• Journal of Species Research
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• v.7 no.1
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• pp.60-72
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• 2018

Our study aimed to discover indigenous prokaryotic species in Korea. A total of 29 bacterial species in the phylum Proteobacteria were isolated from freshwater and sediment of rivers and brackish zones in Korea. From the high 16S rRNA gene sequence similarity (${\geq}98.8%$) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to an independent and predefined bacterial species. To our knowledge, there is no official report or publication that has previously described these 29 species in Korea. Specifically, we identified 10, 12, and seven species of eight, 12, and seven genera that belong to classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, respectively; all are reported as previously unrecorded bacterial species in Korea. The Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs for each are also described.

• Journal of Species Research
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• v.7 no.3
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• pp.193-201
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• 2018

Culturable bacterial diversity was investigated using freshwater and sediment samples collected from the North Han River basin in 2017, as a part of the research program 'Survey of freshwater organisms and specimen collection'. Over a thousand bacterial strains were isolated from the samples and identified based on 16S rRNA gene sequences. Among the bacterial isolates, 22 strains showing higher than 98.7% sequence similarity with validly published bacterial species, but not reported in Korea, were classified as unrecorded species in Korea. The 22 bacterial strains were phylogenetically diverse and assigned to 6 classes, 11 orders, 15 families, and 21 different genera. At the generic level, the unreported species were affiliated with Flavobacterium of the class Flavobacteria, Flexibacter of the class Cytophagia, Blastomonas, Brevundimonas, Elstera, Rhizobium, Roseomonas, Sphingomonas, and Xanthobacter of the class Alphaproteobacteria, Albidiferax, Cupriavidus, Curvibacter, Ferribacterium, Hydrogenophaga, Iodobacter, Limnohabitans, Polaromonas, Undibacterium, and Variovorax of the class Betaproteobacteria, Pseudomonas of the class Gammaproteobacteria, and Arcobacter of the class Epsilonproteobacteria. The unreported bacterial species were further characterized by examining Gram reaction, colonial and cellular morphology, and biochemical properties. The detailed descriptions of 22 strains of the unreported bacterial species are also provided.

• Journal of Life Science
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• v.22 no.2
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• pp.232-238
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• 2012

Kumjungsansung-Makgeolli$^{(R)}$ is a traditional Korean rice wine that is fermented from traditional nuruk and rice. In this study, we performed the PCR-denaturing gradient gel electrophoresis (DGGE) analysis targeting the 16S and 28S rRNA genes to characterize bacterial and fungal diversity during Makgeolli fermentation. The predominant bacteria in the PCR-DGGE profile during Makgeolli fermentation were Lactobacillus spp. (Lactobacillus curvatus, L. kisonensis, L. plantarum, L. sakei, and L. gasseri), Pediococcus spp. (P. acidilactici, P. parvulus, P. agglomerans, and P. pentosaceus), Pantoea spp. (P. agglomerans and P. ananatis), and Citrobacter freundii; these were identified on the base of analysis of 16S rRNA gene sequences. The dominant bacterium during Makgeolli fermentation was L. curvatus. The predominant fungi in PCR-DGGE profile during Makgeolli fermentation were Pichia kudriavzevii, Saccharomyces cerevisiae, Asidia idahoensis, Kluyveromyces marxianus, Saccharomycopsis fibuligera, and Torulaspora delbrueckii, and these were identified on the basis of analysis of 28S rRNA gene sequences. The dominant fungal species during Makgeolli fermentation changed from P. kudriavzevii at 0-2 days incubation to S. cerevisiae at 3-6 days incubation. This study suggests that PCR-DGGE analysis could be a suitable tool for the understanding of microbial diversity and structure during Makgeolli fermentation.

• Journal of Species Research
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• v.10 no.2
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• pp.99-116
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• 2021

In 2018, as a subset study to discover indigenous prokaryotic species in Korea, a total of 18 unreported bacterial strains were discovered. From the high 16S rRNA gene sequence similarity (>98.8%) and formation of a robust phylogenetic clade, it was determined that each strain belonged an independent and predefined bacterial species. There were no official report that these 18 species were previously described in Korea; therefore, one strain of Williamsia, one strain of Rhodococcus, three strains of Microbacterium, three strains of Agromyces, one strain of Arthrobacter, one strain of Paeniglutamicibacter, one strain of Pseudarthrobacter, one strain of Nocardioides, one strain of Fibrella, one strain of Hymenobacter, one strain of Deinococcus, two strains of Fictibacillus, and one strain of Paenibacillus are described as unreported bacterial species in Korea. Gram reaction, basic biochemical characteristics, and colony and cell morphologies are described in the species description section.

