• Parasites, Hosts and Diseases
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• v.34 no.2
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• pp.127-134
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• 1996

Twelve isolates of Accnthamoebc app. assigned to either A. castellanii or A. poIMphoSa, and type strains of A. culbefsoni, A. henIWi, A. pqkestinefiE, and A. astronyxi,s were examined by restriction fragment length polymorphism (RFLP) of a conserved region of small subunit ribosomal RMh gene (ssu rDNA) amplified by polymerase chain reaction (PCR). The PCR products of the isolates measured approximately 910-930 bp, except for that of A. astronyxis which was extraordinarily long, approximately 1,170 bp. Average of estimated sequence divergence of the amplified DNA among the isolates assigned to A. castellanii was 9.8% whereas that among the isolates assigned to A. polvphusn 9.6%. The maximum intraspecific sequence divergence among the isolates assigned to A. costellanii was observed between the Chang and Ma strains (17.3%) while that among the isolates assigned to A. poIWphosa was observed between KA/S3 and KA/S7 strains (16.1%). The both maximum sequence divergences were much greater than the minimum interspecific sequence divergence between A. cnstellnnii and A. polwphasa (2.6%) which appeared between the Castellani (or CCAP 1501/12 g) and KA/S3 strains. The PCR-RFLP patterns of A. culbertsoni, A. healyi, A. palestinensis, and A. ostronvxis were quite diverse from one another and from those of isolates assigned to either A. castellanii or A. polyphoga. It is suggested that taxonomic validity of the isolates assigned to either A. castellnnii or A. polyphoga should be reevaluated.

• Journal of Life Science
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• v.19 no.2
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• pp.277-283
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• 2009

Biogenic amines are generally formed through the decarboxylation of specific free amino acids by exogenous decarboxylases released by microbial species associated with the fish products and fermented feeds. This study was conducted to investigate the properties of e tuna waste regarding the control of degradation of biogenic amines (histamine, tyramine, tryptamine, putrescine, and cadaverine) that might be related with the anti-nutritional factor of the tuna waste that is used for manufacturing domestic fish meal. The values of pH and the salt content were 6.51, 3.35% in tuna waste and 5.58 and 5.83% in tuna fish meal, respectively. The strains and dominant bacteria tested in the tuna waste sample were 9.20, 9.29, 5.67, 7.82 and 7.58 log CFU/g of total bacteria, aerobic plate count (APC), total coliform (TC), Lactobacillus spp. and Bacillus spp., respectively. The main histamine forming-bacteria (HFB) in tuna waste were detected by silica gel thin-layer chromatography (TLC) and 7 histamine-forming bacterial species were isolated among microbes grown in selective medium. The histamine concentration was determined by detection of fluorescence of ο-phthaldialdehyde (OPA) derivatives using HPLC and the date were used to reconfirm the identities of the amine-producing bacteria. The 15 histamine- forming bacteria strains grown in trypicase soy broth (TSB) supplemented with 1% L-histidine (TSBH) were identified as Lactococcus(L.) lactis subsp. lactis, Klebsiella pneummonlae, L. garvieae 36, Vibrio olivaceus, Hafnia alvei and L. garvieae which were main dominant amine - producing strains, and Morganella morganii identified by 16S ribosomal RNA (rRNA) sequencing with PCR amplification. A Phylogenetic tree generated from the 16S rRNA sequencing data showed different phyletic lines that could be readily classified as biogenic amine forming gram-positive and negative bacteria.

• The Plant Pathology Journal
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• v.27 no.4
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• pp.367-371
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• 2011

Multiplex PCR assays were developed for the simultaneous detection of ten important Korean quarantine phytoplasmas. The species-specific primers were designed based on ribosomal protein, putative preprotein translocase Y, immunodominant protein, elongation factor TU, chaperonin protein and the 16S rRNA genes of 'Candidatus (Ca.) Phytoplasma' species. Three main primer sets were prepared from ten designed primer pairs to limit nonspecific amplification as much as possible. The multiplex PCR assay using the three primer sets successfully amplified the correct conserved genes for each 'Ca. Phytoplasma' species. In addition, ten important 'Ca. Phytoplasma' species could be easily determined by recognizing band patterns specific for each phytoplasma species from three primer sets. Moreover, a high sensitivity of multiplex PCR for each primer set was observed for samples containing a low DNA concentration (10 ng/${\mu}l$). This study provides the useful multiplex PCR assay as a convenient method to detect the presence of ten important quarantine phytoplasmas in Korea.

