• Journal of fish pathology
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• v.22 no.3
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• pp.391-400
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• 2009

Genetic identification of 17 fish-derived Aeromonas strains was attempted using 5 housekeeping genes. 16S rRNA, gyrB, rpoD, dnaJ and recA genes from the 17 strains were amplified, and total of 85 amplicons were sequenced. DNA sequences of the strains and type strains of the 17 Aeromonas homology groups were used for genetic identification and phylogenetic analyses. None of the strains was identified as a single species using the 16S rRNA gene, showing the same identities (average = 99.7%) with several Aeromonas species. According to gyrB, rpoD, dnaJ, and recA, 9 strains and RFAS-1 used in this study were identified as A. hydrophila and A. salmonicida, respectively. However, the other strains were closely related to 2 or more Aeromonas species (i.e., A. salmonicida, A. veronii, A. jandaei, A. media and A. troda) depending on the genetic marker used. In this study, gyrB, rpoD, dnaJ and recA gene sequences proved to be advantageous over 16S rRNA for the identification of field Aeromonas isolates obtained from fish. However, there are discrepancies between analyses of different phylogenetic markers, indicating there are still difficulties in genetic identification of the genus Aeromonas using the housekeeping genes used in this study. Advantages and disadvantages of each housekeeping gene should be taken into account when the gene is used for identification of Aeromonas species.

• Korean Journal of Veterinary Research
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• v.34 no.2
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• pp.315-320
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• 1994

The API STAPH-IDENT system was evaluated as a means for identifying Staphylococcus hyicus subsp hyicus straints isolated from swine and poultry. Of 80 strains from swine, 68 (85%) were correctly identified by the API STAPH-IDENT system alone after 5 h of incubation. When results were determined after 24 h of incubation, the accuracy of this system alone was 93.8%. By additional tests in conjunction with the API STAPH-IDENT system, however, all 80 strains could be correctly identified. Of 120 strains from poultry, 87 (72.5%) required additional testing to achieve a correct identification, and 33 (27.5%) were incorrectly identified by this system after 5 h of incubation. After 24 h of incubation, 99 of 120 (82.5%) avian strains were incorrectly identified as Staph epidermidis owing to false-negative mannose and trehalose utilizations. Seventy-seven (96.3%) of swine strains were positive for ${\beta}-glucuronidase$, whereas all 120 strains recovered tram poultry were negative for it.

• Journal of Applied Biological Chemistry
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• v.50 no.4
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• pp.202-210
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• 2007

A total of 45 bacterial strains were isolated from the traditional Korean soybean-fermented food, Chungkookjang. Among these strains, seven strains were selected and identified based on morphological, physiological, and biochemical characteristics, as well as phylogenetic analysis using 16S rDNA sequences. All strains were Gram-positive, aerobic, motile, oxidase-positive, rod-shaped, and endospore-forming bacteria, and produced extracellular enzymes such as amylase, cellulase, lipase, protease, and xylanase. The isolates were grown in the presence of 0-11% (w/v) NaCl. Growth was optimal at pH 6-9 and at temperatures of $30-45^{\circ}C$. According to VITEK automicrobic system tests and supplementary tests, the isolates were similar to several species of the genus Bacillus. The phylogenetic analysis of seven bacterial strains based on comparisons of 16S rDNA sequences, revealed that the strains were closely related to Bacillus species. The identification of strains that produced surfactin was also carried out, based on PCR screening of the sfp gene. Among the seven isolated strains, six yielded a surfactin-positive result with PCR.

