Safety.2023; 255: 114825. 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 s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. 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
- Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
-
Su-Won Jeong , Jeong Eun Han , June-Young Lee , Ji-Ho Yoo , Do-Yeon Kim , In Chul Jeong , Jee-Won Choi , Yun-Seok Jeong , Jae-Yun Lee , So-Yeon Lee , Euon Jung Tak , Hojun Sung , Hyun Sik Kim , Pil Soo Kim , Dong-Wook Hyun , Jin-Woo Bae
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J. Microbiol. 2022;60(6):576-584. Published online April 18, 2022
-
DOI: https://doi.org/10.1007/s12275-022-1604-3
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88
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7
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7
Crossref
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Abstract
-
Three aerobic, Gram-negative, and rod-shaped bacterial strains,
designated strains G4M1T, SM13T, and L12M9T, were isolated
from the gut of Batillaria multiformis, Cellana toreuma, and
Patinopecten yessoensis collected from the Yellow Sea in South
Korea. All the strains grew optimally at 25°C, in the presence
of 2% (w/v) NaCl, and at pH 7. These three strains, which
belonged to the genus Polaribacter in the family Flavobacteriaceae,
shared < 98.8% in 16S rRNA gene sequence and < 86.68%
in whole-genome sequence with each other. Compared with
the type strains of Polaribacter, isolates showed the highest
sequence similarity to P. haliotis KCTC 52418T (< 98.68%),
followed by P. litorisediminis KCTC 52500T (< 98.13%). All
the strains contained MK-6 as their predominant menaquinone
and iso-C15:0 as their major fatty acid. Moreover, all the
strains had phosphatidylethanolamine as their polar lipid
component. In addition, strain G4M1T had two unidentified
lipids and three unidentified aminolipids, strain SM13T had
three unidentified lipids and three unidentified aminolipids,
and strain L12M9T had three unidentified lipids and one unidentified
aminolipid. The DNA G + C contents of strains
G4M1T, SM13T, and L12M9T were 31.0, 30.4, and 29.7 mol%,
respectively. Based on phenotypic, phylogenetic, chemotaxonomic,
and genotypic findings, strains G4M1T (= KCTC 82388T
= DSM 112372T), SM13T (= KCTC 82389T = DSM 112373T),
and L12M9T (= KCTC 62751T = DSM 112374T) were classified
into the genus Polaribacter as the type strains of novel
species, for which the names Polaribacter batillariae sp. nov.,
Polaribacter cellanae sp. nov., and Polaribacter pectinis sp.
nov., respectively, have been proposed.
-
Citations
Citations to this article as recorded by - Polaribacter uvawellassae sp. nov., a Member of the Family Flavobacteriaceae Isolated from Mud Crab (Scylla serrata)
W. M. Lakshani Anuradha Wanasinghe, Wang Xin, Yuan Siliang, Dongru Qiu
Current Microbiology.2025;[Epub] CrossRef - Unique skin microbiome: insights to understanding bacterial symbionts in octopuses
Chelsea O. Bennice, Lauren E. Krausfeldt, W. Randy Brooks, Jose V. Lopez
Frontiers in Marine Science.2024;[Epub] CrossRef - An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef -
Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013
Ju Hye Baek, Mahrukh Butt, Dong Min Han, Jeong Min Kim, Seohui Choi, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef - Validation List no. 207. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef -
Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
Do-Yeon Kim, In-Chul Jeong, So-Yeon Lee, Yun-Seok Jeong, Jeong Eun Han, Euon Jung Tak, June-Young Lee, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef
- Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
-
So-Yeon Lee , Pil Soo Kim , Hojun Sung , Dong-Wook Hyun , Jin-Woo Bae
-
J. Microbiol. 2022;60(5):469-477. Published online March 31, 2022
-
DOI: https://doi.org/10.1007/s12275-022-1647-5
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91
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5
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6
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Abstract
-
Two Gram-stain-negative, mesophilic, strictly aerobic, nonspore
forming, and yellow-pigmented strains with rod-shaped
cells, designated H21R20T and H23M41T, were isolated from
the faeces of an Oriental stork (Ciconia boyciana). Based on
16S rRNA gene sequences, both strains showed the highest
similarity (98.3−98.4%) to the type strain of Lysobacter concretionis.
Phylogenetic analysis based on the 16S rRNA genes
and 92 bacterial core genes showed that strains H21R20T and
H23M41T were robustly clustered with L. concretionis Ko07T.
Whole genome sequencing revealed that the genomes of both
strains were approximately 2.9 Mb in size. The DNA G + C
contents of the H21R20T and H23M41T strains were 67.3 and
66.6%, respectively. The two strains showed 80.1−81.7% average
nucleotide identity with L. concretionis Ko07T. Strain
H21R20T grew optimally at 30°C and pH 8.0 and in the presence
of 0.5–3% (wt/vol) NaCl, while strain H23M41T grew
optimally at 30°C and pH 7.0–8.0 and in the presence of
0–3% (wt/vol) NaCl. Both strains possessed iso-C15:0, iso-C16:0
and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl)
as the major cellular fatty acids, ubiquinone Q-8 as a predominant
quinone, and diphosphatidylglycerol, phosphatidylglycerol,
and phosphatidylethanolamine as the major polar
lipids. A multifaceted investigation demonstrated that strains
H21R20T and H23M41T represent novel species of the genus
Lysobacter, for which we propose the names Lysobacter ciconiae
sp. nov. and Lysobacter avium sp. nov. for strains H21R20T
(= KCTC 82316T = JCM 34832T) and H23M41T (= KCTC
62676T = JCM 33223T), respectively.
