- Rasiella rasia gen. nov. sp. nov. within the family Flavobacteriaceae isolated from seawater recirculating aquaculture system
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Seong-Jin Kim , Young-Sam Kim , Sang-Eon Kim , Hyun-Kyoung Jung , Jeeeun Park , Min-Ju Yu , Kyoung-Ho Kim
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J. Microbiol. 2022;60(11):1070-1076. Published online October 17, 2022
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DOI: https://doi.org/10.1007/s12275-022-2099-7
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A novel bacterium designated RR4-40T was isolated from a
biofilter of seawater recirculating aquaculture system in Busan,
South Korea. Cells are strictly aerobic, Gram-negative, irregular
short rod, non-motile, and oxidase- and catalase-negative.
Growth was observed at 15–30°C, 0.5–6% NaCl (w/v),
and pH 5.0–9.5. The strain grew optimally at 28°C, 3% salinity
(w/v), and pH 8.5. The phylogenetic analysis based on
16S rRNA gene sequences showed that strain RR4-40T was
most closely related to Marinirhabdus gelatinilytica NH83T
(94.16% of 16S rRNA gene similarity) and formed a cluster
with genera within the family Flavobacteriaceae. The values
of the average nucleotide identity (ANI), digital DNA-DNA
hybridization (dDDH), and average amino acid identity (AAI)
between genomes of strain RR4-40T and M. gelatinilytica
NH83T were 72.91, 18.2, and 76.84%, respectively, and the
values against the strains in the other genera were lower than
those. The major fatty acids were iso-C15:0 (31.34%), iso-C17:0
3-OH (13.65%), iso-C16:0 3-OH (10.61%), and iso-C15:1 G
(10.38%). The polar lipids comprised phosphatidylglycerol,
diphosphatidylglycerol, aminophospholipid, aminolipid, glycolipid,
and sphingolipid. The major respiratory quinone was
menaquinone-6 (MK-6) and the DNA G + C content of strain
RR4-40T was 37.4 mol%. According to the polyphasic analysis,
strain RR4-40T is considered to represent a novel genus within
the family Flavobacteriaceae, for which the name Rasiella
rasia gen. nov, sp. nov. is proposed. The type strain is RR4-40T
(= KCTC 52650T = MCCC 1K04210T).
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Citations
Citations to this article as recorded by  - Robiginitalea rubriflava sp. nov. and Robiginitalea insularis sp. nov., isolated from coastal seawaters of the Yellow Sea
Seungyeop Oh, Yeonjung Lim, Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2026; 64(2): e2512009. CrossRef -
Mesohalobacter salilacus sp. nov., a novel halotolerant, flexirubin-type pigment-producing bacterium of the family Flavobacteriaceae
Shuai-Bo Han, Yang-Huan Yu, Xiao-Long He, Jin-Jia Liang, Min Wu, Can Chen, Xue-Wei Xu
International Journal of Systematic and Evolutionary Microbiology
.2025;[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. 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
- Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae
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Jeeeun Park , Young-Sam Kim , Seong-Jin Kim , Sang-Eon Kim , Hyun-Kyoung Jung , Min-Ju Yu , Young Jae Jeon , Kyoung-Ho Kim
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J. Microbiol. 2021;59(6):546-551. Published online April 20, 2021
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DOI: https://doi.org/10.1007/s12275-021-0678-7
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1,081
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A novel bacterium, designated strain RR4-56T, was isolated
from a biofilter of a seawater recirculating aquaculture system.
The 16S rRNA gene sequence analysis showed that the
isolate was closely related to Halovulum dunhuangense YYQ-
30T (92.6%), Albimonas donghaensis DS2T (91.3%), Pontivivens
insulae GYSW-23T (91.3%), and Monaibacterium marinum
C7T (90.9%), belonging to the family Rhodobacteraceae.