• Korean Journal of Microbiology
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• v.44 no.4
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• pp.333-338
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• 2008

Computational analysis of partial rpoB gene sequence (777 bp) was done in this study to identify B. anthracis and its closely related species B. cereus and B. thuringiensis. Sequence data including 17 B. anthracis strains, 9 B. cereus strains, and 7 B. thuringiensis strains were obtained by searching databases. Those sequences were aligned and used for other computational analysis. B. anthracis strains were identificated by in silico restriction enzyme digestion. B. cereus and B. thuringiensis were not segregated by this method. Those sequencing and BLAST search were required to distinguish the two. In actual identification tests, B. anthracis strains could be identified by PCR-RFLP, and B. cereus and B. thuringiensis strains were distinguished by BLAST search with reliable e-value. In this study fast and accurate method for identifying three Bacillus species, and flow chart of identification were developed.

• Mycobiology
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• v.39 no.4
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• pp.299-300
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• 2011

Two species of cultivated Phellinus sp. were identified as P. baumii by internal transcribed spacer (ITS) sequence analysis. The fruit bodies of the examined strains were similar to those of naturally occurring strains, having a bracket-like form, yellow-to-orange color, and poroid hymenial surfaces. The DNA sequences of ITS region of both strains showed a homology of 99% with ITS1 to ITS2 sequences of P. (Inonotus) baumii strain PB0806.

• Journal of Microbiology and Biotechnology
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• v.29 no.4
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• pp.548-557
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• 2019

Staphylococcus species have a ubiquitous habitat in a wide range of foods, thus the ability to identify staphylococci at the species level is critical in the food industry. In this study, we performed rapid identification of Staphylococcus species using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS was evaluated for the identification of Staphylococcus reference strains (n = 19) and isolates (n = 96) from various foods with consideration for the impact of sample preparation methods and incubation period. Additionally, the spectra of isolated Staphylococcus strains were analyzed using principal component analysis (PCA) and a main spectra profile (MSP)-based dendrogram. MALDI-TOF MS accurately identified Staphylococcus reference strains and isolated strains: the highest performance was by the EX method (83.3~89.5% accuracy) at species level identification (EDT, 70.3~78.9% accuracy; DT, less than 46.3~63.2% accuracy) of 24-h cultured colonies. Identification results at the genus level were 100% accurate at EDT, EX sample preparation and 24-h incubation time. On the other hand, the DT method showed relatively low identification accuracy in all extraction methods and incubation times. The analyzed spectra and MSP-based dendrogram showed that the isolated Staphylococcus strains were characterized at the species level. The performance analysis of MALDI-TOF MS shows the method has the potential ability to discriminate between Staphylococcus species from foods in Korea. This study provides valuable information that MALDI-TOF MS can be applied to monitor microbial populations and pathogenic bacteria in the food industry thereby contributing to food safety.

• Journal of Mushroom
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• v.22 no.2
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• pp.37-47
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• 2024

Fluorescent bacteria were isolated from sporocarps that browned into various mushrooms during survey at places of the production in Korea. We examined the pathogenicity, biodiversity, and genetic characteristics of the 19 strains identified as Pseudomonas tolaasii by sequence analysis of 16S rRNA and White Line Assay. The results emphasize the importance of rpoB gene system, fatty acid profiles, specific and sensitive PCR assays, and lipopeptide detection for the identification of P. tolaasii. As a result of these various analyses, 17 strains (CHM03~CHM19) were identified as P. tolaasii. The phylogenetic analysis based on the 16S rRNA gene showed that all strains were clustered closest to P. tolaasii lineage, two strains (CHM01, CHM02) were not identified as P. tolaasii and have completely different genetic characteristics as a result of fatty acids profile, specific and sensitive PCR, lipopetide detection, rpoB sequence and REP-PCR analysis. Pathogenicity tests showed 17 strains produce severe brown discolouration symptoms to button mushrooms and watersoaking of sporophore tissue within three days after inoculation. But two strains did not produce discolouration symptoms. Therefore, these two strains will be further investigated for correct species identification by different biological and molecular characteristics.