-
Citations
Citations to this article as recorded by - Isolation and Characterization of an Antioxidant Aryl Polyene Pigment from Antarctic Bacterium Lysobacter sp. A03
Maria Elisa Pailliè-Jiménez, Paolo Stincone, Jamile Queiroz Pereira, Patricio Román Santagapita, Eliseu Rodrigues, Adriano Brandelli
Molecular Biotechnology.2024;[Epub] CrossRef -
Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022
Claire R. Burbick, Sara D. Lawhon, Erik Munson, Elizabeth Thelen, Amanda Zapp, Anastasia Wilson, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef - Lysobacter changpingensis sp. nov., a novel species of the genus Lysobacter isolated from a rhizosphere soil of strawberry in China
Bang-Yan Niu, Dong-Jun Ren, Fang-Bo Zhang, Hong-Tu Zhu, Hai-Lei Wei, Ming-Chao Ma, Miao Gao
Folia Microbiologica.2023; 68(6): 991. CrossRef -
Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
Do-Yeon Kim, In-Chul Jeong, So-Yeon Lee, Yun-Seok Jeong, Jeong Eun Han, Euon Jung Tak, June-Young Lee, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Validation List no. 207. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef
- Description of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birds
-
So-Yeon Lee , Hojun Sung , Pil Soo Kim , Hyun Sik Kim , Jae-Yun Lee , June-Young Lee , Yun-Seok Jeong , Euon Jung Tak , Jeong Eun Han , Dong-Wook Hyun , Jin-Woo Bae
-
J. Microbiol. 2021;59(11):978-987. Published online September 27, 2021
-
DOI: https://doi.org/10.1007/s12275-021-1323-1
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77
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6
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7
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Abstract
-
Phenotypic and genomic analyses were performed to characterize
two novel species, H23M54T and AMA3305T, isolated
from the faeces of the Oriental stork (Ciconia boyciana) and
the cinereous vulture (Aegypius monachus), respectively. Strains
H23M54T and AMA3305T showed the highest similarities of
16S rRNA gene sequences and complete genome sequences
with Ornithinimicrobium cavernae CFH 30183T (98.5% of 16S
rRNA gene sequence similarity and 82.1% of average nucleotide
identity, ANI) and O. pekingense DSM 21552T (98.5% of
16S rRNA gene sequence similarity and 82.3% of ANI), respectively.
Both strains were Gram-stain-positive, obligate aerobes,
non-motile, non-spore-forming, and coccoid- and rodshaped.
Strain H23M54T grew optimally at 25–30°C and pH
8.0 and in the presence of 1.5–2% (wt/vol) NaCl, while strain
AMA3305T grew optimally at 30°C and pH 7.0 and in the presence
of 1–3% (wt/vol) NaCl. Both strains had iso-C15:0, iso-
C16:0, and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-
methyl) as major cellular fatty acids. MK-8 (H4) was identified
as the primary respiratory quinone in both strains. Strains
H23M54T and AMA3305T possessed diphosphatidylglycerol
and phosphatidylglycerol as major polar lipids. Moreover,
strains H23M54T and AMA3305T commonly contained ribose
and glucose as major sugars and L-ornithine, L-alanine,
glycine, and aspartic acid as major amino acids. The polyphasic
taxonomic data indicate that strains H23M54T and AMA3305T
represent novel species of the genus Ornithinimicrobium. We
propose the names Ornithinimicrobium ciconiae sp. nov. and
Ornithinimicrobium avium sp. nov. for strains H23M54T (= KCTC 49151T = JCM 33221T) and AMA3305T (= KCTC
49180T = JCM 32873T), respectively.
-
Citations
Citations to this article as recorded by - Molecular insight and antimicrobial potential of Actinomycetota isolated from Tanzania’s seagrass sediments
Lucy Dalusi Mbusi, Sylvester Leonard Lyantagaye, Thomas Jacob Lyimo
Biologia.2024; 80(1): 163. CrossRef - Bacterial community of ticks (Acari: Ixodidae) and mammals from Arauca, Colombian Orinoquia
Paula A. Ossa-López, Héctor E. Ramírez-Chaves, María Elena Álvarez López, Gabriel Jaime Castaño Villa, Fredy A. Rivera-Páez
International Journal for Parasitology: Parasites and Wildlife.2024; 24: 100943. CrossRef - Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)
Yuyuan Huang, Suping Zhang, Yuanmeihui Tao, Jing Yang, Shan Lu, Dong Jin, Ji Pu, Wenbo Luo, Han Zheng, Liyun Liu, Jia-fu Jiang, Jianguo Xu
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef - Description of Ornithinimicrobium cryptoxanthini sp. nov., a Novel Actinomycete Producing β-cryptoxanthin Isolated from the Tongtian River Sediments
Yuyuan Huang, Yifan Jiao, Sihui Zhang, Yuanmeihui Tao, Suping Zhang, Dong Jin, Ji Pu, Liyun Liu, Jing Yang, Shan Lu
Journal of Microbiology.2023; 61(4): 379. CrossRef - An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022
Claire R. Burbick, Sara D. Lawhon, Erik Munson, Elizabeth Thelen, Amanda Zapp, Anastasia Wilson, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef - 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 - Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(5): 469. CrossRef
- Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome
-
Dong-Wook Hyun , Jae-Yun Lee , Min-Soo Kim , Na-Ri Shin , Tae Woong Whon , Kyung Hyun Kim , Pil Soo Kim , Euon Jung Tak , Mi-Ja Jung , June Young Lee , Hyun Sik Kim , Woorim Kang , Hojun Sung , Che Ok Jeon , Jin-Woo Bae
-
J. Microbiol. 2021;59(8):793-806.
-
DOI: https://doi.org/10.1007/s12275-021-1165-x
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70
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9
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9
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Abstract
-
Viridans group streptococci are a serious health concern because
most of these bacteria cause life-threatening infections,
especially in immunocompromised and hospitalized individuals.
We focused on two alpha-hemolytic Streptococcus
strains (I-G2 and I-P16) newly isolated from an ileostomy
effluent of a colorectal cancer patient. We examined their pathogenic
potential by investigating their prevalence in human
and assessing their pathogenicity in a mouse model. We also
predicted their virulence factors and pathogenic features by
using comparative genomic analysis and in vitro tests. Using
polyphasic and systematic approaches, we identified the isolates
as belonging to a novel Streptococcus species and designated
it as Streptococcus ilei. Metagenomic survey based on
taxonomic assignment of datasets from the Human Microbiome
Project revealed that S. ilei is present in most human
population and at various body sites but is especially abundant
in the oral cavity. Intraperitoneal injection of S. ilei was
lethal to otherwise healthy C57BL/6J mice. Pathogenomics
and in vitro assays revealed that S. ilei possesses a unique set
of virulence factors. In agreement with the in vivo and in vitro
data, which indicated that S. ilei strain I-G2 is more pathogenic
than strain I-P16, only the former displayed the streptococcal
group A antigen. We here newly identified S. ilei sp.
nov., and described its prevalence in human, virulence factors,
and pathogenicity. This will help to prevent S. ilei strain
misidentification in the future, and improve the understanding
and management of streptococcal infections.
