• Korean Journal of Microbiology
• /
• v.49 no.3
• /
• pp.237-244
• /
• 2013

Bacterial diversities in the guts of sea cucumbers (Apostichopus japonicus) and shrimps (Litopenaeus vannamei) were investigated using barcoded or tag-encoded 454 pyrosequencing of 16S rRNA genes. In sea cucumbers, most of sequences were related to two genera, the genus Propionigenium in the phylum Fusobacteria and an unclassified genus in the family Flavobacteriaceae of phylum Bacteroidetes. Shrimps showed various kinds of genera including Lactococcus, Leuconostoc, Prochlorococcus, and Vibrio as well as the unclassified genera in the families, Flavobacteriaceae, Rhodobacteraceae, Desulfobulbaceae, and Helicobacteraceae and in the order Mycoplasmatales. Unclassified genera containing environmental sequences only are more than half of genera from sea cucumbers and shrimps. Sea cucumbers and shrimps could be unexplored sources of novel microbes and the bacterial diversity of them was revealed by high throughput 454 pyrosequencing.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.1
• /
• pp.112-121
• /
• 2017

Edwardsiella tarda is a gram-negative pathogenic bacterium in aquaculture that can cause hemorrhagic septicemia in fish. Many secreted proteins have already been identified as virulent factors of E. tarda. Moreover, since virulent phenotypes are based on the expression regulation of virulent genes, understanding the expression profile of virulent genes is important. A quantitative RT-PCR is one of the preferred methods for determining different gene expressions. However, this requires the selection of a stable reference gene in E. tarda, which has not yet been systematically studied. Accordingly, this study evaluated nine candidate reference genes (recA, uup, rpoB, rho, topA, gyrA, groEL, rpoD, and 16S rRNA) using the Excel-based programs BestKeeper, GeNorm, and NormFinder under different culture conditions. The results showed that 16S rRNA was more stable than the other genes at different culture growth phases. However, at the same culture time, topA was identified as the reference gene under the conditions of different strains, different culture media, and infection, whereas gyrA was identified under the condition of different temperatures. Thus, in experiments, the expression of gapA and fbaA in E. tarda was analyzed by RT-qPCR using 16S rRNA, recA, and uup as the reference genes. The results showed that 16S rRNA was the most suitable reference gene in this analysis, and that using unsuitable reference genes resulted in inaccurate results.

• Korean Journal of Veterinary Service
• /
• v.32 no.4
• /
• pp.335-341
• /
• 2009

Canine brucellosis produce abortions and infertility in dogs and is currently diagnosed by serological methods such as rapid slide agglutination test with 2-mercaptoethanol (2-ME RSAT) and immunochromatographic assay (ICA). Bacterial isolation is considered gold standard for Brucella diagnosis and the polymerase chain reaction (PCR) is an alternative method to bacterial isolation. A total of 36 whole blood samples were collected from dogs reared in area of Chuncheon and were subjected to serology (2-ME RSAT and ICA for B. canis, Rose Bengal test and C-ELISA for B. abortus), blood culture and 3 types of PCRs (BSCP31, 16s rRNA, and OMP-2). All blood samples were negative by serology and blood cultures. The BCSP31 and the OMP-2 PCR detected 5 samples were positive whereas the 16S rRNA PCR detected all samples were negative as serological methods and blood culture did. From the results observed in the present study, we conclude that 16S rRNA PCR could be used for direct PCR for canine blood samples.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.20
• /
• pp.8883-8886
• /
• 2014