• Journal of Species Research
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• v.10 no.4
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• pp.321-335
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• 2021

In 2020, a total of 12 bacterial strains were isolated from soil after a comprehensive investigation of indigenous prokaryotic species in Korea. It was determined that each strain belonged to independent and predefined bacterial species, with high 16S rRNA gene sequence similarity (>98.7%) and formation of a robust phylogenetic clade with the closest species. This study identified four families in the phylum Actinobacteria, two families in the phylum Proteobacteria, one family in the phylum Bacteroidetes one family in the phylum Firmicutes; and four species in the family Nocardiaceae, two species in the family Nocardioidaceae, one species in the family Cellulomonadaceae, one species in the family Hymenobacter, one species in the family Methylobacteriaceae, one species in the family Microbacteriaceae, one species in the family Bacillaceae and one species in the family Sphingomonadaceae. There is no official report of these 12 species in Korea, so they are described as unreported bacterial species in Korea in this study. Gram reaction, basic biochemical characteristics, colony, and cell morphology are included in the species description section.

• 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.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.205-211
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• 2004

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.900-905
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• 2009

We analyzed succession of the bacterial communities during composting of animal manure in three individual facilities. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) targeting for the bacterial 16S rRNA gene were used to clarify the changes of bacterial community throughout each composting process. Our study revealed that the bacterial community structures differed during the composting process. The bacterial community in composting of facility A showed little change throughout the process. In the compost sample from facility B, its community had a small shift as the temperature increased. In compost from facility C, the temperature dynamically changed; it was shown that various bacterial communities appeared and disappeared as follows: in the initial phase, the members of phylum Bacteroidetes dominated; in the thermophilic phase, some bacteria belonging to phylum Firmicutes increased; towards the end, the community structure consisted of three phyla, Bacteroidetes, Firmicutes, and Proteobacteria. This study provides some information about the bacterial community actually present in field-scale composting with animal manure.

• Journal of Species Research
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• v.7 no.3
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• pp.187-192
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• 2018

During a comprehensive study of indigenous prokaryotic species in South Korea, nine bacterial species in the phylum Bacteroidetes were isolated from freshwater environmental samples that were collected from three major rivers in the Republic of Korea. High 16S rRNA gene sequence similarity (${\geq}98.7%$) and robust phylogenetic clades with the closely related species suggest that each strain was correctly assigned to an independent and predefined bacterial species. There were no previous reports of these nine species in Korea. Within the phylum Bacteroidetes, four species were assigned to the genus Flavobacterium, order Flavobacteriales, and five species to three genera of two families in the order Cytophagales. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

• Korean Journal of Exercise Nutrition
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• v.25 no.4
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• pp.24-37
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• 2021

[Purpose] To determine whether physical activity (PA), primarily the recommended 60 minutes of moderate-to-vigorous PA, is associated with gut bacterial microbiota in 10-year-old children. [Methods] The Block Physical Activity Screener, which provides minutes/day PA variables, was used to determine whether the child met the PA recommendations. 16S rRNA sequencing was performed on stool samples from the children to profile the composition of their gut bacterial microbiota. Differences in alpha diversity metrics (richness, Pielou's evenness, and Faith's phylogenetic diversity) by PA were determined using linear regression, whereas beta diversity (unweighted and weighted UniFrac) relationships were assessed using PERMANOVA. Taxon relative abundance differentials were determined using DESeq2. [Results] The analytic sample included 321 children with both PA and 16S rRNA sequencing data (mean age [SD] =10.2 [0.8] years; 54.2% male; 62.9% African American), where 189 (58.9%) met the PA recommendations. After adjusting for covariates, meeting the PA recommendations as well as minutes/day PA variables were not significantly associated with gut richness, evenness, or diversity (p ≥ 0.19). However, meeting the PA recommendations (weighted UniFrac R² = 0.014, p = 0.001) was significantly associated with distinct gut bacterial composition. These compositional differences were partly characterized by increased abundance of Megamonas and Anaerovorax as well as specific Christensenellaceae_R-7_group taxa in children with higher PA. [Conclusion] Children who met the recommendations of PA had altered gut microbiota compositions. Whether this translates to a reduced risk of obesity or associated metabolic diseases is still unclear.