• Korean Journal of Food Science and Technology
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• v.34 no.6
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• pp.1134-1139
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• 2002

Campylobacter, Arcobacter, and Helicobacter, classified into the same rRNA superfamily VI by taxonomy, cause food-borne diseases, stomach ulcer, and gastric cancer. To detect each strain selectively from contaminated foods, PCR, multiplex-PCR, and restricion fragment length polymorphism (RFLP) were applied on Campylobacter, Arcobacter, and Helicobacter. The same PCR products could be detected using CHA primer targeted for 16S rRNA of Campylobacter, Arcobacter, and Helicobacter. To detect C. jejuni and C. coli from A. butzleri and H. pylori, pg50/pg3 primer targeted for fla A gene was used, and for A. butzleri, Arco2/Butz primer targeted for 23S rRNA was utilized. For H. pylori detection, icd1/icd2 primer targeted for isocitrate dehydrogenase gene was employed, and JEJ1/JEJ2 primer targeted for ceuE gene was effective for C. jejuni detection from the three strains. C. jejuni, C. coli could be separated from A. butzleri and H. pylori through PCR-RFLP using restriction enzyme Dde I. Such primers would be effective for detecting each strain selectively through PCR when C. jejuni, C. coli, A butzleri and H. pylori are contaminated together.

• Journal of Species Research
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• v.12 no.spc2
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• pp.23-32
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• 2023

During screening for indigenous prokaryotic species in Republic of Korea in 2021, a total of 21 bacterial strains assigned to the phylum Bacteroidota were isolated from a variety of environmental habitats including pine cone, seaweed, soil, sea sediment, brackish water and moss. Based on the 16S rRNA gene sequence similarity value of more than 98.7% and formation of a robust phylogenetic clade with the type strain of the closest bacterial species, it was found that the 21 strains belong to independent and recognized bacterial species. There has been no official report that the identified 21 species have been isolated in Republic of Korea up to date. Therefore, 16 species in six genera of two families in the order Flavobacteriales, two species in two genera of two families in the order Cytophagales, one species in one genus of one family in the order Chitinophagales and two species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidota isolated in Republic of Korea. Their Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.

• Journal of Life Science
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• v.24 no.8
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• pp.915-926
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• 2014

The ribosome is a protein synthesizing machinery and a ribonucleoprotein complex that consists of three ribosomal RNAs (23S, 16S and 5S) and 54 ribosomal proteins in bacteria. In the course of ribosome assembly, ribosomal proteins (r-protein) and rRNAs are modified, the r-proteins bind to rRNAs to form ribonucleoprotein complexes which are folded into mature ribosomal subunits. In this process, a number of non-ribosomal trans-acting factors organize the assembly process of the components. Those factors include GTP- and ATP-binding proteins, rRNA and r-protein modification enzymes, chaperones, and RNA helicases. During ribosome biogenesis, they participate in the modifications of ribosomal proteins and RNAs, and the assemblies of ribosomal proteins with rRNAs. Ribosomes can be assembled from a discrete set of components in vitro, and it is notable that in vivo ribosome assembly is much faster than in vitro ribosome assembly. This suggests that non-ribosomal ribosome assembly factors help to overcome several kinetic traps in ribosome biogenesis process. In spite of accumulation of genetic, structural, and biochemical data, not only the entire procedure of bacterial ribosome synthesis but also most of roles of ribosome assembly factors remain elusive. Here, we review ribosome assembly factors involved in the ribosome maturation of Escherichia coli, and summarize the contributions of several ribosome assembly factors which associate with 50S and 30S ribosomal subunits, respectively.

• Annals of Clinical Microbiology
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• v.17 no.1
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• pp.23-27
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• 2014

Rapidly growing mycobacteria are ubiquitous in the environment and are increasingly being recognized as opportunistic pathogens. Recently, a new species, Mycobacteium conceptionense, has been validated from the Mycobacterium fortuitum third biovariant complex by molecular analysis. However, there are few reports, and postsurgical wound infection by this species is rare. We report a case of postsurgical wound infection caused by M. conceptionense in an immunocompetent patient that was identified by a sequencing analysis of 16S rRNA, hps65, and rpoB genes.

• Biomedical Science Letters
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• v.23 no.2
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• pp.96-103
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• 2017

Nocardia species (spp.) are opportunistic pathogen in immunocompromised hosts. The genus Nocardia contains more than 70 species. Nocardia takedensis has been recently reported as a new species of the genus Nocardia. In this study, we describes the first clinical isolate of N. takedensis from the skin lesion in Busan, Korea. For the identification of clinical isolate to the species level as N. takedensis, classical methods (colony morphology, biochemical characteristics, and antimicrobial susceptibility), molecular method (16S rRNA gene sequencing), and MS (mass spectrometry) analysis were conducted. Clinical isolates grew slowly on the culture media (5% sheep blood agar and chocolate agar) under 5% $CO_2$ condition. Especially, carotene pigmentation was detected well on the media. Using mass spectrometry, Nocardia isolate was not identified to the species level. However, molecular method based on 16S rRNA sequencing confirmed the isolate as N. takedensis correctly. N. takedensis isolate was partial positive for acid-fast bacilli on the Ziehl-Neelsen method. And it was observed to be resistance to amoxicillin/clavulanic acid and ciprofloxacin. Our results provide useful information to develop optimal identification protocol of N. takedensis in clinical diagnostic laboratories.

