• Journal of Microbiology and Biotechnology
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• v.28 no.2
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• pp.227-235
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• 2018

Foodborne illness represents a major threat to public health and is frequently attributed to pathogenic microorganisms on fresh produce. Recurrent outbreaks often come from vegetables that are grown close to or within the ground. Therefore, the first step to understanding the public health risk of microorganisms on fresh vegetables is to identify and describe microbial communities. We investigated the phyllospheres on Chinese cabbage (Brassica rapa subsp. pekinensis, N = 54). 16S rRNA gene amplicon sequencing targeting the V5-V6 region of 16S rRNA genes was conducted by employing the Illumina MiSeq system. Sequence quality was assessed, and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using a weighted Fast UniFrac matrix. The average number of sequence reads generated per sample was 34,584. At the phylum level, bacterial communities were composed primarily of Proteobacteria and Bacteroidetes. The most abundant genera on Chinese cabbages were Chryseobacterium, Aurantimonadaceae_g, Sphingomonas, and Pseudomonas. Diverse potential pathogens, such as Pantoea, Erwinia, Klebsiella, Yersinia, Bacillus, Staphylococcus, Salmonella, and Clostridium were also detected from the samples. Although further epidemiological studies will be required to determine whether the detected potential pathogens are associated with foodborne illness, our results imply that a metagenomic approach can be used to detect pathogenic bacteria on fresh vegetables.

• Journal of Microbiology and Biotechnology
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• v.28 no.11
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• pp.1823-1833
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• 2018

Fluorescence in-situ hybridization (FISH) is a common and popular method used to investigate microbial communities in natural and engineered environments. In this study, two specific 16S rRNA-targeted oligonucleotide probes, CLZ and KCLZ, were designed and verified to quantify the genus Clostridium and the species Clostridium kluyveri. The optimal concentration of hybridization buffer solution for both probes was 30% (w/v). The specificity of the designed probes was high due to the use of pellets from pure reference strains. Feasibility was tested using samples of Chinese liquor from the famed Luzhou manufacturing cellar. The effectiveness of detecting target cells appears to vary widely in different environments. In pit mud, the detection effectiveness of the target cell by probes CLZ and KCLZ was 49.11% and 32.14%, respectively. Quantitative analysis by FISH technique of microbes in pit mud and fermented grains showed consistency with the results detected by qPCR and PCR-DGGE techniques, which showed that the probes CLZ and KCLZ were suitable to analyze the biomass of Clostridium spp. and C. kluyveri during liquor fermentation. Therefore, this study provides a method for quantitative analysis of Clostridium spp. and C. kluyveri and monitoring their community dynamics in microecosystems.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.170-179
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• 2017

Tea is the most popular beverage in the world. In fact, there are mainly three different kinds of tea (Green tea, black tea, and post-fermented tea). Post-fermented tea is produced by the microbial fermentation process using sun-dried green tea leaves (Camellia sinensis) as the raw material. Chungtaejeon was a traditional tea introduced in the age of the ancient three states and is the only "Ddeok-cha or Don-cha" culture in the world that survived on the southwestern shore of Republic of Korea. In this study, the structures of the bacterial community involved in the production of oriental traditional post-fermented tea (Chungtaejeon) were investigated using 16S rRNA gene analysis. The 16S rRNA gene analysis of dominant microbial bacteria in post-fermented tea confirmed the presence of Pantoea sp., and Klebsiella oxytoca. Phylogenetic analysis suggested that the taxonomic affiliation of the dominant species in the post-fermented tea was ${\gamma}$-proteobacteria. As a result of the microbial community size analysis, it was confirmed that the size of the microbial communities of Chungtaejeon was the largest compared to other teas

• Journal of fish pathology
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• v.20 no.1
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• pp.25-31
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• 2007

Vibriosis is one of the most important diseases affecting marin fish. In this study, a bacterium belonging to the Vibrio were isolated from maroon clownfish (Premnas biaculeatus) larvae (3～7 days after hatching). The bacterium was identified as Vibrio ponticus KJS1 by 16S rRNA gene sequence analysis. The result of biochemical test using the GN2 microplate (BioLog Inc, USA) showed that it has the ability to use 35 substrates including dextrin and sucrose was detected, could not degrade 52 substrates including α-cyclodextrin, and showed the weak ability to use 7 substrates including glycogen. It was sensitive to oxolinic acid, flumequine, ciprofloxacine, ofloxacin, norfloxacin, nalidixic acid, pefloxacin, and doxycycline hydrochloride.

• Journal of the Korean Institute of Intelligent Systems
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• v.14 no.5
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• pp.545-550
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• 2004

The study of available genotypes (biodiversity analysis) in bacterial communities is of growing importance in several fields such as ecology, environmental technology, clinical diagnostics, etc. These culture-independent genotyping techniques, especially amplifying 16S rRNA genes, attempt to overcome some shortcomings of conventional cultivation method. Biodiversity analysis based on molecular technique were laborious for base-calling chromatogram, trimming primer sites, correcting strand directions, electing representative operation taxonomic units (OTU), etc. Also, biologists wanted intuitively to confirm results of the above processes. For making up these demands, we developed the web application based on Folder-Process-Filter (FPF) modeling with correspondence to classical Model-View-Controller model. The model of web application leads to keep virtues of simplicity and directness for development and management of the stepwise web interfaces. The web application was developed in Perl and CGI on Linux workstation. It can be freely accessed from http://home.pusan.ac.kr/～genome/tools/rat.htm.

