• International Journal of Oral Biology
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• 제45권2호
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• pp.70-75
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• 2020

The aim of this study was to identify strain KCOM 1265 isolated from subgingival plaque at the species level by comparing 16S ribosomal RNA gene (16S rDNA) and genome sequences. The whole genome of strain KCOM 1265 was extracted using the phenol-chloroform extraction method. 16S rDNA was amplified using polymerase chain reaction and sequenced using the dideoxy chain termination method. Pairwise genome comparison was performed using average nucleotide identity (ANI) and genome-to-genome distance (GGD) analyses. The data showed that the percent similarity of 16S rDNA sequence of strain KCOM 1265 was 99.6% as compared with those of Fusobacterium polymorphum ATCC 10953^T and Fusobacterium hwasookii KCOM 1249^T. The ANI values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 95.8% and 93.0%, respectively. The GGD values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 63.9% and 49.6%, respectively. These results indicate that strain KCOM 1265 belongs to F. polymorphum.

• 미생물학회지
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• 제54권1호
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• pp.74-76
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• 2018

최근 Fusobacterium nucleatum subsp. vincentii는 average nucleotide identity 및 genome-to-genome distance 분석법에 의해 Fusobacterium vincentii로 재분류 되었다. F. vincentii는 그람 음성이면서, 혐기성 및 가는 섬유 모양의 세균이다. F. vincentii는 사람의 구강 내 정상세균총의 하나이고, 치주질환에 중요한 역할을 한다. F. vincentii KCOM 2931 균주가 사람 치주염 병소에서 분리되었다. F. vincentii KCOM 2931 균주 유전체 염기서열을 해독하여 보고한다.

• 미생물학회지
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• 제54권1호
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• pp.71-73
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• 2018

최근 Fusobacterium nucleatum subsp. polymorphum는 average nucleotide identity 및 genome-to-genome distance 분석법에 의해 Fusobacterium polymorphum로 재분류 되었다. F. polymorphum 그람 음성이면서, 혐기성 및 가는 섬유 모양의 세균이다. F. polymorphum은 사람의 구강 내 정상세균총의 하나이고, 치주질환의 원인 인자이다. F. polymorphum KCOM 1001 (= ChDC F119) 균주가 사람 치은염 병소의 치은연하치면세균막에서 분리되었다. F. polymorphum KCOM 1001 균주 유전체 염기서열을 해독하여 보고한다.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.562-565
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• 2023

Escherichia coli-specific phage, KFS-EC1, was isolated and purified from a slaughterhouse. The complete genome of the phage was obtained using Illumina MiSeq platforms. Its assembled genome consisted of a single chromosome of 164,715 bp with a GC content of 40.5%. The phage genome contained 170 hypothetical and 101 functional ORFs, and exhibited orthologous average nucleotide identity values of >95% with other E. coli phages belonging to the family Straboviridae. Additionally, phylogenetic analysis revealed that KFS-EC1 was finally classified into the family Straboviridae of the genus Caudoviricetes. The genome has been deposited in GenBank under the accession number NC_055757.1.

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.309-313
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• 2023

Here we report essential features of the draft genome of an AmpC-β-lactamase-producing bacterial isolate obtained from farm tomatoes in South Africa. The isolate designated strain Tom1 featured a genome of 4950426 bp with a G+C% of 59.83. It was identified as Serratia marcescens by ribosomal multilocus sequence typing (rMLST), digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and phylogenetic analysis using reference genomes. Its genome encoded an AmpC-β-lactamase (bla_SST-1), an efflux pump providing tetracycline resistance (tet(41)), and an aminoglycoside acetyltransferase (aac(6')-Ic). Additionally, genes encoding proteins involved in prodigiosin biosynthesis and associated with adherence, biofilm formation, virulence, and pathogenicity were detected.

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.289-292
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• 2023

Thermotolerant Bacillus subtilis NIB353 was isolated from Nuruk, a traditional Korean fermentation starter. The complete B. subtilis NIB353 genome sequence was obtained using MinION and Illumina (MiSeq) platforms. The B. subtilis NIB353 genome sequence was 4,247,447 bp with a GC content of 43%. The B. subtilis NIB353 strain exhibited orthologous average nucleotide identity values of 98.39% and 98.38% with B. subtilis 168 and B. subtilis ATCC6051a, respectively. The genome has been deposited in GenBank under the accession number NZ_CP089148.1.