-
Citations
Citations to this article as recorded by - Microbiota analysis of perimenopausal women experiencing recurrent vaginitis in conjunction with urinary tract infection
Yingying Bi, Yuezhu Wang, Wu Li, Yuhang Chen, Jinlong Qin, Huajun Zheng
BMC Microbiology.2025;[Epub] CrossRef - Characterization of blood microbial population in beef calves with clinical signs of sepsis using 16S rRNA gene sequencing
Giuliano Borriello, Flaminia Valentini, Sara Ferrini, Giorgia Di Muro, Giulia Cagnotti, Elena Grego, Angela Maria Catania, Maria Cristina Stella, Ugo Ala, Patrizia Nebbia, Antonio D’Angelo, Claudio Bellino, Ulrike Gertrud Munderloh
PLOS One.2025; 20(5): e0324469. CrossRef -
Molecular characterization of a novel putative pathogen,
Streptococcus nakanoensis
sp. nov., isolated from sputum culture
Takeaki Wajima, Takashi Sugawara, Emi Tanaka, Kei-ichi Uchiya, Justin R. Kaspar
Microbiology Spectrum.2024;[Epub] CrossRef -
Streptococcus raffinosi sp. nov., isolated from human breast milk samples
Ha Viet Nguyen, Anh Thi Van Trinh, Linh Nguyen Hai Bui, Anh Thi Lan Hoang, Quyen Thi Le Tran, Trung Thanh Trinh
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - Description of Streptococcus dentalis sp. nov., Streptococcus gingivalis sp. nov., and Streptococcus lingualis sp. nov., Isolated from Human Oral Cavities
Beom-Jin Goo, Young-Sik Choi, Do-Hun Gim, Su-Won Jeong, Jee-Won Choi, Hojun Sung, Jae-Yun Lee, Jin-Woo Bae
Journal of Microbiology.2024; 62(11): 973. CrossRef - Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022
Erik Munson, Arianna Carella, Karen C. Carroll, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef - Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Modulation of gut microbiota and fecal metabolites by corn silk among high-fat diet-induced hypercholesterolemia mice
Lin Ding, Shan Ren, Yaoxin Song, Chuangang Zang, Yuchao Liu, Hao Guo, Wenqing Yang, Hong Guan, Jicheng Liu
Frontiers in Nutrition.2022;[Epub] CrossRef - Reclassification of Streptococcus ilei as a later heterotypic synonym of Streptococcus koreensis based on whole-genome sequence analysis
Sanjeet Kumar, Kanika Bansal, Santosh Kumar Sethi
Archives of Microbiology.2022;[Epub] CrossRef
- Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish)
-
Dong-Wook Hyun , Yun-Seok Jeong , Jae-Yun Lee , Hojun Sung , So-Yeon Lee , Jee-Won Choi , Hyun Sik Kim , Pil Soo Kim , Jin-Woo Bae
-
J. Microbiol. 2021;59(6):552-562. Published online April 20, 2021
-
DOI: https://doi.org/10.1007/s12275-021-1036-5
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13
Crossref
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Abstract
-
A polyphasic taxonomic approach was used to characterize
three novel bacterial strains, designated as HDW12AT, HDW-
15BT, and HDW15CT, isolated from the intestine of fish species
Odontobutis interrupta or Siniperca scherzeri. All isolates
were obligate aerobic, non-motile bacteria, and grew optimally
at 30°C. Phylogenetic analysis based on 16S rRNA sequences
revealed that strain HDW12AT was a member of the genus
Nocardioides, and closely related to Nocardioides allogilvus
CFH 30205T (98.9% sequence identities). Furthermore, strains
HDW15BT and HDW15CT were members of the genus Sphingomonas,
and closely related to Sphingomonas lutea JS5T and
Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence
identities), respectively. Strain HDW12AT contained
MK-8 (H4), and strains HDW15BT and HDW15CT contained
Q-10 as the respiratory quinone. Major polar lipid components
of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol,
and phosphatidylinositol, and those of strains
HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol,
phosphatidylglycerol, phosphatidylethanolamine,
and phosphatidylcholine. The G + C content of strains
HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and
65.5%, respectively. The results of phylogenetic, phenotypic,
chemotaxonomic, and genotypic analyses suggest that strain
HDW12AT represents a novel species within the genus Nocardioides,
and strains HDW15BT and HDW15CT represent
two novel species within the genus Sphingomonas. We propose
the names Nocardioides piscis for strain HDW12AT (= KACC
21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis
for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM
33738T), and Sphingomonas sinipercae for strain HDW15CT
(= KACC 21342T = KCTC 72589T = JCM 33739T).