Background: Tetracycline is an antibiotic widely used for the treatment of Helicobacter pylori infection, but its effectiveness is decreasing due to increasing bacterial resistance. The aim of this study was to investigate the occurrence of 16S rRNA mutations associated with resistance or reduced susceptibility to tetracycline ofHelicobacter pylori by real-time PCR (RT-PCR) assays from culture. Materials and Methods: Tetracycline susceptibility and minimal inhibition concentration (MIC) was determined by the Epsilometer test (Etest) method. A LightCycler assay developed to detect these mutations was applied to DNA extracted from culture. The 16S rRNA of these isolates was sequenced and resistance-associated mutations were identified. From 104 isolates of H. pylori examined, 11 showed resistance to tetracycline. Results: LightCycler assay was applied to DNA extracted from 11 tetracycline-susceptible and 11 tetracycline resistance H. pylori isolates. In our study the sequencing of the H. pylori wild types in 16 s rRNA gene were AGA 926-928 with MIC (0.016 to $0.5{\mu}g/ml$), while the sequencing and MIC for resistant were GGA and AGC, (0.75 to $1.5{\mu}g/ml$), respectively. Also we found a novel mutation in 2 strains with $84^{\circ}C$ as their melting temperatures and exhibition of an A939C mutation. Conclusions: We conclude that real-time PCR is an excellent method for determination of H. pylori tetracycline resistance related mutations that could be used directly on biopsy specimens.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.7
• /
• pp.1112-1121
• /
• 2018

Jeotgal is a Korean traditional fermented seafood with a high concentration of salt. In this study, we isolated lactic acid bacteria (LAB) from galchi (Trichiurus lepturus, hairtail) and myeolchi (Engraulis japonicas, anchovy) jeotgal on MRS agar and MRS agar containing 5% NaCl (MRS agar+5% NaCl), and identified them by using 16S rRNA gene sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as culture-dependent methods. We also performed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) as a culture-independent method to identify bacterial communities. Five samples of galchi-jeotgal and seven samples of myeolchi-jeotgal were collected from different regions in Korea. A total of 327 and 395 colonies were isolated from the galchi- and myeolchi-jeotgal samples, respectively. 16S rRNA gene sequencing and MALDI-TOF MS revealed that the genus Pediococcus was predominant on MRS agar, and Tetragenococcus halophilus on MRS agar+5% NaCl. PCR-DGGE revealed that T. halophilus, Tetragenococcus muriaticus, and Lactobacillus sakei were predominant in both types of jeotgal. T. halophilus was detected in all samples. Even though the same species were identified by both culture-dependent and -independent methods, many species identified by the culture-dependent methods were not in the bacterial list identified by the culture-independent methods. The distribution of bacteria in galchi-jeotgal was more diverse than in myeolchi-jeotgal. The diverse LAB in galchi- and myeolchi-jeotgals can be further studied as candidates for starter cultures to produce fermented foods.

• Microbiology and Biotechnology Letters
• /
• v.42 no.4
• /
• pp.377-385
• /
• 2014

In this study, a wastewater treatment system for hypersaline wastewater utilizing the Hypersaline Wastewater Treatment Community (HWTC) has been developed. The hypersaline wastewater treatment efficiency and microbial community of the HWTC were investigated. The average removal efficiencies of chemical oxygen demand were 84% in an HRT of 2.5 days. Microbial community analysis, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments and 16S rRNA gene clone library, revealed community diversity. The 16S rRNA gene analysis of dominant microbial bacteria in 4% hypersaline wastewater confirmed the presence of Halomonas sp. and Paenibacillus sp. Phylogenetic analysis suggested that the taxonomic affiliation of the dominant species in the HWTC was ${\gamma}$-proteobacteria and firmicutes. These results indicate the possibility that an appropriate hypersaline wastewater treatment system can be designed using acclimated sludge with a halophilic community.