The strain was aerobic, Gram-negative, rod-shaped, oxidasepositive,
and catalase-negative. Its optimum temperature,
pH, and salinity for growth were 25–30°C, pH 8.5, and 2–3%
NaCl (w/v), respectively. Its growth occurred at 15–35°C, pH
5.0–9.5, and 0–7% NaCl (w/v). It contained ubiquinone-10
(Q-10), a respiratory quinone, and the major cellular fatty
acids were 11-methyl C18:1 ω7c (31.9%), C18:1 ω6c (30.4%),
and C19:0 cyclo ω8c (16.1%). The polar lipids present in the
strain were phosphatidylglycerol, an unidentified phospholipid,
and an unidentified aminolipid. The strain had one
4,373,045 bp circular chromosome with G + C contents of
65.9 mol% including 4,169 genes, 4,118 coding sequences
(CDSs), 3 rRNAs, and 45 tRNAs. Genome annotation predicted
some gene clusters related to the degradation of several
types of organic matter such as protocatechuate, catechol,
and phthalate. Based on the polyphasic characteristics,
RR4-56T represents a novel genus and species in the family
Rhodobacteraceae, for which the name Pikeienuella piscinae
gen. nov., sp. nov. was proposed. The type strain is RR4-56T
(= KCTC 52648T = DSM 107918T).
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Citations
Citations to this article as recorded by - Systematic degradation process of petroleum hydrocarbons by an integrated bacterial consortium under bottom seawater and surface seawater environments
Lin Lin, Jia Ning, Chunhui Li, Linlin Zhang, Yu Gao, Wang Bo, Ke Shi
Environmental Technology.2025; 46(5): 752. CrossRef -
Paludibacillus litoralis gen. nov., sp. nov.: a novel species of a novel genus in the family Paracoccaceae, isolated from the sediment of a tidal flat located in Zhoushan, China
Dong-yan He, Jia-wei Gao, Yu-ruo Wang, Ke Cao, Yun-fei Cao, Yang Li, Lu-yao Wang, Xing-cheng Wang, Lin Xu, Cong Sun
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater
Jili Wang, Yuling Zhang, Yang Ding, Hewei Song, Ting Liu, Yi Zhang, Weiqing Xu, Yujia Shi
Chemosphere.2023; 311: 137173. CrossRef - 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
- Pukyongia salina gen. nov., sp. nov., a novel genus in the family Flavobacteriaceae
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Young-Sam Kim , Seong-Jin Kim , Yeon Hee Jang , Kyoung-Ho Kim
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J. Microbiol. 2020;58(6):456-462. Published online April 22, 2020
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DOI: https://doi.org/10.1007/s12275-020-9310-5
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1,005
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A Gram-negative aerobic bacterium, designated RR4-38T,
was isolated from a biofilter in a seawater recirculating aquaculture
system (RAS) in Busan, South Korea. The bacteria
were irregular, short, rod-shaped, non-motile, oxidase-positive,
and catalase-negative. Growth of the strain RR4-38T
was observed at 15–35°C (optimum, 25–30°C), pH 5.5–9.5
(optimum, pH 8.0), and in the presence of 0–5% (w/v) NaCl
(optimum, 3%). Phylogenetic analysis based on the 16S rRNA
gene sequences showed that the strain RR4-38T formed a distinct
lineage with close genera Ulvibacter (≤ 95.01% 16S rRNA
gene sequence similarity), Aureitalea (94.74%), Aureisphaera
(≤ 93.27%), and Jejudonia (93.07%) that all belong to the
family Flavobacteriaceae. Whole-genome sequence comparison
revealed that the ANI (average nucleotide identity) and
digital DDH (DNA-DNA hybridization) values between strain
RR4-38T and the two closest strains, Ulvibacter antarcticus
DSM 23424T and Aureitalea marina S1-66T, were 68.96–
69.88% and 17.4–19%, respectively. The genome analysis
revealed that the strain might be involved in biodegradation
of organic debris produced by farmed fish in aquaculture
systems. The predominant respiratory quinone was menaquinone
MK-6 and the major cellular fatty acids were iso-
C15:0 (26.5%), iso-C17:0 3-OH (16.4%), iso-C15:1 G (15%), and
iso-C16:0 3-OH (9.6%). The major cellular polar lipids were
diphosphatidylglycerol, phosphatidylethanolamine, unidentified
aminolipids, and glycolipids. Based on phenotypic, chemotaxonomic,
and phylogenetic features, strain RR4-38T represents
a novel genus and species in the family Flavobacteriaceae,
for which the name Pukyongia salina gen. nov., sp.
nov. is proposed. The type strain is RR4-38T (= KCTC 52651T
= DSM 108068T).
