• Proceedings of the Korean Environmental Sciences Society Conference
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• 2003.11b
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• pp.233-235
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• 2003

한국 서해안과 남해안 47개소의 해수와 mud 시료로부터 광합성세균으로 유추되는 13개의 균주를 분리하였고, agar-shake tube method와 RAPD-PCR을 이용하여 4개 서로 다른 균주를 순수분리 하였다. 4개의 균주 중 폐수분해능이 가장 뛰어난 균을 선정하여, 형태학적, 배양적, 생화학적 특성 및 16S rRNA sequencing에 의한 동정결과 purple, sulfur bacteria 쪽에 가까웠으나 형태학적, 배양학적, 생화학적 특성이 purple, non-sulfur bacteria의 Rhodobacter 속에 가장 근접하여, Rhodobacter sp. EGH-24로 명명하였다.

• Fisheries and Aquatic Sciences
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• v.22 no.7
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• pp.14.1-14.8
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• 2019

Olive flounder (Paralichthys olivaceus) is the major species developed for aquaculture in South Korea. Over the long history of olive flounder aquaculture, complex and diverse diseases have been a major problem, negatively impacting industrial production. Vibriosis is a prolific disease which continuously damages olive flounder aquaculture. A bacterial disease survey was performed from January to June 2017 on 20 olive flounder farms on Jeju Island. A total of 1710 fish were sampled, and bacteria from the external and internal organs of 560 fish were collected. Bacterial strains were identified using 16 s rRNA sequencing. Twenty-seven species and 184 strains of Vibrio were isolated during this survey, and phylogenetic analysis was performed. Bacterial isolates were investigated for the distribution of pathogenic and non-pathogenic species, as well as bacterial presence in tested organs was characterized. V. gigantis and V. scophthalmi were the dominant non-pathogenic and pathogenic strains isolated during this survey, respectively. This study provides data on specific Vibrio spp. isolated from cultured olive flounder in an effort to provide direction for future research and inform aquaculture management practices.

• 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
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• v.44 no.2
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• pp.155-161
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• 2006

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63 % (137 of 217) in the standard PCR method to about 34 % (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: ${\alpha},\;{\beta},\;{\gamma}-$ Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

• Journal of Microbiology and Biotechnology
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• v.24 no.11
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• pp.1464-1472
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• 2014

The microbial community structures of two continuous stirred tank reactors digesting turkey manure with pine wood shavings as well as chicken and swine manure were investigated. The reactor fed with chicken/swine wastes displayed the highest organic acids concentration (up to 15.2 g/l) and ammonia concentration (up to 3.7 g/l ammonium nitrogen) and generated a higher biogas yield (up to $366ml/g_{VS}$) compared with the reactor supplied with turkey wastes (1.5-1.8 g/l of organic acids and 1.6-1.7 g/l of ammonium levels; biogas yield was up to $195ml/g_{VS}$). The microbial community diversity was assessed using both sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Additionally, methanogens were analyzed using methyl coenzyme M reductase alpha subunit (mcrA) genes. The bacterial community was dominated by members of unclassified Clostridiales with the prevalence of specific clostridial phylotypes in each reactor, indicating the effect of the substrate type on the community structure. Of the methanogenic archaea, methanogens of the genus Methanosarcina were found in high proportions in both reactors with specific methanosarcinas in each reactor, whereas the strict hydrogenotrophic methanogens of Methanoculleus sp. were found at significant levels only in the reactor fed with chicken/swine manure (based on the analyses of 16S rRNA gene). This suggests that among methanogenic archaea, Methanosarcina species which have different metabolic capabilities, including aceticlastic and hydrogenotrophic methanogenesis, were mainly involved in anaerobic digestion of turkey wastes.

• Journal of Veterinary Science
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• v.25 no.5
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• pp.72.1-72.14
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• 2024

Importance: Identifying bovine mastitis agents using molecular methods to reveal their phylogenetic relationships and antimicrobial resistance profiles is essential for developing up-to-date databases in mastitis cases that cause severe economic losses. Objective: This study examined bacterial mastitis agents in cows with clinical and subclinical mastitis observed in various dairy cattle farms to reveal their phylogenetic relationships and antibiotic resistance properties. Methods: Sixty-two clinical and subclinical bovine mastitis milk samples were collected from 15 dairy farms. The polymerase chain reaction (PCR) was used to amplify the 16S rRNA gene regions of the bacteria. The 16S rRNA gene sequences obtained from sequencing include the V4-V6 regions. The strains were compared using a similarity analysis method that produced phylogenetic trees using the Molecular Evolutionary Genetics Analysis 11 program. Antibiotic susceptibilities were determined using the Kirby-Bauer disk diffusion method. Results: Sixty-three bacteria were isolated and identified in this study. The most isolated bacteria from all mastitis cases were Staphylococcus spp. (30.2%), Escherichia coli (25.4%), Streptococcus spp. (14.3%), and Aerococcus spp. (7.9%), respectively. The phylogenetic trees were drawn from the 16S rRNA sequences. Some of these bacteria showed resistance to different types of antibiotics at varying rates. Conclusions and Relevance: The bacteria isolated in this study originated from environmental sources. Regular cleaning of barns and proper hygiene practices are essential. Regular screenings for mastitis should be conducted in herds instead of the random or empirical use of antibiotics.