-
Citations
Citations to this article as recorded by - Description of Streptococcus dentalis sp. nov., Streptococcus gingivalis sp. nov., and Streptococcus lingualis sp. nov., Isolated from Human Oral Cavities
Beom-Jin Goo, Young-Sik Choi, Do-Hun Gim, Su-Won Jeong, Jee-Won Choi, Hojun Sung, Jae-Yun Lee, Jin-Woo Bae
Journal of Microbiology.2024; 62(11): 973. CrossRef - Sphingomonas flavescens sp. nov., isolated from soil
Hyosun Lee, Dhiraj Kumar Chaudhary, Dong-Uk Kim
Archives of Microbiology.2024;[Epub] CrossRef - Nocardioides limicola sp. nov., an alkaliphilic alkane degrading bacterium isolated from oilfield alkali-saline soil
Lin Zhu, Biyue Yang, Wenjun Guo, Xinyu Hu, Shenkui Liu, Xiang Xiao, Wei Wei
Antonie van Leeuwenhoek.2024;[Epub] CrossRef - An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef - The probiotic roles of Lactiplantibacillus plantarum E2 as a dietary supplement in growth promotion and disease resistance of juvenile large yellow croaker (Larimichthys crocea)
Ruizhe Liu, Shan Wang, Dongliang Huang, Yulu Huang, Tianliang He, Xinhua Chen
Aquaculture.2024; 578: 740082. CrossRef - Phylogeny, phenotypic characteristics and pathogenicity of Sphingomonas sp. and Erwinia persicina as bacterial causal agents of lettuce diseases in southwest of Iran
Vahid Keshavarz-Tohid, Somayeh Ebrahimi
Physiological and Molecular Plant Pathology.2023; 127: 102124. CrossRef - Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza
Xiaohui Chen, Zhouqing Zheng, Feina Li, Xiao Ma, Feng Chen, Mingsheng Chen, Li Tuo
Systematic and Applied Microbiology.2023; 46(2): 126391. CrossRef -
Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
Ji-Ho Yoo, Jeong Eun Han, June-Young Lee, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Hojun Sung, Euon Jung Tak, Hyun Sik Kim, Pil Soo Kim, Jee-Won Choi, Do-Yeon Kim, In Chul Jeong, Do-Hun Gim, Seo Min Kang, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef -
Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
Do-Yeon Kim, In-Chul Jeong, So-Yeon Lee, Yun-Seok Jeong, Jeong Eun Han, Euon Jung Tak, June-Young Lee, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Intergenerational Transfer of Persistent Bacterial Communities in Female Nile Tilapia
Yousri Abdelhafiz, Jorge M. O. Fernandes, Claudio Donati, Massimo Pindo, Viswanath Kiron
Frontiers in Microbiology.2022;[Epub] CrossRef - Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef -
Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease
Jae-Yun Lee, Woorim Kang, Na-Ri Shin, Dong-Wook Hyun, Pil Soo Kim, Hyun Sik Kim, June-Young Lee, Euon Jung Tak, Hojun Sung, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef - Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome
Dong-Wook Hyun, Jae-Yun Lee, Min-Soo Kim, Na-Ri Shin, Tae Woong Whon, Kyung Hyun Kim, Pil Soo Kim, Euon Jung Tak, Mi-Ja Jung, June Young Lee, Hyun Sik Kim, Woorim Kang, Hojun Sung, Che Ok Jeon, Jin-Woo Bae
Journal of Microbiology.2021; 59(8): 792. CrossRef
- Leucobacter coleopterorum sp. nov., Leucobacter insecticola sp. nov., and Leucobacter viscericola sp. nov., isolated from the intestine of the diving beetles, Cybister brevis and Cybister lewisianus, and emended description of the genus Leucobacter
-
Dong-Wook Hyun , Hojun Sung , Pil Soo Kim , Ji-Hyun Yun , Jin-Woo Bae
-
J. Microbiol. 2021;59(4):360-368. Published online January 26, 2021
-
DOI: https://doi.org/10.1007/s12275-021-0472-6
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78
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8
Web of Science
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9
Crossref
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Abstract
-
Three novel bacterial strains, HDW9AT, HDW9BT, and
HDW9CT, isolated from the intestine of the diving beetles
Cybister lewisianus and Cybister brevis, were characterized as
three novel species using a polyphasic approach. The isolates
were Gram-staining-positive, strictly aerobic, non-motile,
and rod-shaped. They grew optimally at 30°C (pH 7) in the
presence of 0.5% (wt/vol) NaCl. Phylogenetic analysis based
on the 16S rRNA gene sequences revealed that they belong
to the genus Leucobacter and are closely related to L. denitrificans
M1T8B10T (98.4–98.7% sequence similarity). Average
nucleotide identity (ANI) values among the isolates were
76.4–84.1%. ANI values for the isolates and the closest taxonomic
species, L. denitrificans KACC 14055T, were 72.3–73.1%.
The isolates showed ANI values of < 76.5% with all analyzable
Leucobacter strains in the EzBioCloud database. The
genomic DNA G + C content of the isolates was 60.3–62.5%.
The polar lipid components were phosphatidylglycerol, diphosphatidylglycerol,
and other unidentified glycolipids, phospholipids,
and lipids. The major cellular fatty acids were anteiso-
C15:0, iso-C16:0, and anteiso-C17:0. MK-10 was the major
respiratory quinone, and MK-7 and MK-11 were the minor
respiratory quinones. The whole-cell sugar components of the
isolates were ribose, glucose, galactose, and mannose. The
isolates harbored L-2,4-diaminobutyric acid, L-serine, L-lysine,
L-aspartic acid, glycine, and D-glutamic acid within the
cell wall peptidoglycan. Based on phylogenetic, phenotypic,
chemotaxonomic, and genotypic analyses, strains HDW9AT,
HDW9BT, and HDW9CT represent three novel species within
the genus Leucobacter. We propose the name Leucobacter
coleopterorum sp. nov. for strain HDW9AT (= KACC 21331T
= KCTC 49317T = JCM 33667T), the name Leucobacter insecticola
sp. nov. for strain HDW9BT (= KACC 21332T =
KCTC 49318T = JCM 33668T), and the name Leucobacter viscericola
sp. nov. for strain HDW9CT (= KACC 21333T =
KCTC 49319T = JCM 33669T).