-
Citations
Citations to this article as recorded by - Autumnicola aciditolerans sp. nov., a novel member of the genus Autumnicola isolated from tidal flat in Zhoushan
Yang Li, Dong-Yan He, Jia-Wei Gao, Ke Cao, Yun-Fei Cao, Xing-Cheng Wang, Lin Xu, Yan Bai, Can Chen, Cong Sun
Antonie van Leeuwenhoek.2026;[Epub] CrossRef - Two new members of the family Aerococcaceae: Tuanshanicoccus yangjingiae gen. nov., sp. nov. and Tuanshanicoccus lijuaniae sp. nov., isolated from the trachea of Marmota himalayana
Gui Zhang, Yanpeng Cheng, Yue Liu, Dong Jin, Shan Lu, Weiguang Li, Ji Pu, Yajun Ge, Caiyun Ma, Wenbo Luo, Jianguo Xu
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Assessing the impacts of fine sediment removal on endogenous pollution release and microbial community structure in the shallow lakes
Ying Yu, Zengliang Yu, Jingang Jiang, Lifang Wu, Huiyun Feng
Science of The Total Environment.2023; 897: 165410. CrossRef - 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 - Constantimarinum furrinae gen. nov., sp. nov., a marine bacterium isolated from saline volcanic rock aquifer (lava seawater) at Jeju Island, Republic of Korea
Sung-Hyun Yang, Hyun-Myung Oh, Mi-Jeong Park, Dongil Jang, Kae Kyoung Kwon
Journal of Microbiology.2022; 60(1): 11. CrossRef -
Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov., isolated from Tibetan Plateau wildlife
Gui Zhang, Yuyuan Huang, Jing Yang, Xin-He Lai, Dong Jin, Shan Lu, Yanpeng Cheng, Caixin Yang, Ji Pu, Junrong Liang, Ying Huang, Jianguo Xu
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef - Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae
Jeeeun Park, Young-Sam Kim, Seong-Jin Kim, Sang-Eon Kim, Hyun-Kyoung Jung, Min-Ju Yu, Young Jae Jeon, Kyoung-Ho Kim
Journal of Microbiology.2021; 59(6): 546. CrossRef
- Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.
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Dong-Shan An , Muhammad Zubair Siddiqi , Kyoung-Ho Kim , Hong-Shan Yu , Wan-Taek Im
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J. Microbiol. 2018;56(1):24-29. Published online January 4, 2018
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DOI: https://doi.org/10.1007/s12275-018-7107-6
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1,040
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A taxonomic study was conducted on BR7-21T, a bacterial
strain isolated from the soil of a ginseng field in Baekdu
Mountain. Comparative studies of the 16S rRNA gene sequence
showed that the isolate was most closely related to
Conexibacter woesei DSM 14684T, Solirubrobacter pauli ATCC
BAA-492T, Patulibacter minatonensis JCM 12834T, with 93.8%,
92.4%, and 91.5% sequence similarity, respectively; each genus
represented a family in the order Solirubrobacterales. Strain
BR7-21T was Gram-reaction positive, non-spore forming,
aerobic, non-motile, and short rod-shaped. It grew well on
half-strength R2A medium. The G + C content of the genomic
DNA was 73.9%. It contained meso-diaminopimelic acid in
the cell wall and the major menaquinones were MK-7(H4)
and MK-8(H4). The major fatty acids were summarized as
(C16:1 ω7c/iso-C15:0 2-OH), iso-C16:0, and C17:0 cyclo. On the
basis of polyphasic evidence, it was proposed that strain BR7-
21T should be placed in a new genus and species, for which
the name Baekduia soli gen. nov., sp. nov. was proposed with
the type strain BR7-21T (= KCTC 22257T = LMG 24797T). The
family Baekduiaceae fam. nov. is proposed to encompass
the genus Baekduia gen. nov.