• Microbiology and Biotechnology Letters
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• v.39 no.2
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• pp.175-181
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• 2011

Kimchi is a group of traditional fermented vegetable foods in Korea and known to be the product of a natural mixed-fermentation process carried out principally by lactic acid bacteria (LAB). According to microbial results based on conventional identification, Leuconostoc mesenteroides and Lactobacillus plantarum were considered to be responsible for the good taste and over-ripening of kimchi, respectively. However, with the application of phylogenetic identification, based on 16S ribosomal RNA gene similarities, a variety of Leuconostoc and Lactobacillus species not detected in the previous studies have been isolated, together with a species in the genus Weissella. Additionally, Lactobacillus sakei has been accepted as the most populous LAB in over-ripened kimchi. In this study, Leuconostoc and Weissella species inhibiting the growth of Lb. sakei were isolated from kimchi for future applications to do with kimchi fermentation. From 25 kimchi samples, 378 strains in the genera Leuconostoc and Weissella were isolated and 68 strains identified as Lc. mesenteroides, Lc. citreum, Lc. lactis, W. cibaria, W. confusa, and W. paramesenteroides exhibited growth inhibition against Lb. sakei. Most of the strains also had antagonistic activities against Lb. brevis, Lb. curvatus, Lb. paraplantarum, Lb. pentosus, and Lb. plantarum. Their antagonistic activities against Lb. sakei were more remarkable at lower temperatures of incubation.

• Journal of Microbiology
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• v.43 no.2
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• pp.209-212
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• 2005

The purpose of this study was to develop species-specific PCR primers for use in the identification and detection of Actinobacillus actinomycetemcomitans. These primers target variable regions of the 168 ribosomal RNA coding gene (rDNA). We assessed the specificity of the primers against 9 A. actinomycetemcomitans strains and 11 strains (3 species) of the Haemophilus genus. Primer sensitivity was determined by testing serial dilutions of the purified genomic DNAs of A. actinomycetemcomitans ATCC$ 33384^$T Our obtained data revealed that we had obtained species-specific amplicons for all of the tested A. actinomycetemcomitans strains, and that none of these amplicons occurred in any of the other species. Our PCR protocol proved able to detect as little as 4 fg of A. actinomycetemcomitans chromosomal DNA. Our findings suggest that these PCR primers are incredibly sensitive, and should prove suitable for application in epidemiological studies, as well as the diagnosis and monitoring of periodontal pathogens after treatment for periodontitis.

• Tuberculosis and Respiratory Diseases
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• v.67 no.3
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• pp.239-243
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• 2009

Delftia acidovorans is a gram-negative motile rod found ubiquitously in soil and in water. Confirmed isolation from clinical infections is rare, and has been documented mostly in immunocompromised patients or those with indwelling catheters. A 53-year-old man was referred for the evaluation of a huge mass-like lesion found incidentally by chest X-ray. The lesion occupied more than half of the right lung and was diagnosed as a large loculated pleural effusion by CT scan. Bloody pus was drained through a percutaneous catheter, and D. acidovorans, identified by the Vitek GN card and confirmed by amplification of 16S ribosomal RNA and sequencing analysis, was isolated repeatedly from the drained pus. The patient was treated with imipenem/cilastatin to which the organism was sensitive. This is a rare report of chronic empyema associated with D. acidovorans in the respiratory system of an immunocompetent patient.

• International Journal of Oral Biology
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• v.38 no.2
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• pp.55-59
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• 2013

TM7 is an uncultivated organism which is present in extremely diverse environments. Members of the Dialister genus are difficult to culture as a result of which many of these strains remain uncultivated. It has been suggested that TM7 and Dialister bacteria may belong to a group of suspected periodontal pathogens. In our current study, the presence of the sebacteria in Korean dental plaque samples was assessed using PCR detection methods with specific primers for 16S ribosomal RNA genes. The experimental group included 84 volunteers (35 males and 49 females). Plaque samples were collected from 4 non-adjacent proximal sites of the molar areas of the mandible in each subject and pooled. TM7 was detectable in 56% and the Dialister genus in 27.5% of the volunteers. Both TM7 and Dialister were present in 20.3% of volunteers. We found that 36.9% of the volunteers were negative for both bacteria. Further studies to evaluate the prevalence of these putative pathogenic bacteria in the Korean population are warranted.