• Journal of Species Research
• /
• v.8 no.2
• /
• pp.191-196
• /
• 2019

In 2015 and 2017, the National Institute of Biological Resources has isolated four unrecorded prokaryotic species designated as R-1-5, R-2-13, R-2-1, and R-1-8 from the peatland soil of Yongneup. Phylogenetic analysis based on 16S rRNA gene sequence similarity determined the four strains (R-1-5, R-2-13, R-2-1, R-1-8) were most closely related to Curvibacter lanceolatus (99.93%), Massilia brevitalea (98.7%), Pseudomonas lini (99.54%), and Pseudomonas vancouverensis (99.93%), respectively. The four unrecorded strains belong to the phylum Proteobacteria, in which the genera Curvibacter and Massilia are assigned to the class Betaproteobacteria, and the genus Pseudomonas to the class Gammaproteobacteria. Since there are no publications or official reports on these four strains, these four species are new records to Korea. The strains were further characterized by Gram reaction, colony and cell morphology, basic biochemical properties, and phylogenetic position. Descriptive information of the four unrecorded species is provided.

• Journal of Microbiology
• /
• v.44 no.5
• /
• pp.572-576
• /
• 2006

To obtain primary idea on oral bacterium species that are generally present in periodotally healthy Koreans, the oral bacterial flora in the saliva of four periodontally healthy Koreans at different ages (5, 32, 35, 65) was investigated in this study. For this investigation, 16S rRNA gene clone libraries were generated from the saliva of the four healthy Koreans, and 50 clones were randomly selected from each saliva clone library and sequenced. Totally, 37 different kinds of bacterial 16S rRNA gene sequences were identified based on sequence homology search through GenBank database. The 37 kinds of saliva clone sequences were classified to 14 genera and 2 uncultured and 1 unidentified bacteria. Among the 14 identified genera, Streptococcus, Prevotella, and Veillollella were common genera, and Streptococcus was dominant genus that accounted for 7 different species. Among the seven Streptococcus species, S. salivarius appeared as the most common species. More numbers of species belonging to the genera Streptococcus and Prevotella was present in saliva from ages 32 and 35. While saliva from ages 5 and 65 showed more numbers of species belonging to the genera Rothia, including potential pathogenic species. Overall, saliva of a young child and a senior showed higher bacterial diversity than that of young adults.

• Journal of Microbiology
• /
• v.44 no.4
• /
• pp.432-438
• /
• 2006

Twelve actinomycete strains were isolated from Egyptian soil. The isolated actinomycete strains were then screened with regard to their potential to generate antibiotics. The most potent of the producer strains was selected and identified. The cultural and physiological characteristics of the strain identified. the strain as a member of the genus Streptomyces. The nucleotide sequence of the 16S rRNA gene (1.5kb) of the most potent strain evidenced a 99% similarity with Streptomyces spp. and S. aureofaciens 16S rRNA genes, and the isolated strain was ultimately identified as Streptomyces sp. MAR01. The extraction of the fermentation broth of this strain resulted in the isolation of one major compound, which was active in vitro against gram-positive, gram-negative representatives and Candida albicans. The chemical structure of this bioactive compound was elucidated based on the spectroscopic data obtained from the application of MS, IR, UV, $^1H$ NMR, $^{13}C$ NMR, and elemental analysis techniques. Via comparison to the reference data in the relevant literature and in the database search, this antibiotic, which had a molecular formula of $C_{19}H_{29}NO_2$ and a molecular weight of 303.44, was determined to differ from those produced by this genus as well as the available known antibiotics. Therefore, this antibiotic was designated Meroparamycin.

• ALGAE
• /
• v.35 no.1
• /
• pp.1-15
• /
• 2020

Two strains isolated from a subtropical region in China, were morphologically identified as a Nostoc-like species, but its taxonomic identity was unknown. In this study, these two strains were taxonomically and phylogenetically characterized based on polyphasic approach combining morphological and genetic characteristics. Though both were virtually indistinguishable from Nostoc in field and cultured material, these two strains were phylogenetically distinct from Nostoc based on 16S rRNA phylogeny. The 16S-23S internal transcribed spacer rRNA secondary structure of these strains showed the unique pattern of D1-D1', Box-B, and V3 helix, which distinguished them from other Nostoc-like heterocytous genera. A unique cluster separated from Nostoc sensu stricto supports the establishment of Violetonostoc gen. nov. with the type species as Violetonostoc minutum sp. nov.