-
Citations
Citations to this article as recorded by - Biogenic Silver Nanoparticles Produced by Soil Rare Actinomycetes and Their Significant Effect on Aspergillus-derived mycotoxins
Mohamed N. Abd El-Ghany, Salwa A. Hamdi, Shereen M. Korany, Reham M. Elbaz, Ahmed N. Emam, Mohamed G. Farahat
Microorganisms.2023; 11(4): 1006. CrossRef -
Leucobacter tenebrionis sp. nov., isolated from the gut of Tenebrio molitor
Yu Ying, Bo Yuan, Tingting Liu, Xiaoshuan Bai, Haifeng Zhao
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef -
Leucobacter allii sp. nov. and Leucobacter rhizosphaerae sp. nov., isolated from rhizospheres of onion and garlic, respectively
Seunghwan Kim, Tomomi Asano, Hanako Naito, Moriyuki Hamada, Hang-Yeon Weon, Soon-Wo Kwon, Jun Heo
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef -
Leucobacter chinensis sp. nov., with plant growth-promoting potential isolated from field soil after seven-years continuous maize cropping
Jie Zhu, Juan Che, Xin Jiang, Mingchao Ma, Dawei Guan, Li Li, Fengming Cao, Baisuo Zhao, Yaowei Kang, Ji Zhao, Delong Kong, Yiqing Zhou, Zhiyong Ruan, Jun Li
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Changes of gut microbiota in colorectal cancer patients with Pentatrichomonas hominis infection
Hongbo Zhang, Yanhui Yu, Jianhua Li, Pengtao Gong, Xiaocen Wang, Xin Li, Yidan Cheng, Xiuyan Yu, Nan Zhang, Xichen Zhang
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef - Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(5): 469. CrossRef - Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef -
Leucobacter soli sp. nov., from soil amended with humic acid
Peter Kämpfer, John A. McInroy, Dominique Clermont, Meina Neumann-Schaal, Alexis Criscuolo, Hans-Jürgen Busse, Stefanie P. Glaeser
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef - Fate of Functional Bacterial and Eukaryotic Community Regulated by Earthworms during Vermicomposting of Dewatered Sludge, Studies Based on the 16S rDNA and 18S rDNA Sequencing of Active Cells
Jun Yang, Kui Huang, Lansheng Peng, Jianhui Li, Aozhan Liu
International Journal of Environmental Research and Public Health.2021; 18(18): 9713. CrossRef
- 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 description of the genus Vagococcus
-
Dong-Wook Hyun , Euon Jung Tak , Pil Soo Kim , Jin-Woo Bae
-
J. Microbiol. 2021;59(2):132-141. Published online December 23, 2020
-
DOI: https://doi.org/10.1007/s12275-021-0485-1
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76
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6
Web of Science
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6
Crossref
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Abstract
-
A polyphasic taxonomic approach was used to characterize
two novel bacterial strains, HDW17AT and HDW17BT, isolated
from the intestine of the diving beetle Cybister lewisianus,
and the dark diving beetle Hydrophilus acuminatus,
respectively. Both strains were Gram-positive and facultative
anaerobic cocci forming cream-colored colonies. The isolates
grew optimally at 25°C, pH 7, in the presence of 0.3% (wt/vol)
NaCl. Phylogenetic analysis based on 16S rRNA gene sequences
and genome sequences showed that the isolates were
members of the genus Vagococcus, and strain HDW17AT was
closely related to Vagococcus fessus CCUG 41755T (98.9% of
16S rRNA gene sequence similarity and 74.3% of average
nucleotide identity [ANI]), whereas strain HDW17BT was
closely related to Vagococcus fluvialis NCFB 2497T (98.9% of
16S rRNA gene sequence similarity and 76.6% of ANI). Both
strains contained C16:0, and C18:1 ω9c as the major cellular fatty
acids, but C16:1 ω9c was also observed only in strain HDW17BT
as the major cellular fatty acid. The respiratory quinone of the
isolates was MK-7. The major polar lipid components were
phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol.
The genomic DNA G + C content of strains
HDW17AT and HDW17BT were 36.6 and 34.4%, respectively.
Both strains had cell wall peptidoglycan composed of the
amino acids L-alanine, glycine, D-glutamic acid, L-tryptophan,
L-lysine, and L-aspartic acid, and the sugars ribose, glucose,
and galactose. Based on phylogenetic, phenotypic, chemotaxonomic,
and genotypic analyses, strains HDW17AT and
HDW17BT represent two novel species in the genus Vagococcus.
We propose the name Vagococcus coleopterorum sp.
nov. for strain HDW17AT (= KACC 21348T = KCTC 49324T
= JCM 33674T) and the name Vagococcus hydrophili sp. nov.
for strain HDW17BT (= KACC 21349T = KCTC 49325T =
JCM 33675T).
-
Citations
Citations to this article as recorded by -
Vagococcus proximus sp. nov. and Vagococcus intermedius sp. nov., originating from modified atmosphere packaged broiler meat
Per Johansson, Elina Jääskeläinen, Elina Säde, Johanna Björkroth
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - A case of Vagococcus fluvialis isolated from the bile of a patient with calculous cholecystitis
Dan Zhang, Xiaosu Wang, Jingdan Yu, Zheng Dai, Qichao Li, Litao Zhang
BMC Infectious Diseases.2023;[Epub] CrossRef -
Vagococcus luciliae sp. nov., isolated from the common green bottle fly Lucilia sericata
Juan Guzman, Anja Poehlein, Rolf Daniel, Peter Kämpfer, Andreas Vilcinskas
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Effects of different doses of electron beam irradiation on bacterial community of Portunus trituberculatus
Huijuan Pan, Qi Yu, Chenru Qian, Haitao Shao, Jiajun Han, Yongyong Li, Yongjiang Lou
Food Bioscience.2021; 42: 101198. CrossRef - Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish)
Dong-Wook Hyun, Yun-Seok Jeong, Jae-Yun Lee, Hojun Sung, So-Yeon Lee, Jee-Won Choi, Hyun Sik Kim, Pil Soo Kim, Jin-Woo Bae
Journal of Microbiology.2021; 59(6): 552. 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
-
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
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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
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- Acinetobacter apis sp. nov., Isolated from the Intestinal Tract of a Honey Bee, Apis mellifera
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Pil Soo Kim , Na-Ri Shin , Joon Yong Kim , Ji-Hyun Yun , Dong-Wook Hyun , Jin-Woo Bae
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J. Microbiol. 2014;52(8):639-645. Published online August 1, 2014
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DOI: https://doi.org/10.1007/s12275-014-4078-0
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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).
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Citations
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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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69
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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
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Journal of Microbiology.2022; 60(6): 576. CrossRef - Actinoplanes solisilvae sp. nov., Isolated from Birch Forest Soil
Qingyun Ma, Qi Zhang, Xu Jiang, Delong Kong, Xiaoyan Han, Huiying Xue, Yiqing Zhou, Yuqin Zhang, Wei Zhang, Zhiyong Ruan
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Miho Watanabe, Hisaya Kojima, Manabu Fukui
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Dyella halodurans sp. nov., isolated from lower subtropical forest soil
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Dyella lipolytica sp. nov., a lipolytic bacterium isolated from lower subtropical forest soil
Liang Tang, Mei-hong Chen, Xi-chen Nie, Meng-ran Ma, Li-hong Qiu
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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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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).