• Korean Journal of Microbiology
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• v.52 no.1
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• pp.65-73
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• 2016

The aim of this study was to investigate the UV-resistance of radiation-resistant bacteria isolated from the water of Han River, South Korea. The water sample was irradiated with 3 kGy gamma radiation prior to isolation. Radiation-resistant bacterial strains were isolated by standard serial dilution method on R2A and 1/10 diluted R2A agar. The resulting purely isolated 60 cultures of bacteria were analysed for UV resistance and used in further studies. Based on the comparative analyses of 16S rRNA gene sequences, the bacterial isolates were divided into 3 phyla (4 genera): the phylum Deinococcus-Thermus (the genus Deinococcus) was 61.7%, Bacteroidetes (Hymenobacter and Spirosoma) was 23.4%, and Firmicutes (Exiguobacterium) was 15%. The results suggested that twenty-nine isolates are candidates new species belonging to Deinococcus, Hymenobacter, and Spirosoma, or other new genera. Nine bacterial strains were selected among the novel candidates and the UV-resistance analysis was conducted. All the candidate bacterial strains showed high UV resistance, similar to that of D. radiodurans R1.

• Fisheries and Aquatic Sciences
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• v.23 no.7
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• pp.18.1-18.10
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• 2020

During June 2017, we collected two postflexion larvae (6.01 and 7.56 mm in standard length [SL]) and two juveniles (7.72 and 9.62 mm SL) belonging to Myctophidae in the waters of Jejudo Island. Those four individuals were identified as Diaphus garmani, which had not been reported in Korea. They were distinguished from Benthosema pterotum by melanophores in the abdominal cavity (absent in D. garmani vs. present in B. pterotum) and the development of photophores (developed in D. garmani vs. rudimentary in B. pterotum) when shorter than 10.0 mm SL. Analysis of 16S rRNA sequences showed that the sequences of four individuals matched those of adult D. garmani (Kimura 2-parameter distance: 0.6-0.8%). This is the first record of larvae and juveniles of D. garmani in Korean waters, and we propose a new Korean name, Gar-ma-ni-sat-bi-neul-chi.

• Journal of Species Research
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• v.10 no.1
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• pp.23-45
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• 2021

For the collection of indigenous prokaryotic species in Korea, 77 strains within the phylum Actinobacteria were isolated from various environmental samples, fermented foods, animals and clinical specimens in 2019. Each strain showed high 16S rRNA gene sequence similarity (>98.8%) and formed a robust phylogenetic clade with actinobacterial species that were already defined and validated with nomenclature. There is no official description of these 77 bacterial species in Korea. The isolates were assigned to 77 species, 31 genera, 18 families, 14 orders and 2 classes of the phylum Actinobacteria. All the strains except one Coriobacteriia strain were affiliated within the class Actinomycetia. Among them, the orders Streptomycetales and Microbacteriales were predominant. A number of strains were isolated from forest soils, riverside soils, and ginseng cultivated soils. Twenty-nine strains were isolated from 'Protected Ecosystem and Scenery Areas'. Morphological properties, basic biochemical characteristics, isolation source and strain IDs are described in the species descriptions.

• Journal of fish pathology
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• v.18 no.2
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• pp.133-146
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• 2005

A bacteriological survey in maricultured fish farms was conducted in Korea from 2002 to 2004. A total number of 166 Vibrio isolates were collected from diseased fishes, including olive flounder (133 isolates), black rock fish (8 isolates), red sea bream (6 isolates), shrimp (5 isolates), black sea bream (4 isolates), abalone (3 isolates) and other fishes (7 isolates). All isolates were phenotypically characterized and then groups were obtained using the traditional biochemical test. Representative isolates of each group were genotypically characterized with sequencing the 16S rRNA genes or 16S-23S intergenic space genes. Above 14 species of Vibrio were identified as V. ichthyoenteri (45 strains), V. alginolyticus (34 strains), V. harveyi (32 strains), Ph. damselae subsp. damselae (Formerly V. damsela, 10 strains), V. campbellii (6 strains), V. costicola-like (6 strains), V. fisheri (5 stains), V. fluvialis (4 strains) and others Vibrio sp. (24 strains) by combining of biochemial and genetic characteristics.

• Fisheries and Aquatic Sciences
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• v.16 no.2
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• pp.109-116
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• 2013

Eighteen specimens of juvenile Mugilidae were collected in October 2012 from the southern coastal waters of Jeju Island, and identified based on analysis of their mitochondrial DNA16S rRNA sequences. Seventeen specimens of Oedalechilus labiosus and a single specimen of Ellochelon vaigiensis were found, constituting a new record for these species among Korean ichthyofauna. O. labiosus is identified by the angle at the posterior end of its mouth, which contains a round notch, a darkish dorsal margin of the pectoral fin, the presence of 33-36 lateral line scales, and 23-24 vertebrae. E. vaigiensis is identified by dark dorsal and pectoral fins, the presence of 26 lateral line scales, and 25 vertebrae. The proposed Korean name for Oedalechilus is 'Sol-ip-sung-eo-sok' and that for Ellochelon is 'Nup-jeok-ggo-ri-sung-eo-sok'. The proposed Korean names for the species are 'Sol-ip-sung-eo' and 'Nup-jeok-ggo-ri-sung-eo' for O. labiosus and E. vaigiensis, respectively. We present a key for identification of the Mugilidae family of species from Korea, and include these two newly recorded species.