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Citations
Citations to this article as recorded by - Integrative phylogenomics, polyphasic taxonomy, and metagenomics expand the characterized taxonomic diversity of Thermoleophilia
Shuai Li, Xin‐Ran Wang, Xu‐Rui Li, Jia‐Rui Han, Wen‐Hui Lian, Jie Huang, Jun Liu, Wei Zhang, Yong‐Hong Liu, Bao‐Zhu Fang, Cui‐Ping Tian, Lei Dong, Wen‐Jun Li
Journal of Systematics and Evolution.2026;[Epub] CrossRef -
Actinomycetota bioprospecting from ore-forming environments
César Aguilar, Amir Alwali, Madeline Mair, Lorena Rodriguez-Orduña, Haydeé Contreras-Peruyero, Ramya Modi, Carson Roberts, Nelly Sélem-Mojica, Cuauhtemoc Licona-Cassani, Elizabeth Ivy Parkinson
Microbial Genomics
.2024;[Epub] CrossRef -
Svornostia abyssi gen. nov., sp. nov. isolated from the world’s deepest silver–uranium mine currently devoted to the extraction of radon-saturated water
Gabriela Kapinusova, Jachym Suman, Michal Strejcek, Petr Pajer, Tomas Cajthaml, Pavel Ulbrich, Meina Neumann-Schaal, Ondrej Uhlik
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef -
Baekduia alba sp. nov., a novel representative of the order Solirubrobacterales isolated from temperate grassland soil
Selma Vieira, Katharina J. Huber, Alicia Geppert, Jacqueline Wolf, Meina Neumann-Schaal, Mathias Müsken, Jörg Overmann
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef -
Paraconexibacter antarcticus sp. nov., a novel actinobacterium isolated from Antarctic tundra soil
Chol Song Kim, Zhenyu Liu, Xiaoya Peng, Kun Qin, Jun Huang, Jingjing Niu, Yixuan Liu, Jia Liu, Mingjing Sun, Fang Peng
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - High-Resolution Indicators of Soil Microbial Responses to N Fertilization and Cover Cropping in Corn Monocultures
Nakian Kim, Chance W. Riggins, María C. Zabaloy, Marco Allegrini, Sandra L. Rodriguez-Zas, María B. Villamil
Agronomy.2022; 12(4): 954. CrossRef -
Capillimicrobium parvum gen. nov., sp. nov., a novel representative of Capillimicrobiaceae fam. nov. within the order Solirubrobacterales, isolated from a grassland soil
Selma Vieira, Katharina J. Huber, Alicia Geppert, Jacqueline Wolf, Meina Neumann-Schaal, Manja Luckner, Gerhard Wanner, Mathias Müsken, Jörg Overmann
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2019; 69(5): 1247. CrossRef
- Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing
-
Da-Eun Lee , Jinhwan Lee , Young-Mog Kim , Jeong-In Myeong , Kyoung-Ho Kim
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J. Microbiol. 2016;54(4):296-304. Published online April 1, 2016
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DOI: https://doi.org/10.1007/s12275-016-5571-4
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1,168
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Bacterial diversity in a seawater recirculating aquaculture
system (RAS) was investigated using 16S rRNA amplicon
sequencing to understand the roles of bacterial communities
in the system. The RAS was operated at nine different combinations
of temperature (15°C, 20°C, and 25°C) and salinity
(20‰, 25‰, and 32.5‰). Samples were collected from five
or six RAS tanks (biofilters) for each condition. Fifty samples
were analyzed. Proteobacteria and Bacteroidetes were most
common (sum of both phyla: 67.2% to 99.4%) and were inversely
proportional to each other. Bacteria that were present
at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes
(2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%);
they were preferentially present in packed bed biofilters, mesh
biofilters, and maturation biofilters. The three biofilters showed
higher diversity than other RAS tanks (aerated biofilters, floating
bed biofilters, and fish tanks) from phylum to operational
taxonomic unit (OTU) level. Samples were clustered
into several groups based on the bacterial communities. Major
taxonomic groups related to family Rhodobacteraceae and
Flavobacteriaceae were distributed widely in the samples. Several
taxonomic groups like [Saprospiraceae], Cytophagaceae,
Octadecabacter, and Marivita showed a cluster-oriented distribution.