- Rhodopirellula rosea sp. nov., a Novel Bacterium Isolated from an Ark Clam Scapharca broughtonii
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Seong Woon Roh , Hae-Won Lee , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Na-Lae Lim , Daekyung Kim , Jin-Woo Bae
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J. Microbiol. 2013;51(3):301-304. Published online June 28, 2013
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DOI: https://doi.org/10.1007/s12275-013-3210-x
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16
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Abstract
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A novel Gram-negative, motile, and ovoid-shaped strain, LHWP3T, which belonged to the family Planctomycetaceae in the phylum Planctomycetes, was isolated from a dead ark clam Scapharca broughtonii collected during a mass mortality event on the south coast of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the isolate was most closely related to the type strain of Rhodopirellula baltica, with a shared 16S rRNA gene sequence similarity of 94.8%. The isolate grew optimally at 30°C in 4–6% (w/v) NaCl, and at pH 7. The major isoprenoid quinone was menaquinone-6 (MK-6). The dominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified polar lipids. The predominant cellular fatty acids were C16:0, C18:1 ω9c, and C18:0. The genomic DNA G+C content of strain LHWP3T was 53.0 mol%. Based on polyphasic taxonomic analyses, strain LHWP3T should be classified as a novel species in the genus Rhodopirellula in the family Planctomycetaceae, for which the name Rhodopirellula rosea sp. nov. is proposed. The type strain is LHWP3T (=KACC 15560T =JCM 17759T).
- Ruminococcus faecis sp. nov., Isolated from Human Faeces
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Min-Soo Kim , Seong Woon Roh , Jin-Woo Bae
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J. Microbiol. 2011;49(3):487-491. Published online June 30, 2011
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DOI: https://doi.org/10.1007/s12275-011-0505-7
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44
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Abstract
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Bacterial strain Eg2T, an anaerobic, Gram-positive, non-motile, and non-spore-forming coccus, was isolated from human faeces. The optimal temperature for its growth was 37°C. Oxidase activity was negative, but catalase activity was positive. The strain was able to hydrolyze esculin and to produce acids from the fermentation
of several substrates, including glucose. Lactic and acetic acids were the main products of glucose fermentation. The major fatty acids present in this strain were C16:0, C14:0, and C18:1 cis11 DMA. The G+C content was 43.4 mol%. Based on the 16S rRNA gene sequence, strain Eg2T was closely related to species of the genus Ruminococcus (96.3% similarity to R. torques and 96.2% similarity to R. lactaris), and its taxonomic position was placed within the Clostridium cluster XIVa. Based on phenotypic, chemotaxonomic, genotypic, and phylogenetic evidence, we propose that this novel strain be assigned to the genus Ruminococcus and be named Ruminococcus faecis sp. nov. The type strain is Eg2T (=KCTC 5757T =JCM 15917T).
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Citations
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- NOTE] Oceanobacillus kimchii sp. nov. Isolated from a Traditional Korean Fermented Food
-
Tae Woong Whon , Mi-Ja Jung , Seong Woon Roh , Young-Do Nam , Eun-Jin Park , Kee-Sun Shin , Jin-Woo Bae
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J. Microbiol. 2010;48(6):862-866. Published online January 9, 2011
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DOI: https://doi.org/10.1007/s12275-010-0214-7
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Abstract
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A moderate halophile, strain X50T, was isolated from mustard kimchi, a traditional Korean fermented food. The organism grew under conditions ranging from 0-15.0% (w/v) NaCl (optimum: 3.0%), pH 7.0-10.0 (optimum: pH 9.0) and 15-45°C (optimum: 37°C). The morphological, physiological, and biochemical features and the 16S rRNA gene sequences of strain X50T were characterized. Colonies of the isolate were creamcolored and the cells were rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X50T belongs to the genus Oceanobacillus and is closely related phylogenetically to the type strain O. iheyensis HTE831T (98.9%) and O. oncorhynchi subsp. oncorhynchi R-2T (97.0%). The cellular fatty acid profiles predominately included anteiso-C15:0 and iso-C15:0. The G+C content of the genomic DNA of the isolate was 37.9 mol% and the major isoprenoid quinone was MK-7. Analysis of the 16S rRNA gene sequences, DNA-DNA relatedness and physiological and biochemical tests indicated genotypic and
phenotypic differences among strain X50T and reference species in the genus Oceanobacillus. Therefore, strain X50T was proposed as a novel species and named Oceanobacillus kimchii. The type strain of the new species is X50T (=JCM 16803T =KACC 14914T =DSM 23341T).
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Citations
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Biologia.2022; 77(8): 2405. CrossRef - Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley
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Evolutionary Bioinformatics.2022;[Epub] CrossRef - First Case of Bacteremia and Epididymo-orchitis Caused by Oceanobacillus oncorhynchi subspecies incaldanensis in an Immunocompetent Patient
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Draft Genome Sequence of an
Oceanobacillus
sp. Strain Isolated from Soil in a Burial Crypt
Ilargi Martínez-Ballesteros, Ylenia Arizaga, Joseba Bikandi, Javier Garaizar, Giulia Ganau, Bianca Paglietti, Manuela Murgia, Massimo Deligios, Salvatore Rubino
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Oceanobacillus halophilus sp. nov., a novel moderately halophilic bacterium from a hypersaline lake
Mohammad Ali Amoozegar, Maryam Bagheri, Ali Makhdoumi, Mahdi Moshtaghi Nikou, Seyed Abolhassan Shahzadeh Fazeli, Peter Schumann, Cathrin Spröer, Cristina Sánchez-Porro, Antonio Ventosa
International Journal of Systematic and Evolutionary Microbiology
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Jean-Christophe Lagier, Saber Khelaifia, Esam Ibraheem Azhar, Olivier Croce, Fehmida Bibi, Asif Ahmad Jiman-Fatani, Muhammad Yasir, Huda Ben Helaby, Catherine Robert, Pierre-Edouard Fournier, Didier Raoult
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Oceanobacillus arenosus sp. nov., a moderately halophilic bacterium isolated from marine sand
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Oceanobacillus limi sp. nov., a moderately halophilic bacterium from a salt lake
Mohammad Ali Amoozegar, Maryam Bagheri, Ali Makhdoumi-Kakhki, Maryam Didari, Peter Schumann, Cathrin Spröer, Cristina Sánchez-Porro, Antonio Ventosa
International Journal of Systematic and Evolutionary Microbiology
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Cong Yu, Shaolan Yu, Zenghu Zhang, Zhao Li, Xiao-Hua Zhang
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Oceanobacillus
luteolus sp. nov., isolated from soil
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Bacillaceae
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Oceanobacillus indicireducens sp. nov., a facultative alkaliphile that reduces an indigo dye
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Oceanobacillus
chungangensis sp. nov., isolated from a sand dune
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.2011; 61(5): 1011. CrossRef
- NOTE] Halomonas jeotgali sp. nov., a New Moderate Halophilic Bacterium Isolated from a Traditional Fermented Seafood
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Min-Soo Kim , Seong Woon Roh , Jin-Woo Bae
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J. Microbiol. 2010;48(3):404-410. Published online June 23, 2010
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DOI: https://doi.org/10.1007/s12275-010-0032-y
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36
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27
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Abstract
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A moderate halophilic, Gram-negative, non-motile, rod-shape, and aerobe designated as strain HwaT was isolated from traditional fermented Korean seafood, which presented as a single cell or paired cells. Optimal growth occurred at 25°C in 10% (w/v) salts at pH 7.0-8.0; however, growth occurred in a temperature range of
10-32°C, a salts concentration of 5-25% (w/v) and pH 5.0-10.0. Tests for oxidase and catalase were positive. The cells produced poly-β-hydroxybutyric acid, but not exopolysaccharide. Based on the 16S rRNA gene sequence, not only was there low similarity between strain HwaT and all other species (94.1% similarity with H. subglaciescola DSM 4683T, 94.0% similarity with H. sulfidaeris Esulfide1T, 93.6% similarity with H. cerina SP4T and 93.0% similarity with H. halodurans DSM 5160T), but the phylogenetic analysis revealed that the isolate may be classified as a novel species belonging to the genus Halomonas in the class Gammaproteobacteria.
