• Korean Journal of Microbiology
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• v.51 no.2
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• pp.148-155
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• 2015

The diversity of endobacteria in the edible part (cap and stipe) king oyster mushroom (Pleurotus eryngii) was investigated using 16S rRNA sequence analysis. The bacterial 16S rRNA libraries were constructed from the body cap (BC) and the body stipe (BS) of the king oyster mushroom. The twenty sequenced BC clones were divided into four groups and the largest group was affiliated with the Firmicutes (40% of clones). While, the twenty sequenced BS clones could be divided into six groups and the largest group was affiliated with the Actinobacteria (40% of clones). The predominant bacterial family from both the cap and stipe of the mushroom was corresponded with the Gram positive bacteria (62.5%).

• Journal of Life Science
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• v.26 no.10
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• pp.1202-1206
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• 2016

Unicellular cyanobacterial strains of Subsections I and II and filamentous cyanobacterial strains of Subsection III have been shown to be polyphyletic, heterocystous strains of Subsections IV and V, both of which were previously reported to be monophyletic. In this study, the small subunit ribosomal RNA (16S rRNA) sequences of 13 strains of cyanobacteria - one strain, Oscillatoria nigro-viridis PCC7112, of the Subsection III, 6 strains including genus Anabaena, Nostoc, Tolypothrix, Calothrix and Scytonema of the Subsection IV, and 6 strains including genus Hapalosiphon, Fischerella and Chlorogloeopsis of the Subsection V - were determined. The phylogenetic analysis of cyanobacteria was carried out using the 16S rRNA sequences. The results of the phylogenetic analyses of 16S rRNA sequences, based on Neighbour-joining, maximum-parsimony, and maximum-likelihood methods, indicated that the members of Subsection IV were not monophyletic but polyphyletic. In addition, the phylogenetic results strongly indicated that the genus Scytonema in Subsection IV could be a common ancestor of heterocystous cyanobacteria in Subsection IV and V. Furthermore, the phylogenetic analyses revealed that the genus Anabaena could be phylogenetically diverse and that cyanobacterial strains in Subsection IV might be polyphyletic, whereas those in Subsection V could be monophyletic, as reported before. The results for the genus Anabaena indicate that it should be reclassified.

• Korean Journal of Veterinary Service
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• v.35 no.4
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• pp.289-294
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• 2012

Mycoplasmas are highly fastidious bacteria, difficult to culture and slow growing. Infections with Mycoplasma species can cause a variety of problems in living organisms and in vitro cell cultures. In this study, we investigated the usefulness of a genus-specific consensus PCR analysis method to detect Mycoplasma species. The developed consensus primer pairs MycoF and MycoR were designed specifically to amplify the 16S ribosomal RNA gene (rRNA) of Mycoplasma species by the optimized PCR system. The developed consensus PCR system effectively amplified 215 bp of Mycoplasma genus-specific region of 16S rRNA. In conclusion, we recommend this consensus PCR for monitoring Mycoplasma species in animals, human and cell culture system.

• Journal of the Korean Applied Science and Technology
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• v.40 no.4
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• pp.881-889
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• 2023

The genus Hymenobacter, type genus of the family Hymenobacteraceae and a member of the phylum Bacteroidota includes gram-negative and red-pigmented rods. Those bacteria have been isolated from various environments of the earth. I isolated a red-pigmented, gram-negative rod from a pond in the campus of the Changwon University, Changwon, Kyeongnam and designated this bacterium as strain B2. Strain B2 was further analyzed phylogenetically and biochemically, and concluded as a member of genus Hymenobacter. BLAST search of the 16S rRNA gene sequence of strain B2 showed its homology lower than 98.7% with those sequences of the other bacteria whose 16S rRNA gene sequences have been reported. Fatty acid composition of the strain B2 was analyzed and its major fatty acids are summed feature 3(C_16:1 ω7c and/or C_16:1 ω6c, 22.8%), iso-C_15:0 (16.2%), anteiso-C_15:0(12.9%), C_16:1ω5c(12.4%) and summed feature 4 (iso-C_17:1 I/anteiso-C_17:1)(9.5%) showing significant differences in fatty acid compositions between strain B2 and the other known Hymenobacter species. DNA sequence of 16S rRNA gene of strain B2 was deposited in genbank under accession number OQ318247.

• Parasites, Hosts and Diseases
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• v.51 no.4
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• pp.401-412
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• 2013

Because of an increased number of Acanthamoeba keratitis (AK) along with associated disease burdens, medical professionals have become more aware of this pathogen in recent years. In this study, by analyzing both the nuclear 18S small subunit ribosomal RNA (18S rRNA) and mitochondrial 16S rRNA gene loci, 27 clinical Acanthamoeba strains that caused AK in Japan were classified into 3 genotypes, T3 (3 strains), T4 (23 strains), and T5 (one strain). Most haplotypes were identical to the reference haplotypes reported from all over the world, and thus no specificity of the haplotype distribution in Japan was found. The T4 sub-genotype analysis using the 16S rRNA gene locus also revealed a clear subconformation within the T4 cluster, and lead to the recognition of a new sub-genotype T4i, in addition to the previously reported sub-genotypes T4a-T4h. Furthermore, 9 out of 23 strains in the T4 genotype were identified to a specific haplotype (AF479533), which seems to be a causal haplotype of AK. While heterozygous nuclear haplotypes were observed from 2 strains, the mitochondrial haplotypes were homozygous as T4 genotype in the both strains, and suggested a possibility of nuclear hybridization (mating reproduction) between different strains in Acanthamoeba. The nuclear 18S rRNA gene and mitochondrial 16S rRNA gene loci of Acanthamoeba spp. possess different unique characteristics usable for the genotyping analyses, and those specific features could contribute to the establishment of molecular taxonomy for the species complex of Acanthamoeba.

