• Journal of Microbiology and Biotechnology
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• 제21권4호
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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.

• 한국미생물·생명공학회지
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• 제29권2호
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• pp.78-83
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• 2001

본 연구는 phytic acid를 myo-inositol과 무기태인으로 분해시키는 효소인 phytase 생산균주의 분리 및 효소생산의 배지최적하에 관한 것이다. 1차로 calcium phytate를 기질로 함유한 phytase screening 배지를 이용하여 phytase 생산을 나타내는 균주 35가지를 이용하여 분리한 후, sodium phytate를 기질로 하여 재현성 있는 phytase 활성을 나타내는 균주 12가지를 선발하였다. 12개의 균주 중 BHI broth에서 배양한 조효소액의 phytase 활성이 가장 우수한 것으로 나타난 YH100을 선발하여 주사현미경 관찰, 16S rRNA sequence 분석, GC conten(mol%) 조성, 지방산 분석, API 20E kit를 이용한 test 결과 Enterobacter cloacae로 동정되어, 이 균주를 Enterobacter cloacae YH100이라 명명하였다. Enterobacter cloacae YH100에 의한 phytase 생산을 위한 최적 배지 조성을 파악한 결과 glucose 2.0%(w/v), peptone 1.0%(w/v), beef extract 1.0%(w/v), KCI 0.1%(w/v), sodium phytate 0.1%(w/v)로 나타났다.

• Journal of Microbiology and Biotechnology
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• 제28권2호
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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.

• 한국식품저장유통학회지
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• 제17권2호
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• pp.301-306
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• 2010

본 연구에서는 계육 창상부위의 원인이 되는 세균을 동정하였다. 계육의 등과 다리 창상 부위로부터 무작위 선별법을 통해 총 10주의 균주를 분리하였다. 순수 분리 배양된 균주의 세포막 지방산 조성 분석 결과, 5 균주가 높은 유효성을 지녔으며, Shigella sonnei, Proteus mirabilis, Escherichia coli로 동정되었다. 또한 16S rRNA sequence를 실시한 결과, 동정된 균주는 Shigella sonnei(99%), Proteus mirabilis(99%) 그리고 Escherichia coli(99%)와 높은 염기서열 상동성을 나타냈다. 따라서 본 연구에서 조사된 계육의 등과 다리 부위 주요 창상 원인균은 Shigella sonnei, Proteus mirabilis, Escherichia coli인 것으로 밝혀졌다.

• 미생물학회지
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• 제50권1호
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• pp.67-72
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• 2014

담배식물과 담배재배 토양으로부터 최소배지에 유일 탄소원으로 니코틴을 첨가한 배지(MB/N)를 이용하여 니코틴을 분해하는 새로운 균주의 분리를 시도하였다. 16S rRNA 유전자의 염기서열 분석과 표현형 시험 및 형태학적 시험으로 분리균주들은 Micrococcaceae 과의 Arthrobacter 속에 포함되는 균주로 판명되었다. NU15는 Arthrobacter nicotinovorans와 99.8%의 상동성을 보였고, NU11는 Arthrobacter equi와 98.2%의 상동성을 보여 신주일 가능성이 있었다. 두 균주 모두 양성의 간구균이며, catalase 양성, oxidase 음성이었다. 신주일 가능성이 있는 NU11균주의 니코틴 분해를 확인하기 위하여 MB/N 액체배지에서 배양하면서 니코틴 특이적으로 나타내는 260 nm에서의 흡광도가 감소를 측정한 결과, 니코틴이 균주에 의해 특이적으로 분해되는 것을 확인 할 수 있었으며, 분해균들은 니코틴 오염을 복원하는데 사용될 수 있을 것으로 생각된다.

• Journal of Microbiology and Biotechnology
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• 제26권8호
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• pp.1375-1382
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• 2016

The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. Strain CBA1132 had nine putative CRISPRs and the genome contained genes encoding metal resistance determinants: copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR). Strain CBA1132 was related to Halobacterium noricense, with 99.2% 16S rRNA gene sequence similarity. Based on the comparative genomic analysis, strain CBA1132 has distinctly evolved; moreover, essential genes related to nitrogen metabolism were only detected in the genome of strain CBA1132 among the reported genomes in the genus Halobacterium. This genome sequence of Halobacterium noricense CBA1132 may be of use in future molecular biological studies.