• Korean Journal of Microbiology
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• v.47 no.2
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• pp.130-136
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• 2011

Five strains of Actinomyces were isolated from freshwater sponges, Baikalospongia and Lubomirskia, in Lake Baikal. By 16S rRNA sequencing, isolates were identified as Streptomyces griseoplanus, S. halstedii, S. violascens, S. flavovirens, and S. microflavus. Isolates had different characteristics of growth temperature, carbon utilization, enzyme activity, and cellular fatty acid composition. Optimum growth conditions of isolates were $30-37^{\circ}C$, pH 8-9, and 0-1.5% salt concentrations. Major fatty acid compositions were anteiso-$C_{15:0}$, iso-$C_{15:0}$, and iso-$C_{16:0}$. Strain ATS-BA-19 had DNase and chitinase activities and strain ATS-BA-16 had cellulase and protease activities. Colonies of strain ATS-BA-15 and ATS-BA-19 made inhibition zone of Pseudomonas aeruginosa.

• Journal of Life Science
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• v.28 no.9
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• pp.1118-1126
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• 2018

In this study, investigated the general characteristics and diagnostic methods types of streptococcosis among various fish disease pathogens that caused a lot of economic damaged to aquaculture fish based on the previous research paper. Streptococcosis infection of fish is considered a reemerging disease affecting a variety of wild and cultured fish throughout the world. Calssifiacation of Gram positive cocci based on DNA-DNA hybridization coupled with 16S sequencing has shown that at least five different species are considered of significance as fish pathogens: Lactococcus garvieae, L. piscium, Streptococcus iniae, S. agalactiae, S. paruberis, Vagococcus salmoninarum. Symptoms of infection with streptococcosis disease such as body color change, eyeball abnormality, gill discoloration, bleeding, abdominal distension, swelling of the kidney and spleen. In addition, it usually occurs from June to October when the water temperature rise a lot of fish death. Currently, 16S rRNA, 16S-23S rRNA intergenic spacer region (ISR), Random Amplified polymorphic DNA (RAPD), Ribotyion (RT), Loop-mediated isothermal amplification (LAMP) are among the methods for diagnosing streptococcosis. Among them, the LAMP method, which is high applicable to the aquaculture farm has attracted the spotlight, but due to problems such as confirmation of results. This seems to minimize the economic loss of streptococcosis which complements the problem so that it can be easily used from the diagnosis to the results confirmation.

• Journal of fish pathology
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• v.19 no.2
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• pp.127-139
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• 2006

From 2002 to 2004, various vibrios were isolated from the olive flounder, Paralichthys olivaceus of culturing size with disease signs. During this survey, it was known that the high proportion of Vibrio ichthyoenteri was occupied among the isolated vibrios. Generally, V. ichthyoenteri is well known as the pathogen of bacterial enteritis of olive flounder larvae. The aim of the present study was the compare the characteristics of two groups of V. ichthyoenteri, culturing sized olive flounder, and larvae of olive flounder showing the intestinal necrosis. The research was focused on the physiology, biochemistry, genetics in the two bacterial groups. The physiological and biochemical characteristics of the tested strains were very similar. The intergenic spacer (IGS) region between the 16S and 23S rRNA genes of 21 isolated strains and 3 reference strains, V. ichthyoenteri, were investigated by PCR fragment length typing and DNA sequencing. After the isolated strains were identified as V. ichthyoenteri, not only phenotypic characteristics of the isolated and reference strains but also homology of 16S-23S IGS of all isolated strains and reference strains as 99.1~100%. The V. ichthyoenteri showed 4 specific 16S-23S patterns and contained no-tRNA, tRNAGlu(TTC) , tRNAIle(GAT) tRNAAla(TGC) type .

• Microbiology and Biotechnology Letters
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• v.48 no.3
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• pp.276-286
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• 2020

Probiotics are live microorganisms that, when administered in adequate amounts, confer health benefits to the host. This study was conducted for the isolation of potential lactic acid bacteria (LAB) with probiotic properties from goat milk and yogurt. Several tests were conducted in vitro using the standard procedures for evaluating the inhibitory spectra of LAB against pathogenic bacteria; tolerance to NaCl, bile salt, and phenol; hemolytic, milk coagulation, and bile salt hydrolase activities; gastrointestinal transit tolerance; adhesion properties; and antibiotic susceptibility. Among 40 LAB strains screened according to culture characteristics, five isolates exhibited antagonistic properties. Three were identified as Pediococcus acidilactici, and two were identified as Enterococcus faecium, exploiting 16S rRNA gene sequencing. All the isolates succeeded in the gastrointestinal transit tolerance assay and successively colonized mucosal epithelial cells. Based on the results of these in vitro assays, both P. acidilactici and E. faecium can be considered as potential probiotic candidates.