• Journal of Food Hygiene and Safety
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• v.33 no.4
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• pp.280-288
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• 2018

In this study, an approach for the analysis of the five cephalopod species (octopus, long-arm octopus, squid, wet-foot octopus, beka squid) consumed in the Republic of Korea is developed. The samples were collected from the Southeast Asian countries Thailand, Indonesia, Vietnam, and China. The SYBR-green-based real-time qPCR method, based on the mitochondrial DNA genome of the five cephalopods was developed and validated. The intergroup variations in the mitochondrial DNA are evident in the bioinformatic analysis of the mitochondrial genomic DNA sequences of the five groups. Some of the highly-conserved and slightly-variated regions are identified in the mitochondrial cytochrome-c-oxidase subunit I (COI) gene, 16s ribosomal RNA (16s rRNA) gene, and 12s ribosomal RNA (12s rRNA) gene of these groups. To specify each five cephalopod groups, specific primer sets were designed from the COI, 16s rRNA and 12s rRNA regions. The specific primer sets amplified the DNA using the SYBR-green-based real-time PCR system and 11 commercially secured animal tissues: Octopus vulgaris, Octopus minor, Todarodes pacificus, Dosidicus gigas, Sepia esculenta, Amphioctopus fangsiao, Amphioctopus aegina, Amphioctopus marginatus, Loliolus beka, Loligo edulis, and Loligo chinensis. The results confirmed by a conveient way to calculate relative amplification levels between different samples in that it directly uses the threshold cycles (Ct)-value range generated by the qPCR system from these samples. This genomic DNA-based molecular technique provides a quick, accurate, and reliable method for the taxonomic classification of the animal tissues using the real-time qPCR.

• Korean Journal of Medicinal Crop Science
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• v.16 no.3
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• pp.195-198
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• 2008

Karyotypic analysis and FISH (fluorescence in situ hybridization) with 45S and 5S rRNA genes were carried out in Persicaria tinctoria H Gross. The somatic metaphase chromosomes were ranged from 2.25 ${\mu}m$ to 1.50 ${\mu}m$ in length. Chromosome number was 2n = 4x = 40 with the basic number of x = 10. The chromosome complement of the species consisted of 16 pairs of metacentrics (chromososomes 1,2,3,4,6,7,8,9, 10, 11, 12, 13, 15, 18, 19 and 20) and 4 pairs of submetacentrics (chromosome 5, 14, 16 and 17). The karyotype formula was K(2n) = 4x = 32 m + 8 sm. In FISH analysis, three pairs of 45S rRNA gene loci on the terminal region of submetacentrics (chromosomes 5, 16 and 17) and two pairs of 5S rRNA gene loci on the centromeric region of metacentrics (chromosomes 9 and 11) were detected, respectively.

• Korean Journal of Food Science and Technology
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• v.32 no.6
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• pp.1331-1335
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• 2000

The WL6 strain isolated from Kimchi could not be made scientific name because it was identified as three species, i.e., Leuconostoc mesenternides ssp cremoris, Leu. mesenteroides ssp. dextranicum or Lactobacillus bifermentans when it was tested by API kit or Biolog system methods. The unidentifiable WL6 strain was finally reclassified as Lactobacillus bifermentans by genetic identification using two PCR-based specific sequence primer sets which were originated from homologous pepN and 16S rRNA genes.

• Journal of Veterinary Clinics
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• v.31 no.1
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• pp.36-39
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• 2014

Many bacteria colonized in the horse semen affect quality of the sperm and some may cause infection in the mare reproductive tract and infertility of susceptible mare. This study was initiated to determine the prevalence of bacteria in testes of Jeju horses by determining rRNA sequence. The samples were swabed from the testes of nine Jeju horses (aged from 8 to 12 months after birth). Bacteria isolated from testes were identified by 16S rDNA sequencing. 1.6-kbp PCR products for 16S rRNA coding region were obtained using the universal primers. The PCR products were further purified and sequenced. Maximum similar species were found by BLAST search in the GenBank DNA database. BLAST results showed that the sequences were similar to those of Acinetobacter sp (A. schindleri, A. ursingii)., Bacillus cereus, Corynebacterium glutamicum, Escherichia coli, Gamma proteobacterium, Micrococcus luteus, Pseudomonas mendocina, Shigella sonnei, Sphingomonas sp., Staphylococcus sp (S. cohnii, S. saprophyticus, S. xylosus)., and Stenotrophomonas maltophilia. DNA sequences for 16S rRNA is provided useful informations for species identification of pathogenic microorganisms for the reproductive organs in horses.

• Microbiology and Biotechnology Letters
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• v.38 no.3
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• pp.263-272
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• 2010

One hundred sixty three strains showing different colony morphological characteristics on different concentration of marine agar (MA) plates were isolated from ambient seawater near Dokdo island. Bacterial diversity and distributions were studied by phylogenetic analysis of the partial 16S rRNA gene sequences. One hundred sixty three strains were partially sequenced and analyzed phylogenetically. They were composed of 5 phyla, of which gamma-proteobacteria (58%), alpha-proteobacteria (20%), bacteriodetes (16%) were predominant. They were affiliated with 90 species. The 16S rRNA sequence similarity of the isolates was in 93.3 to 100 % range to reported sequence data. Thirty six isolates of among them were assumed to be novel species candidates based on similarity analysis of the 16S rRNA gene sequences. Overall, Proteobacteria and Bacteriodetes of the Dokdo coastal sea water showed a high diversity.