• Korean Journal of Ecology and Environment
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• v.55 no.4
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• pp.352-359
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• 2022

Recently, with the development of genetic technology, interest in environmental DNA (eDNA) to study biodiversity according to molecular biological approaches is increasing. Environmental DNA has many advantages over traditional research methods for biological communities distributed in the environment but highly depends on the established base sequence database. This study conducted a comprehensive analysis of the habitat status and classification at the genus level, which is mainly used in eDNA (12S rRNA, 16S rRNA, 18S rRNA, COI, and CYTB), focusing on Korean registration taxon groups (phytoplankton, zooplankton, macroinvertebrates, and fish). As a result, phytoplankton and zooplankton showed the highest taxa proportion in 18S rRNA, and macroinvertebrates observed the highest ratio in the nucleotide sequence database in COI. In fish, all genes except 18S rRNA showed a high taxon ratio. Based on the Korean registration taxon group, the gene construction of the top 20 genera according to bio density observed that most of the phytoplankton were registered in 18S rRNA, and the most significant number of COI nucleotide sequences were established in macroinvertebrates. In addition, it was confirmed that there is a nucleotide sequence for the top 20 genera in 12S rRNA, 16S rRNA, and CYTB in fish. These results provided comprehensive information on the genes suitable for eDNA research for each taxon group.

• 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.

• Journal of Microbiology and Biotechnology
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• v.20 no.2
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• pp.245-253
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• 2010

The base sequences representing human- and cow-specific 168 rRNA gene markers identified in a T-RFLP analysis were recovered from clone libraries. The human- and cow-specific primers were designed from these sequences and their specificities were analyzed with fecal DNAs from human, cow, and pig. The AllBac primer set showed positive results for all human, cow, and pig samples, whereas the human-specific primer set showed positive result only for the human sample but not for the cow or pig samples. Likewise, the cow-specific primer set showed positive results only for the cow sample but not for the human or pig samples. Real-time PCR assay with these primers was developed for the identification and quantification of fecal pollution in the river water. The human- and cow-specific markers were detected in the order of 9 $\log_{10}$ copies per gram wet feces, which were two orders of magnitude lower than those of total Bacteroidales. For the river water samples, the human-specific marker was detected in $1.7-6.2\;\log_{10}$ copies/100 ml water, which was 2.4-4.9 orders of magnitude lower than those of total Bacteroidales. There was no significant correlation between total Bacteroidales and conventional fecal indicators, but there was a high correlation between Bacteroidales and the human-specific marker. This assay could reliably identify and quantify the fecal pollution sources, enabling effective measures in the watersheds and facilitating water quality management.

• The Plant Pathology Journal
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• v.29 no.4
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• pp.465-470
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• 2013

In January 2012, spreading type petunia cv. Wave Pink plants showing an abnormal growth habit of sprouting unusual multiple plantlets from the lateral buds were collected from a greenhouse in Gwacheon, Gyeonggi Province, Korea. The presence of phytoplasma was investigated using PCR with the primer pairs P1/P6, and R16F1/R1 for nested-PCR. In the nested PCR, 1,096 bp PCR products were obtained, and through sequencing 12 Pet-Stol isolates were identified. Comparison of the nucleotide sequences of 16S rRNA gene of the 12 Pet-Stol isolates with other phytoplasmas belonging to aster yellows or Stolbur showed that Pet-Stol isolates were members of Stolbur. The presence of phytoplasma in petunia was also confirmed by microscopic observation of the pathogens. In this study, Stolbur phytoplasma was identified from spreading type petunia cultivars by sequence analysis of 16S rRNA gene of phytoplasma and microscopic observation of phytoplasma bodies. This is the first report of Stolbur phytoplasma in commercial Petunia hybrida cultivars.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.421-429
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• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

• Korean journal of applied entomology
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• v.39 no.4
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• pp.211-226
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• 2000

Genetic divergence and phylogenetic relationships among the major Korean fireflies (Hotaria papariensis, Luciola lateralis, and Pyrocoelia rufa) were studied. A portion of mitochondrial COI (403 bp) and 165 rRNA (490~504 bp) genes were sequenced, and the GenBank-registered, homologous 165 rRNA sequences of Japanese fireflies were compared (27 species of Lampyridae, one of Lycidae, and one of Rhgophthalmidae). Greatest DNA and/or amino acid sequence divergence was found when P rufa, belonging to Lampyrinae was compared with H. papariensis and L. lateralis, both belong-ing to Luciolinae, confirming the current taxonomic status of the species. In the PAUP and PHYLIP analyses with 165 rRNA data, grouping of the two geographic samples of H. papariensis with H. tsushimana validate the use of generic name, Hotaria. Nevertheless, lack of sister-group relationship of the two geographic samples of H. papariensis renders further investigation on this group . Although the Korean and Japanese L. lateralis formed a strong monophyletic group, a substantial genetic differentiation was detected between them (2.9% of 165 rRNA gene sequence divergence). Finally, the geographic samples of Korean p. rufa strongly formed a group with Japanese p. rufa, warranting the use of generic name, Pyrocoelia, but the genetic distance observed between the Cheju-Island individual and all others requires further investigation on this subject. Summarized, this study supports the current taxonomic status of the Korean fireflies in that each respectively formed a strong monophyletic group with its own species or genus.