The predominant fatty acids of strain HwaT were C18:1 ω7c, C16:0, C12:0 3-OH and C16:1 ω7c/C15:0 iso 2-OH. The DNA G+C content was calculated as 61.7 mol%. Based on phenotypic, genotypic, and phylogenetic characteristics, it is proposed that the strain designated as HwaT be assigned to the genus Halomonas as
Halomonas jeotgali sp. nov. (=KCTC 22487T =JCM 15645T).
- Phenotypic Characterization and Genomic Analysis of the Shigella sonnei Bacteriophage SP18
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Kyoung-Ho Kim , Ho-Won Chang , Young-Do Nam , Seong Woon Roh , Jin-Woo Bae
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J. Microbiol. 2010;48(2):213-222. Published online May 1, 2010
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DOI: https://doi.org/10.1007/s12275-010-0055-4
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49
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12
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Abstract
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A novel bacteriophage that infects Shigella sonnei was isolated from the Gap River in Korea, and its phenotypic and genomic characteristics were investigated. The virus, called SP18, showed morphology characteristic of the family Myoviridae, and phylogenetic analysis of major capsid gene (gp23) sequences classified it as a T4-like phage. Based on host spectrum analysis, it is lytic to S. sonnei, but not to Shigella flexneri, Shigella boydii or members of the genera Escherichia and Salmonella. Pyrosequencing of the SP18 bacteriophage genome revealed a 170-kb length sequence. In total, 286 ORFs and 3 tRNA genes were identified, and 259 ORFs showed similarity (BLASTP e-value<0.001) to genes of other bacteriophages. The results from comparative genomic analysis indicated that the enterophage JS98, isolated from human stool, is the closest relative of SP18. Based on phylogenetic analysis of gp23 protein-coding sequences, dot plot comparison and BLASTP analysis of genomes, SP18 and JS98 appear to be closely related to T4-even phages. However, several insertions, deletions, and duplications indicate differences between SP18 and JS98. Comparison of duplicated gp24 genes and the soc gene showed that duplication events are responsible for the differentiation and evolution of T4-like bacteriophages.
- Application of Quantitative Real-Time PCR for Enumeration of Total Bacterial, Archaeal, and Yeast Populations in Kimchi
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Eun-Jin Park , Ho-Won Chang , Kyoung-Ho Kim , Young-Do Nam , Seong Woon Roh , Jin-Woo Bae
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J. Microbiol. 2009;47(6):682-685. Published online February 4, 2010
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DOI: https://doi.org/10.1007/s12275-009-0297-1
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58
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37
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Abstract
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Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45×106 which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.
- Halorubrum cibi sp. nov., an Extremely Halophilic Archaeon from Salt-Fermented Seafood
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Seong Woon Roh , Jin-Woo Bae
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J. Microbiol. 2009;47(2):162-166. Published online May 2, 2009
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DOI: https://doi.org/10.1007/s12275-009-0016-y
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60
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21
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Abstract
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Strain B31T is a Gram-staining-negative, motile, and extremely halophilic archaeon that was isolated from salt-fermented seafood. Its morphology, physiology, biochemical features, and 16S rRNA gene sequence were determined. Phylogenetic analysis of its 16S rRNA gene sequence and composition of its major polar lipids placed this archaeon in the genus Halorubrum of the family Halobacteriaceae. Strain B31T showed 97.3, 97.2, and 96.9% 16S rRNA similarity to the type strains of Halorubrum alkaliphilum, Hrr. tibetense, and Hrr. vacuolatum, respectively. Its major polar lipids were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulfated diglycosyl diether (S-DGD). Genomic DNA from strain B31T has a 61.7 mol% G+C content. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified genotypic and phenotypic differences between strain B31T and other Halorubrum species. The type strain of the novel species is B31T (=JCM 15757T =DSM 19504T).