Phaeobacter and Sediminicola-related reads were
detected frequently and abundantly at low temperature. Nitrifying
bacteria were detected frequently and abundantly in
the three biofilters. Phylogenetic analysis of the nitrifying bacteria
showed several similar OTUs were observed widely
through the biofilters. The diverse bacterial communities and
the minor taxonomic groups, except for Proteobacteria and
Bacteroidetes, seemed to play important roles and seemed
necessary for nitrifying activity in the RAS, especially in packed
bed biofilters, mesh biofilters, and maturation biofilters.
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Citations
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Spieck Eva
International Journal of Aquaculture and Fishery Sciences.2017; : 051. CrossRef
- Analysis of Bacterial Diversity in Sponges Collected from Chuuk and Kosrae Islands in Micronesia
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In-Hye Jeong , Kyoung-Ho Kim , Hyi-Seung Lee , Jin-Sook Park
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J. Microbiol. 2014;52(1):20-26. Published online January 4, 2014
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DOI: https://doi.org/10.1007/s12275-014-3619-x
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936
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3
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Abstract
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The bacteria resident in sponges collected from Chuuk Lagoon
and Kosrae Island of Micronesia were investigated using the
16S rRNA gene PCR-tagged pyrosequencing method. These
sponges were clustered into 5 groups based on their bacterial
composition. Diversity indexes and cumulative rank abundance
curves showed the different compositions of bacterial
communities in the various groups of sponges. Reads related
to the phylum Chloroflexi were observed predominantly
(9.7–68.2%) in 9 sponges of 3 groups and unobserved in the
other 2 groups. The Chloroflexi-containing group had similar
bacterial patterns at the phylum and lower taxonomic levels,
for example, significant proportions of Acidobacteria, Gemmatimonadetes,
SBR1093, and PAUC34f were observed in
most members of this group. The three groups in the Chloroflexi-
containing group, however, showed some minor
differences in the composition and diversity. The other two
groups contained high proportions of Proteobacteria (>87%)
or Bacteroidetes (>61%) and different composition and diversity
compared to the Chloroflexi-containing group and each
other. Four pairs of specimens with the same species showed
similar bacterial profiles, but, the bacteria in sponges were
highly specific at the individual level.
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Citations
Citations to this article as recorded by - Identification of marine sponge-associated bacteria of the Saint Martin's island of the Bay of Bengal emphasizing on the prevention of motile Aeromonas septicemia in Labeo rohita
Sulav Indra Paul, Md. Mahbubur Rahman, Mohammad Abdus Salam, Md. Arifur Rahman Khan, Md. Tofazzal Islam
Aquaculture.2021; 545: 737156. CrossRef - First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing
Akram Najafi, Maryam Moradinasab, Iraj Nabipour
Frontiers in Microbiology.2018;[Epub] CrossRef - Acidobacteriaappear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid
Aileen O’Connor-Sánchez, Adán J Rivera-Domínguez, César De los Santos-Briones, Lluvia K López-Aguiar, Yuri J Peña-Ramírez, Alejandra Prieto-Davo
Biological Research.2014;[Epub] CrossRef
- Analysis of Bacterial Diversity in Sponges Collected off Chujado, an Island in Korea, Using Barcoded 454 Pyrosequencing: Analysis of a Distinctive Sponge Group Containing Chloroflexi
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In-Hye Jeong , Kyoung-Ho Kim , Jin-Sook Park
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J. Microbiol. 2013;51(5):570-577. Published online October 31, 2013
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DOI: https://doi.org/10.1007/s12275-013-3426-9
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909
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0
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13
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Abstract
PDF