• Parasites, Hosts and Diseases
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• v.40 no.1
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• pp.25-31
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• 2002

We describe a riboprinting scheme for identification of unknown Acanthamoeba isolates at the species level. It involved the use of PCR-RFLP of small subunit ribosomal RNA gene (riboprint) of 24 reference strains by 4 kinds of restriction enzymes. Seven strains in morphological group I and III were identified at species level with their unique sizes of PCR product and riboprint type by Rsa 1. Unique RFCP of 17 strains in group II by Dde I. Taq I and Hae III were classified into: (1) four taxa that were identifiable at the species level. (2) a subgroup of 4 taxa and a pair of 2 taxi that were identical with each other. and (3) a species complex of 7 taxa assigned to A. castellanii complex that were closely related. These results were consistent with those obtained by 18s rDNA sequence analysis. This approach provides an alternative to the rDNA sequencing for rapid identification of a new clinical isolate or a large number of environmental isolates of Acanthamoeba.

• Journal of Microbiology and Biotechnology
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• v.6 no.5
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• pp.340-346
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• 1996

In order to find out if staphylococci occur in significant numbers in Korean fermented fish products, a total of 40 different fermented fish products were collected from different markets in Korea and analyzed for their physico-chemical and microbiological states. The pH, salt concentration and water activity of the products were measured and the total viable cell count and the number of Staphylococcus grown on mannitol salt agar were determined. The identification of the strains of Staphylococcus were made by API Staph Strip and MIS identification kits, and the physiological properties of the identified strains were further characterized by different conventional methods. The pH, salt content and water activity of fermented fish samples varied widely from 4.8 to 7.1, 7.4-28.7$%$ and 0.77-0.84, repectively, depending on the type of product. The total viable cell count varied from $10^4-10^9$ cfu/ml, and most of the samples had $10^5-10^6$ cfu/ml No correlation was found between the viable cell count and the pH, NaCl concentration and water activity of the samples. Among the 35 colonies identified as Staphylococcus strains by the identification kits, S. xylosus was the most frequently occurring strain marking 17, and S. warneri was 8, S. epidermidis 4 and S. cohnii 2. S. hominis, S. saprophyticus, S. haemolyticus and S. aureus were also identified once each. In some samples (K-3, P-6, K-8, G-5 and G-10), 2-3 different species of Staphylococcus were found. Considering the region of sampling, among the 10 samples from Kunsan 5 were identified as S. warneri, while in the other regions S. xylosus was predominant. Although the physiological characteristics of the identified strains were generally consistent with those in Bergey's Manual, some discrepances were also observed. All the strains were highly salt tolerant, growing in the media containing over 18$%$ NaCl. All the strains except S. aureus (G-11) showed negative in hemolysis activity, plasma coagulation and DNase tests. All the strains including S. aureus (G-11) showed negative in enterotoxin test.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.48-55
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• 2004

Six strains of an obligate predatory bdellovibrio isolate that preys on Burkholderia glumae in rice paddy field water and rhizosphere soil, were identified and characterized. The numbers of Bdellovibrio cells varied from $3.2{\times}10^3$ to $9.2{\times}10^3$ plaque-forming unit/g after enrichment in cells of B. glumae. Prey range tests with six Bdellovibrio strains and 17 prey strains of rice-pathogenic, antibiosis-related, or nitrogen-fixing bacteria resulted in unique predation patterns in related prey cells. Strain BG282 had the widest prey range on 7 plant pathogenic bacteria among the 17 prey strains tested. However, no predation occurred with strains of Azospirillum brasilense, Paenibacillus polymyxa, Pseudomonas fluorescens, P. putida, and Serratia marcescens that are associated with antibiosis or nitrogen fixation in the rice ecosystem. Identification was confirmed by the presence of typical bdelloplast in the prey cells of B. glumae and by a PCR assay using B. bacteriovorus-specific primers. Furthermore, 16S rDNA sequencing of the six bdellovibrio strains showed a homology range of 97.2% to 99.2% to the type strain of B. bacteriovorus.