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- Henriciella marina gen. nov., sp. nov., a Novel Member of the Family Hyphomonadaceae Isolated from the East Sea
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Zhe-Xue Quan , Dan-Ning Zeng , Yi-Ping Xiao , Seong Woon Roh , Young-Do Nam , Ho-Won Chang , Jung-Hoon Yoon , Hee-Mock Oh , Jin-Woo Bae
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J. Microbiol. 2009;47(2):156-161. Published online May 2, 2009
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DOI: https://doi.org/10.1007/s12275-008-0290-0
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Abstract
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A bacterial strain, designated Iso4T, was isolated from the East Sea of Korea and was subjected to a polyphasic taxonomy study including phenotypic and chemotaxonomic characteristics as well as 16S rRNA gene sequence analysis. Cells of the strain were Gram-negative, motile, non-budding, non-stalked, and strictly aerobic. Strain Iso4T grew optimally at 20°C in the presence of 1~2% (w/v) NaCl and at pH 6.9~7.6. The major respiratory quinone was Q-10 and the major cellular fatty acids were C18:1 ω7c (53.5%), C17:1 ω5c (11.7%), C17:1 ω6c (8.1%), C16:0 (7.8%), C17:0 (4.8%), C15:0 (2.9%), and C16:1 ω5c (2.2%). The DNA G+C content of strain Iso4T was 56.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Iso4T formed a monophyletic clade in the family Hyphomonadaceae, supported by high bootstrap value and was most closely related to the genus Hyphomonas (92~94%), a member of marine bacteria in the family. The phenotypic, genotypic, and chemotaxonomic evidences also suggest strain Iso4T represents a novel genus and species in the family Hyphomonadaceae, for which the name Henriciella gen. nov., sp. nov. is proposed. The type strain is Iso4T (=KCTC 12513T =DSM 19595T =JCM 15116T).
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- NOTE] Aliihoeflea aestuarii gen. nov., sp. nov., a Novel Bacterium Isolated from Tidal Flat Sediment
-
Seong Woon Roh , Kyoung-Ho Kim , Young-Do Nam , Ho-Won Chang , Min-Soo Kim , Kee-Sun Shin , Jung-Hoon Yoon , Hee-Mock Oh , Jin-Woo Bae
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J. Microbiol. 2008;46(5):594-598. Published online October 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0196-x
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Abstract
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A novel Gram-negative and rod-shaped bacterium, designated N8T, was isolated from tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences showed that N8T strain is associated with the family Phyllobacteriaceae: two uncultured clones (98.4 and 99.8% 16S rRNA gene sequence similarity) and the genus Mesorhizobium (≤97.0%). The novel strain formed a separate clade with uncultured clones in the phylogenetic tree based on 16S rRNA gene sequences. Cellular fatty acid profiles predominately comprised C18:1 ω7c and C19:0 cyclo ω8c. The major isoprenoid quinone is ubiquinone-10 and genomic DNA G+C content is 53.4 mol%. The polyphasic taxonomic study indicates that the novel strain N8T represents a novel species of the new genus in the family Phyllobacteriaceae, named Aliihoeflea aestuarii. The type strain is N8T (= KCTC 22052T= JCM 15118T= DSM 19536T).
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DOI: https://doi.org/10.1007/s12275-008-0189-9
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52
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38
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Abstract
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A novel bacterium B9T was isolated from tidal flat sediment. Its morphology, physiology, biochemical features, and 16S rRNA gene sequence were characterized. Colonies of this strain are yellow and the cells are Gram-negative, rod-shaped, and do not require NaCl for growth. The 16S rRNA gene sequence similarity indicated that strain B9T is associated with the genus Lysobacter (≤ 97.2%), Xanthomonas (≤ 96.8%), Pseudomonas (≤ 96.7%), and Luteimonas (≤ 96.0%). However, within the phylogenetic tree, this novel strain shares a branching point with the species Luteimonas composti CC-YY255T (96.0%). The DNA-DNA hybridization experiments showed a DNA-DNA homology of 23.0% between strain B9T and Luteimonas mephitis B1953/27.1T. The G+C content of genomic DNA of the type strain is 64.7 mol% (SD, 1.1). The predominant fatty acids are iso-C11:0, iso-C15:0, iso-C16:0, iso-C17:0, iso-C17:1 ω9c, and iso-C11:0 3-OH. Combined analysis
of the 16S rRNA gene sequences, fatty acid profile, and results from physiological and biochemical tests indicated that there is genotypic and phenotypic differentiation of the isolate from other Luteimonas species. For these reasons, strain B9T was proposed as a novel species, named Luteimonas aestuarii. The type strain of the new species is B9T (= KCTC 22048T, DSM 19680T).
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Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae
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J. Microbiol. 2008;46(5):491-501. Published online October 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0199-7
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Abstract
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The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).
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- Characterization of the Depth-Related Changes in the Microbial Communities in Lake Hovsgol Sediment by 16S rRNA Gene-Based Approaches
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Young-Do Nam , Youlboong Sung , Ho-Won Chang , Seong Woon Roh , Kyoung-Ho Kim , Sung-Keun Rhee , Jung-Chan Kim , Joo-Yong Kim , Jung-Hoon Yoon , Jin-Woo Bae
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J. Microbiol. 2008;46(2):125-136. Published online June 11, 2008
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DOI: https://doi.org/10.1007/s12275-007-0189-1
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Abstract
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The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial
<br>communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39~42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta- and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria
<br>(some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly deteced by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the
<br>archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing
<br>depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.
- Arthrobacter soli sp. nov., a Novel Bacterium Isolated from Wastewater Reservoir Sediment
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Seong Woon Roh , Youlboong Sung , Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Jung-Hoon Yoon , Che Ok Jeon , Hee-Mock Oh , Jin-Woo Bae
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J. Microbiol. 2008;46(1):40-44.
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DOI: https://doi.org/10.1007/s12275-007-0239-8
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Abstract
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A novel Gram-positive bacterium, designated SYB2T, was isolated from wastewater reservoir sediment, and a polyphasic taxonomic study was conducted based on its morphological, physiological, and biochemical features, as well as the analysis of its 16S rRNA gene sequence. During the phylogenetic analysis of the strain SYB2T, results of a 16S rRNA gene sequence analysis placed this bacterium in the genus Arthrobacter within the family Micrococcaceae. SYB2T and Arthrobacter protophormiae ATCC 19271T, the most closely related species, both exhibited a 16S rRNA gene sequence similarity of 98.99%. The genomic DNA G+C content of the novel strain was found to be 62.0 mol%. The predominant fatty acid composition was anteiso-C15:0, anteiso-C17:0, iso-C16:0, and iso-C15:0. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness, as well as physiological and biochemical tests, showed genotypic and phenotypic differences between strain SYB2T and other Arthrobacter species. The type strain of the novel species was identified as SYB2T (= KCTC 19291T= DSM 19449T).
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