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The bacterial diversity of 14 sponges belonging to 5 different orders that were collected around Chuja Island, Korea was investigated using barcoded 454 pyrosequencing. The sponges contained many unidentified bacterial groups (e.g. more than half of the taxa at the family level) that were known only in environmental sequences and obtained from culture-independent methods. Five of the sponges were clustered into one notable group (CF group), which was distinguished from the other sponges in accordance with bacterial composition (the other sponges may be separated into more groups but clustering is not clear). The CF group contained high amounts of Chloroflexi (25.0–47.7%) and moderate amounts of Gemmatimonadetes (2.3–7.0%), AncK6 (0.6–2.2%), PAUC34f (0.8–6.0%), Acidobacteria (3.7–9.6%), and SBR1093 (1.8–5.6%) exclusively or almost exclusively to this group. Sponges in the CF group also showed higher diversity (e.g. Shannon index) than the other sponges and contained group-specific taxonomic lineages (e.g. class or family level) from group-specific phyla and even from the Proteobacteria and Actinobacteria, which were detected in all sponges at the phylum level. The CF group may be one of the most distinctive groups in sponges in terms of bacterial diversity.
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Citations
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In-Hye Jeong, Kyoung-Ho Kim, Hyi-Seung Lee, Jin-Sook Park
Journal of Microbiology.2014; 52(1): 20. CrossRef - Bacterial Diversity of the South Pacific Sponge, Dactylospongia metachromia Based on DGGE Fingerprinting
In-Hye Jeong, Jin-Sook Park
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- Comparative Genomic Analysis of Bacteriophage EP23 Infecting Shigella sonnei and Escherichia coli
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Ho-Won Chang , Kyoung-Ho Kim
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J. Microbiol. 2011;49(6):927-934. Published online December 28, 2011
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DOI: https://doi.org/10.1007/s12275-011-1577-0
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675
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0
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21
Crossref
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Abstract
PDF
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Bacteriophage EP23 that infects Escherichia coli and Shigella sonnei was isolated and characterized. The bacteriophage morphology was similar to members of the family Siphoviridae. The 44,077 bp genome was fully sequenced using 454 pyrosequencing. Comparative genomic and phylogenetic analyses showed that EP23 was most closely related to phage SO-1, which infects Sodalis glossinidius and phage SSL-2009a, which infects engineered E. coli. Genomic comparison indicated that EP23 and SO-1 were very similar with each other in terms of gene order and amino acid similarity, even though their hosts were separated in the level of genus. EP23 and SSL-2009a displayed high amino acid similarity between their genes, but there was evidence of several recombination events in SSL-2009a. The results of the comparative genomic analyses further the understanding of the evolution and relationship between EP23 and its bacteriophage relatives.
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Citations
Citations to this article as recorded by - Bacteriophage Treatment Induces Phenotype Switching and Alters Antibiotic Resistance of ESBL Escherichia coli
Árpád Rózsa, László Orosz, Nikoletta Szemerédi, Gabriella Spengler, Gábor Kecskeméti, Otília Vágó, Károly Péter Sárvári, Diana Szabó, Zoltán Szabó, Katalin Burián, Dezső Péter Virok
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Viruses.2023; 15(2): 379. CrossRef -
Complete Genome Sequences of Five SO-1-Like
Siphoviridae
Bacteriophages That Infect
Enterobacteriales
Madelyn G. Purnell, Kyle Andersen, Adam Bell, Jared T. Briscoe, Hannah M. F. Brown, Emilee L. Carr, Justen Doney, Parker F. Folsom, Cheyanne Green, Evan H. Harris, Elisa Huhem, R. Matthew Jensen, Liberty Johnson, Carter Jones, Andrew S. Lambert, Emily Loe
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Jing Xu, Ruiyang Zhang, Xinyan Yu, Xuesen Zhang, Genyan Liu, Xiaoqiu Liu
Frontiers in Microbiology.2021;[Epub] CrossRef - Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca)
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Frontiers in Veterinary Science.2021;[Epub] CrossRef - Isolation, characterization, and genomic analysis of the novel T4-like bacteriophage ΦCJ20
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Food Science and Biotechnology.2021; 30(5): 735. CrossRef - Ecology, Structure, and Evolution of Shigella Phages
Sundharraman Subramanian, Kristin N. Parent, Sarah M. Doore
Annual Review of Virology.2020; 7(1): 121. CrossRef - Genomic and Proteomic Characterizations of Sfin-1, a Novel Lytic Phage Infecting Multidrug-Resistant Shigella spp. and Escherichia coli C
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Lawrence D. Goodridge
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- 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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816
View
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1
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12
Crossref
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Abstract
PDF
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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.