• Journal of Life Science
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• v.20 no.8
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• pp.1214-1220
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• 2010

Imipenem-resistant bacteria were isolated from clinical specimens taken from hospitalized patients in Suncheon, Korea. Fifty-four isolates were phylogenetically analyzed based on 16S rRNA gene and gyrB gene sequence comparisons. Isolates were affiliated with Pseudomonas aeruginosa (30 strains; 55.6%), Acinetobacter baumannii (21; 38.9%), Enterobacter hormaechei (2) and Pseudomonas putida (2). Twenty-two isolates produced metallo-$\beta$-lactamase (MBL); 12 Acinetobacter baumannii strains, 7 Pseudomonas aeruginosa strains, 2 P. putida strains and 1 Enterobacter hormaechei strain. Antibiotic susceptibility of the isolates was determined using the disc diffusion method and Vitek system. Strains producing metallo-$\beta$-lactamase (type IMP & VIM) were more resistant to antibiotics ceftazidime, aztreonam, amikacin and gentamicin than to strains producing OXA and SHV type of $\beta$-lactamase.

• Korean Journal of Ichthyology
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• v.22 no.3
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• pp.201-205
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• 2010

One specimen of a natural hybrid of an Oplegnathus (Oplegnathus fasciatus $\times$ Oplegnathus punctatus) was found in Tongyeong, Korea in August 2008. We, herein, describe its morphological and genetic characteristics and compare them with those of O. fasciatus and O. punctatus. In morphology, the hybrid showed many distinctive black rounded blotches on body sides and four faint vertical bars, being in those features similar to O. punctatus. Although the counts and measurements of the hybrid mostly overlapped between O. fasciatus and O. punctatus, the Oplegnathus hybrid resembled O. punctatus in the ratio of pelvic-fin length in standard length: Oplegnathus hybrid (26.7%) was closer to O. punctatus (26.4%) than to O. fasciatus (17.2~23.6%). In genetics, as a result of analysis of 510 base pair sequences of mitochondrial DNA 16S rRNA, the hybrid was closer to O. fasciatus (d=0.000~0.010) than to O. punctatus (d=0.020). Our results suggest that the natural hybridization represented by the subject specimen occurred between an O. fasciatus female and an O. punctatus male.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.4
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• pp.586-593
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• 2016

A new methanogen was isolated from an anaerobic digester using pig slurry in South Korea. Only one strain, designated KOR-1, was characterized in detail. Cells of KOR-1 were straight or crooked rods, non-motile, 5 to $15{\mu}m$ long and $0.7{\mu}m$ wide. They stained Gram-positive and produced methane from $H_2+CO_2$ and formate. Strain KOR-1 grew optimally at $38^{\circ}C$. The optimum pH for growth was 7.0. The strain grew at 0.5% to 3.0% NaCl, with optimum growth at 2.5% NaCl. The G+C content of genomic DNA of strain KOR-1 was 41 mol%. The strain tolerated ampicillin, penicillin G, kanamycin and streptomycin but tetracycline inhibited cell growth. A large fragment of the 16S rRNA gene (~1,350 bp) was obtained from the isolate and sequenced. Comparison of 16S rRNA genes revealed that strain KOR-1 is related to Methanobacterium formicicum (98%, sequence similarity), Methanobacterium bryantii (95%) and Methanobacterium ivanovii (93%). Phylogenetic analysis of the deduced mcrA gene sequences confirmed the closest relative as based on mcrA gene sequence analysis was Methanobacterium formicicum strain (97% nucleic acid sequence identity). On the basis of physiological and phylogenetic characteristics, strain KOR-1 is proposed as a new strain within the genus Methanobacterium, Methanobacterium formicicum KOR-1.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.584-591
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• 2015

This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.568-572
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• 2015

Acetes chinensis is an economically important shrimp that belongs to the Sergestidae family; following fermentation, A. chinensis' economic value, however, is low in China, and much of the catch in China is exported to Korea at a low price, thus leading to potential false labeling. For this reason, we developed a simple method to identify A. chinensis' origin using allele-specific polymerase chain reaction (PCR). Ten single nucleotide polymorphisms (SNPs) were identified from partial (i.e., 570 bp) DNA sequence analysis of the mitochondrial 16s rRNA gene in 96 Korean and 96 Chinese individual shrimp. Among 10 SNP sites, four sites were observed in populations from both countries, and two sites located in the middle with SNP sites at their 3'-ends were used to design allele-specific primers. Among the eight internal primers, the C220F primer specific to the Chinese A. chinensis population amplified a DNA fragment of 364 bp only from that population. We were able to identify the A. chinensis population origin with 100% accuracy using multiplex PCR performed with two external primers and C220F primers. These results show that the 16S rRNA gene that is generally used for the identification of species can be used for the identification of the origin within species of A. chinensis, which is an important finding for the fair trade of the species between Korea and China.