• Journal of Species Research
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• 제8권2호
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• pp.176-190
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• 2019

A total of 38 bacterial strains within the classes Bacilli and Deinococci were isolated from various sources in Korea. Samples were collected from animal intestine, urine, soil, tidal flat mud, and kimchi. In the sequence comparison and phylogenetic analysis of 16S rRNA sequences, the 38 isolates were assigned to the classes Bacilli and Deinococci with sequence similarities more than 98.7%. Twenty-four strains and 13 strains were classified the order Bacillales and Lactobacillales in the class Bacilli, respectively. In the order Bacillales, there were nine species in the genus Bacillus, seven species in the genus Paenibacillus, and the remaining eight species in the genera Domibacillus, Halobacillus, Virgibacillus, Lysinibacillus, Paenisporosarcina, Planococcus, Savagea, and Staphylococcus. In the order Lactobacillales, there were four species in the genus Lactobacillus, three species in the genus Leuconostoc, three species in the genus Lactococcus, and the remaining three species in the genera Aerococcus, Enterococcus, and Streptococcus. One species was related to the genus Deinococcus of the order Deinococcales. Most of the isolated strains were Gram-stain-positive, but some were Gram-stain-variable or Gram-stain-negative. Cells were rod or cocci-shaped. Based on the results of 16S rRNA analysis, we report 38 strains as previously unrecorded species to Korea, and the basic characteristics of strains are described herein.

• Journal of Species Research
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• 제10권2호
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• pp.117-133
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• 2021

In 2019, 43 bacterial strains were isolated from food, soil, marine environments, human, and animals related sources from the Republic of Korea. Based on the analysis of 16S rRNA gene sequence, these isolates were allocated to the phyla Bacteroidetes and Firmicutes as unrecorded species in Korea. The 10 Bacteroidetes strains were classified into the families Bacteroidaceae, Chitinophagaceae, Cytophagaceae, Flavobacteriaceae, and Prolixibacteraceae (of the orders Bacteroidales, Chitinophagales, Cytophagales, Flavobacteriales, and Marinilabiliales, respectively). The 33 Firmicutes strains belonged to the families Bacillaceae, Paenibacillaceae, Planococcaceae, Staphylococcaceae, Clostridiaceae, Lachnospiraceae, Peptostreptococcaceae, Enterococcaceae, Lactobacillaceae, Leuconostocaceae, and Streptococcaceae (of the orders Bacillales, Clostridiales, and Lactobacillales). These unrecorded bacteria were determined based on taxonomic criterion (>98.7%; 16S rRNA gene sequence similarity). In addition, their phylogenetic affiliation, as well as cell and colony morphologies, staining reactions, and physiological and biochemical properties were investigated. Therefore, we report 43 isolates as unrecorded species, and described basic features, isolation source, and locations of these strains.

• Journal of Species Research
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• 제12권2호
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• pp.165-173
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• 2023

Bacterial communities inhabiting islands play a vital role in the functioning and formation of a unique, isolated ecosystem. Nevertheless, there has been a lack of systematic research on the indigenous microbiological resources of the islands in Korea. To excavate microbial resources for further studies on the metabolism and biotechnological potential, a standard dilution plating was applied to coastal seawater samples collected from islands along the west coast of the Korean Peninsula, including Deokjeokdo, Baengnyeongdo, and Daebudo in 2022. A total of 2,007 bacterial strains were isolated from the samples as single colonies and identified using 16S rRNA gene sequence analyses. A total of 20 strains, with ≥98.7% 16S rRNA gene sequence similarity to bacterial species having validly published names but not reported in Korea, were designated as unrecorded bacterial species in Korea. The unrecorded bacterial strains were phylogenetically diverse and belonged to four phyla, five classes, 12 orders, 17 families, and 18 genera. The unreported species were assigned to Algimonas, Amylibacter, Notoacmeibacter, Roseibium, and Terasakiella of the class Alphaproteobacteria; Alteromonas, Congregibacter, Marinagarivorans, Marinicella, Oceanospirillum, Psychromonas, Thalassotalea, Umboniibacter, and Vibrio of the class Gammaproteobacteria; Lutibacter and Owenweeksia of the class Flavobacteriia; Paenibacillus of the class Bacilli; and Pelagicoccus of the class Opitutae. The taxonomic characteristics of the unreported species, including morphology, biochemistry, and phylogenetic position are provided in detail.

• Journal of Species Research
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• 제12권4호
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• pp.374-414
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• 2023

As part of a comprehensive investigation of indigenous prokaryotic species in Republic of Korea in 2022, 156 bacterial strains were isolated from diverse environmental habitats. These strains were assigned to six phyla, namely Acidobacteriota, Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of robust phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Acidobacteriota, one species belonging to the phylum Deinococcota, 28 species belonging to the phylum Actinomycetota, 19 species belonging to the phylum Bacillota, 19 species belonging to the phylum Bacteroidota, and 88 species belonging to the phylum Pseudomonadota (comprising 34 species of the class Alphaproteobacteria, 20 species of the class Betaproteobacteria, and 34 species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 156 isolates in Republic of Korea, they are reported as unrecorded species in Republic of Korea. The Gram stain, colony and cell morphology, basic biochemical characteristic, isolation source, and strain ID of each species are described in the species descriptions.