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Citations
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Haixiao Jin, Youhong Zhong, Yiting Wang, Chuanyu Zhang, Jin Guo, Xiaona Shen, Cunxiang Li, Ying Huang, Haoming Xiong, Peng Wang, Wei Li
Viruses.2022; 14(12): 2740. CrossRef - Isolation, characterization, and genomic analysis of the novel T4-like bacteriophage ΦCJ20
Jaegon Kim, Jong Pyo Chae, Gyeong-Hwuii Kim, Jae-Won Kim, Na-Gyeong Lee, Jun-Ok Moon, Sung-Sik Yoon
Food Science and Biotechnology.2021; 30(5): 735. CrossRef - Molecular Characteristics of Novel Phage vB_ShiP-A7 Infecting Multidrug-Resistant Shigella flexneri and Escherichia coli, and Its Bactericidal Effect in vitro and in vivo
Jing Xu, Ruiyang Zhang, Xinyan Yu, Xuesen Zhang, Genyan Liu, Xiaoqiu Liu
Frontiers in Microbiology.2021;[Epub] CrossRef - Ecology, Structure, and Evolution of Shigella Phages
Sundharraman Subramanian, Kristin N. Parent, Sarah M. Doore
Annual Review of Virology.2020; 7(1): 121. CrossRef - Genomic and Proteomic Characterizations of Sfin-1, a Novel Lytic Phage Infecting Multidrug-Resistant Shigella spp. and Escherichia coli C
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Manonmani Soundararajan, Rudolf von Bünau, Tobias A. Oelschlaeger
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Current Microbiology.2015;[Epub] CrossRef - Isolation and development of bioluminescent reporter phages for bacterial dysentery
D. A. Schofield, D. J. Wray, I. J. Molineux
European Journal of Clinical Microbiology & Infectious Diseases.2015; 34(2): 395. CrossRef - Bacteriophages for managingShigellain various clinical and non-clinical settings
Lawrence D. Goodridge
Bacteriophage.2013; 3(1): e25098. CrossRef - Comparative genomic analysis of bacteriophage EP23 infecting Shigella sonnei and Escherichia coli
Ho-Won Chang, Kyoung-Ho Kim
The Journal of Microbiology.2011; 49(6): 927. CrossRef
- 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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764
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33
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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.