• Mycobiology
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• 제38권3호
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• pp.166-170
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• 2010

Gummy stem blight is a major foliar disease of muskmelon (Cucumis melo L.). In this study, morphological characteristics and rDNA internal transcribed spacer (ITS) sequences were analyzed to identify the causal organism of this disease. Morphological examination of the Jeonbuk isolate revealed that the percentage of monoseptal conidia ranged from 0% to 10%, and the average length $\times$ width of the conidia was 70 ($\pm$ 0.96) $\times$ 32.0 ($\pm$ 0.15) ${\mu}m$ on potato dextrose agar. The BLAST analysis showed nucleotide gaps of 1/494, 2/492, and 1/478 with identities of 485/492 (98%), 492/494 (99%), 491/494 (99%), and 476/478 (99%). The similarity in sequence identity between the rDNA ITS region of the Jeonbuk isolate and other Didymella bryoniae from BLAST searches of GenBank was 100% and was 95.0% within the group. Nucleotide sequences of the rDNA ITS region from pure culture ranged from 98.2% to 99.8%. Phylogenetic analysis with related species of D. bryoniae revealed that D. bryoniae is a monophyletic group distinguishable from other Didymella spp., including Ascochyta pinodes, Mycosphaerella pinodes, M. zeae-maydis, D. pinodes, D. applanata, D. exigua, D. rabiei, D. lentis, D. fabae, and D. vitalbina. Phylogenetic analysis, based on rDNA ITS sequence, clearly distinguished D. bryoniae and Didymella spp. from the 10 other species studied. This study identified the Jeonbuk isolate to be D. bryoniae.

• 식물병연구
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• 제28권2호
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• pp.98-107
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• 2022

The incidence of Tomato brown rugose fruit virus (ToBRFV) and biological and molecular characterization of the Palestinian isolates of ToBRFV are described in this study. Symptomatic leaf samples obtained from Solanum lycopersicum L. (tomatoes) and Nicotiana tabacum L. (cultivated tobacco) plants were tested for tobamoviruses infection by reverse transcription polymerase chain reaction. Tomato leaf samples collected from Tulkarm and Qalqilia are infected with ToBRFV-PAL with an infection rate of 76% and 72.5%, respectively. Leaf samples collected from Jenin and Nablus were found to be mixed infected with ToBRFV-PAL and Tobacco mosaic virus (TMV) (100%). Sequence analysis of the ToBRFV-PAL genome showed that the net average nucleotide divergence between ToBRFV/F48-PAL strain and the Israeli and Turkish strains was 0.0026398±0.0006638 (±standard error of mean), while it was 0.0033066±0.0007433 between ToBRFV/F42-PAL and these two isolates. In the phylogenetic tree constructed with the complete genomic sequence, all the ToBRFV isolates were clustered together and formed a sister branch with the TMV. The sequenced Palestinian isolates of ToBRFV-PAL shared the highest nucleotide identity with the Israeli ToBRFV isolate suggesting that the virus was introduced to Palestine from Israel. The findings of this study enhance our understanding of the biological and molecular characteristics of ToBRFV which would help in the management of the disease.

• Journal of Microbiology and Biotechnology
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• 제33권8호
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• pp.1084-1090
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• 2023

The strain KIST612, initially identified as E. limosum, was a suspected member of E. callanderi due to differences in phenotype, genotype, and average nucleotide identity (ANI). Here, we found that E. limosum ATCC 8486^T and KIST612 are genetically different in their central metabolic pathways, such as that of carbon metabolism. Although 16S rDNA sequencing of KIST612 revealed high identity with E. limosum ATCC 8486^T (99.2%) and E. callanderi DSM 3662^T (99.8%), phylogenetic analysis of housekeeping genes and genome metrics clearly indicated that KIST612 belongs to E. callanderi. The phylogenies showed that KIST612 is closer to E. callanderi DSM 3662^T than to E. limosum ATCC 8486^T. The ANI between KIST612 and E. callanderi DSM 3662^T was 99.8%, which was above the species cut-off of 96%, Meanwhile, the ANI value with E. limosum ATCC 8486^T was not significant, showing only 94.6%. The digital DNA-DNA hybridization (dDDH) results also supported the ANI values. The dDDH between KIST612 and E. callanderi DSM 3662^T was 98.4%, whereas between KIST612 and E. limosum ATCC 8486^T , it was 57.8%, which is lower than the species cut-off of 70%. Based on these findings, we propose the reclassification of E. limosum KIST612 as E. callanderi KIST612.

• 미생물학회지
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• 제54권1호
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• pp.81-83
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• 2018

Neisseria 속 균주 KEM232는 사람 평활면 치아우식 부위로부터 분리하였다. 균주 KEM232의 유전체는 G + C 비율이 58.5%, 2,369개의 유전자와 2,210개의 단백질 코딩 유전자, 108개의 위유전자, 51개의 RNA 유전자 그리고 한 개의 CRISPR array를 포함한 단일 원형 염색체로 구성되었으며 그 크기는 2,371,912 bp였다. 균주 KEM232의 최 근연종은 Neisseria baciliformis 로서 두 균주 사이의 16S rRNA 유전자 염기서열의 유사도는 96.8% 그리고 유전체의 평균 염기 동일성은 84%였다.