• Animal Systematics, Evolution and Diversity
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• v.39 no.4
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• pp.264-271
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• 2023

The edible jellyfish Rhopilema esculentum occurs in waters throughout northeastern Asia, including in Korea, China, and Japan. In Korean waters, R. esculentum has appeared in two regions (Gangwha and Muan). Based on the appearance of young medusae and coastal distribution records, these two regions may be key R. esculentum breeding sites. In the present study, we investigate and compare the genetic structure of R. esculentum in the two regions using mitochondrial sequences (16S ribosomal RNA and cytochrome c oxidase subunit I). The genetic diversity of the R. esculentum population at Ganghwa exceeded that of the population at Muan. Despite considerable geographic separation (400 km) between the two regions(Gangwha and Muan), our haplotype network suggests that the Gangwha and Muan populations of R. esculentum are related. The simple and monotonous genetic structure of the Muan population shows that R. esculentum emergence is relatively recent. In contrast, the Gangwha population shows evolution. Moreover, jellyfish of the Gangwha population are genetically diverse and remain constant despite environmental fluctuations in the Han River. The Gangwha area is considered to be the old origin of R. esculentum in Korea.

• Korean Journal of Ichthyology
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• v.36 no.3
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• pp.288-294
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• 2024

A juvenile of long-snout tonguefish, Symphurus longirostris belonging to the family Cynoglossidae, was collected from the waters around Jeju Island, Korea in August 2023. Molecular analysis revealed that our juvenile specimen was identical to S. longirostris adult from Japan (Kimura-2-parameter distance, d=0.002) based on mitochondrial DNA 16S ribosomal RNA region sequences 475 base pairs, and differed from its congeneric S. orientalis (d=0.199). The juvenile of S. longirostris has the following morphological traits: obvious dermal spots on both sides of the bases of the dorsal and anal fins; and peritoneum bluish black on its dorsalmost aspect. The juvenile of S. longirostris is also distinguished from S. orientalis in that they do not have a patch of melanophores above the abdominal cavity on the ocular-side. This is the first record of S. longirostris in Korea, and we propose a new Korean name "Gin-ko-bo-seop-seo-dae" for this species.

• Journal of Ginseng Research
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• v.40 no.2
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• pp.97-104
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• 2016

Background: Rhizobacteria play an important role in plant defense and could be promising sources of biocontrol agents. This study aimed to screen antagonistic bacteria and develop a biocontrol system for root rot complex of Panax notoginseng. Methods: Pure-culture methods were used to isolate bacteria from the rhizosphere soil of notoginseng plants. The identification of isolates was based on the analysis of 16S ribosomal RNA (rRNA) sequences. Results: A total of 279 bacteria were obtained from rhizosphere soils of healthy and root-rot notoginseng plants, and uncultivated soil. Among all the isolates, 88 showed antagonistic activity to at least one of three phytopathogenic fungi, Fusarium oxysporum, Fusarium solani, and Phoma herbarum mainly causing root rot disease of P. notoginseng. Based on the 16S rRNA sequencing, the antagonistic bacteria were characterized into four clusters, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetesi. The genus Bacillus was the most frequently isolated, and Bacillus siamensis (Hs02), Bacillus atrophaeus (Hs09) showed strong antagonistic activity to the three pathogens. The distribution pattern differed in soil types, genera Achromobacter, Acidovorax, Brevibacterium, Brevundimonas, Flavimonas, and Streptomyces were only found in rhizosphere of healthy plants, while Delftia, Leclercia, Brevibacillus, Microbacterium, Pantoea, Rhizobium, and Stenotrophomonas only exist in soil of diseased plant, and Acinetobacter only exist in uncultivated soil. Conclusion: The results suggest that diverse bacteria exist in the P. notoginseng rhizosphere soil, with differences in community in the same field, and antagonistic isolates may be good potential biological control agent for the notoginseng root-rot diseases caused by F. oxysporum, Fusarium solani, and Panax herbarum.