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- Aliihoeflea aestuarii gen. nov., sp. nov., a Novel Bacterium Isolated from Tidal Flat Sediment
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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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- Luteimonas aestuarii sp. nov., Isolated from Tidal Flat Sediment
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Seong Woon Roh , Kyoung-Ho Kim , Young-Do Nam , Ho-Won Chang , Min-Soo Kim , Jung-Hoon Yoon , Hee-Mock Oh , Jin-Woo Bae
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J. Microbiol. 2008;46(5):525-529. Published online October 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0189-9
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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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- Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People
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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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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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- Comamonas granuli sp. nov., Isolated from Granules Used in a Wastewater Treatment Plant
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Kyoung-Ho Kim , Leonid N. Ten , Qing-Mei Liu , Wan-Taek Im , Sung-Taik Lee
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J. Microbiol. 2008;46(4):390-395. Published online August 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0019-0
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Abstract
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A Gram-negative, motile, rod-shaped, non-spore-forming bacterial strain, designated as Ko03T, was isolated from microbial granules, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The isolate was positive for catalase and oxidase, but negative for gelatinase and β-galactosidase. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evoluionary radiation occupied by the genus Comamonas, its closest neighbors being Comamonas koreensis KCTC 12005T (95.9% sequence similarity), Comamonas nitrativorans DSM 13191T (95.7%), and Comamonas odontotermitis LMG 23579T (95.7%). Strain Ko03T had a genomic DNA G+C content of 68.4 mol% and the predominant respiratory quinone was Q-8. The major fatty acids were C16:1 ω7c (44.7%), C16:0 (28.1%), C18:1 (16.1%), and C10:0 3-OH (3.5%). These chemotaxonomic results supported the affiliation of strain Ko03T to the genus Comamonas. However, low 16S rRNA gene sequence similarity values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Ko03T from recognized Comamonas species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Ko03T represents a novel species of the genus Comamonas, for which the name Comamonas granuli sp. nov. is proposed. The type strain is Ko03T (= KCTC 12199T= NBRC 101663T).
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Citations
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Comamonas endophytica sp. nov., a novel indole acetic acid producing endophyte isolated from bamboo in China
Jinjun Yue, Fu Yang, Youtie Xiao, Seqiao Lin, Zhengping He, Siyu Wang, Jiayi Zhao, Jinling Yuan, Lubin Li, Lei Liu
International Journal of Systematic and Evolutionary Microbiology
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Rahul Kadam, Sangyeol Jo, Kamonwan Khanthong, Jonghwa Lee, Heewon Jang, Jungyu Park
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Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea
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International Journal of Systematic and Evolutionary Microbiology
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Genomic Analysis of Carbapenem-Resistant
Comamonas
in Water Matrices: Implications for Public Health and Wastewater Treatments
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Comamonas suwonensis sp. nov., isolated from stream water in the Republic of Korea
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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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709
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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.
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- 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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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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S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(2): 421. CrossRef - Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment
S. W. Roh, K.-H. Kim, Y.-D. Nam, H.-W. Chang, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(6): 1359. CrossRef - Halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood
Seong Woon Roh, Jin-Woo Bae
The Journal of Microbiology.2009; 47(2): 162. CrossRef - Nitratireductor basaltis sp. nov., isolated from black beach sand
K.-H. Kim, S. W. Roh, H.-W. Chang, Y.-D. Nam, J.-H. Yoon, C. O. Jeon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(1): 135. CrossRef - Phylogenetic Characterization of Two Novel Commensal Bacteria Involved with Innate Immune Homeostasis inDrosophila melanogaster
Seong Woon Roh, Young-Do Nam, Ho-Won Chang, Kyoung-Ho Kim, Min-Soo Kim, Ji-Hwan Ryu, Sung-Hee Kim, Won-Jae Lee, Jin-Woo Bae
Applied and Environmental Microbiology.2008; 74(20): 6171. CrossRef - Marinobacter goseongensis sp. nov., from seawater
S. W. Roh, Z.-X. Quan, Y.-D. Nam, H.-W. Chang, K.-H. Kim, S.-K. Rhee, H.-M. Oh, C. O. Jeon, J.-H. Yoon, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(12): 2866. CrossRef - Genomics of biological wastewater treatment
Roland J. Siezen, Marco Galardini
Microbial Biotechnology.2008; 1(5): 333. CrossRef - List of new names and new combinations previously effectively, but not validly, published
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(9): 1993. CrossRef - Luteimonas aestuarii sp. nov., isolated from tidal flat sediment
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Min-Soo Kim, Jung-Hoon Yoon, Hee-Mock Oh, Jin-Woo Bae
The Journal of Microbiology.2008; 46(5): 525. CrossRef - Marinomonas basaltis sp. nov., a marine bacterium isolated from black sand
H.-W. Chang, S. W. Roh, K.-H. Kim, Y.-D. Nam, J.-H. Yoon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(12): 2743. CrossRef - 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
The Journal of Microbiology.2008; 46(5): 594. CrossRef
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