• Journal of Life Science
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• v.21 no.6
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• pp.788-795
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• 2011

Accurate identification for pathogenic bacterium is an essential element in the clinical microbiology laboratory. We studied molecular analysis involving the identification of Chyseobacterium indologenes and evaluated the seventeen isolates in Korea with the 16S rRNA gene of the ribosome to estimate phylogenetic relationships within the genus Chyseobacterium in GenBank. The aligned data sets for C. indologenes were 1,176 nucleotides. Sequence variation within the C. indologenes was mostly due to nucleotide substitutions. Korean C. indologenes isolates were not strikingly different from the same species found in the other countries. However, the rates of base substitution in Korean C. indologenes isolates were higher than those of other C. indologenes isolates in GenBank. C. indologenes was placed as a sister species to C. isbiliense, C. hominis, C. hispanicum, C. molle, C. hungaricum, and C. pallidum.

• Mycobiology
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• v.28 no.1
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• pp.11-16
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• 2000

The nucleotide sequences of the internal transcribed spacer (ITS) regions of the ribosomal DNA including the 5.8S ribosomal RNA gene (rDNA) have been determined for 11 species in order to analyze their intrageneric relationships. The total length of these sequences ranged from 530 nucleotides for Trichoderma reesei KCTC 1286 to 553 nucleotide for Trichoderma koningii IAM 12534. Generally speaking, the length of ITS1 region was about 30 nucleotides longer than that of the ITS2 region. Also, the sequences of 5.8S rDNA were more conserved in length and variation than those of ITS regions. Although the variable ITS sequences were often ambiguously aligned, the conserved sites were also found. Thus, a neighbor-joining tree was constructed using the full sequence data of the ITS regions and the 5.8S rDNA. The Trichoderma genus used to be grouped on the basis of the morphological features and especially the shape of phialides needs to be reexamined. The phylogenetic tree displayed the presence of monophylogeny in the species of Trichoderma. Therefore, it was difficult to distinguish the intrageneric relationships in the Trichoderma genus.

• Korean Journal of Microbiology
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• v.46 no.4
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• pp.352-358
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• 2010

Bacterial community composition in activated sludge wastewater treatment bioreactors were analyzed using 16S rRNA gene-based pyrosequencing for the four different wastewater treatment processes. Sequences within the orders Rhodocyclales, Burkholderiales, Sphingobacteriales, Myxococcales, Xanthomonadales, Acidobacteria group 4, Anaerolineales, Methylococcales, Nitrospirales, and Planctomycetales constituted 54-68% of total sequences retrieved in the activated sludge samples, which demonstrated that a few taxa constituted majority of the activated sludge bacterial community. The relative ratio of the order members was different for each treatment process, which was assumed to be affected by different operational and environmental conditions of each treatment process. In addition, activated sludge had very diverse bacterial species (Chao1 richness estimate: 1,374-2,902 operational taxonomic units), and the diversity was mainly originated from rare species. Particularly, the bacterial diversity was higher in membrane bioreactor than conventional treatment processes, and the long solids retention time of the operational strategy of the membrane bioreactor appeared to be appropriate for sustaining diverse slow growing bacteria. This study investigating bacterial communities in different activated sludge processes using a high-throughput pyrosequencing technology would be helpful for understanding microbial ecology in activated sludge and for improving wastewater treatment in the future.

• Molecules and Cells
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• v.22 no.1
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• pp.78-88
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• 2006

The phylogeny of the subfamily Tephritinae (Diptera: Tephritidae) was reconstructed from mitochondrial 16S ribosomal RNA gene sequences using 53 species representing 11 currently recognized tribes of the Tephritinae and 10 outgroup species. The minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) monophyly of the Tephritinae was strongly supported; (2) a sister group relationship between the Tephritinae and Plioreocepta was supported by the Bayesian tree; (3) the tribes Tephrellini, Myopitini, and Terelliini (excluding Neaspilota) were supported as monophyletic groups; (4) the non-monophyletic nature of the tribes Dithrycini, Eutretini, Noeetini, Tephritini, Cecidocharini, and Xyphosiini; and (5) recognition of 10 putative tribal groups, most of which were supported strongly by the statistical tests of the interior branches. Our results, therefore, convincingly suggest that an extensive rearrangement of the tribal classification of the Tephritinae is necessary. Since our sampling of taxa heavily relied on the current accepted classification, some lineages identified by the present study were severely under-sampled and other possible major lineages of the Tephritinae were probably not even represented in our dataset. We believe that our results provide baseline information for a more rigorous sampling of additional taxa representing all possible major lineages of the subfamily, which is essential for a comprehensive revision of the tephritine tribal classification.