• 산업식품공학
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• 제21권2호
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• pp.174-179
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• 2017

For preliminary molecular typing, PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) is the method of choice. In this study, 14 bacterial strains were isolated from different Korean food sources, identified using 16S rRNA gene sequencing, and characterized through RAPD-PCR. Two PCR primers (239 and KAY3) generated a total of 130 RAPD bands, 14 distinct PCR profiles, 10 polymorphic bands, one monomorphic band, and four unique bands. Dendrogram-based analysis with primer 239 showed that all 14 strains could be divided into seven clades out of which clade VII had the maximum of seven. In contrast, dendrogram analysis with the primer KAY3 divided the 14 L. citreum strains into four clades out of which clade IV consisted of a maximum of 10 strains out of 14. This research identified and characterized bacterial populations associated with different Korean foods. The proposed RAPD-PCR method, based on sequence amplification, could easily identify and discriminate the lactic acid bacteria species at the strain-specific level and could be used as a highly reliable genomic fingerprinting tool.

• Journal of Applied Biological Chemistry
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• 제66권
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• pp.394-403
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• 2023

지속 가능하고 친환경적인 농업 관행을 추구하기 위해 우리는 40년이 넘는 장기간 동안 화학 비료를 사용하지 않은 토양에 서식하는 근권 박테리아에 대한 광범위한 연구를 수행하였다. 이번 조사를 통해 식물생장촉진 근권박테리아 총 80종을 분리하고 이들의 식물생장 증진 가능성을 평가했다. 이러한 분리균중에서 Burkholderia cepacia CD2는 가장 우수한 식물 성장촉진 활성과 생장능을 나타내어 추가 분석을 위한 최적의 후보균주로 선정되었다. Burkholderia cepacia CD2는 인 가용화 능력, 사이드로포어 생산, 탈질화 능력, 아질산 이온 활용능력 및 요소분해효소 활성을 포함하여 식물 성장에 도움이 되는 다양한 유익한 특성을 나타내었다. 이러한 특성은 식물의 성장과 발달에 긍정적인 영향을 미치는 것으로 잘 알려져 있다. 균주의 분류학적 분류를 검증하기 위해 16S rRNA 유전자 서열분석을 통해 Burkholderia 속 내 위치를 확인하여 계통발생 관계에 대한 추가 통찰력을 제공하였다. 식물 생장 촉진 특성의 기본 메커니즘을 더 깊이 조사하기 위해 우리는 CD2에서 식물 생장촉진과 관련된 특정 유전자의 존재를 확인하려고 하였다. 이를 달성하기 위해 옥스포드 나노포어를 활용하여 전장 유전체 시퀀싱을 수행하였다. CD2 게놈에 대한 전장유전체 분석을 통해 식물 생장 개선에 중추적 요인으로 생각되는 하위 시스템 기능을 확인하였다. 이러한 발견을 바탕으로 Burkholderia cepacia CD2는 미생물 비료로 작용하여 화학 비료에 대한 지속 가능한 대안을 제공할 수 있는 잠재력을 가지고 있다는 결론을 내릴수 있다.

• 식물병연구
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• 제30권1호
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• pp.88-94
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• 2024

In July 2021, symptoms of soft rot were observed on the stems of Ficus carica in Yeongam, Jeollanamdo, Korea. To accurately diagnose the cause, infected stem was collected and bacterial strain was isolated. Among these, the pathogenic strain KNUB-08-21 was identified as Pectobacterium aroidearum through 16S rRNA gene sequencing and phylogenetic analysis based on the concatenated sequences of the dnaX, leuS, and recA genes. The affiliation of the isolate with this bacterial species was also confirmed by its biochemical characteristics obtained using API ID 32 GN system. Artificial inoculation confirmed the strain's pathogenicity in figs, causing significant damage to both stems and fruits. To our knowledge, this is the first report of P. aroidearum causing soft rot disease in F. carica in Korea.

• Journal of Animal Science and Technology
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• 제64권6호
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• pp.1144-1172
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• 2022

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

• KSBB Journal
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• 제30권5호
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• pp.239-244
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• 2015

Bacterial vaginosis (BV) is caused by microbial imbalance of the vaginal ecosystem and overgrowth of anaerobic bacteria. The antibiotic treatment often results in very high recurrence of BV because it disturbs the vaginal ecosystem. The high recurrence rates suggest a need for alternative therapeutic methods and probiotics are being recognized as alternative or additional treatment method for BV. The purpose of this study was to investigate how human vaginal isolates of Lactobacillus spp. inhibit the BV-associated pathogen Gardnerella vaginalis. Results show that selected strains significantly reduced the viability of G. vaginalis. Among these selected strains KLB410 and KLB416 were further selected based on acid/bile tolerance and identified through 16S rRNA gene sequencing being Lactobacillus plantarum. Further studies are underway to demonstrate that the selected strain can be applied as potential probiotics for recovering vaginal ecosystem.

• Journal of Microbiology and Biotechnology
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• 제27권3호
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• pp.561-572
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• 2017

The global commercial cultivation of transgenic crops, including glyphosate-tolerant soybean, has increased widely in recent decades with potential impact on the environment. The bulk of previous studies showed different results on the effects of the release of transgenic plants on the soil microbial community, especially rhizosphere bacteria. In this study, comparative analyses of the bacterial communities in the rhizosphere soils and surrounding soils were performed between the glyphosate-tolerant soybean line NZL06-698 (or simply N698), containing a glyphosate-insensitive EPSPS gene, and its control cultivar Mengdou12 (or simply MD12), by a 16S ribosomal RNA gene (16S rDNA) amplicon sequencing-based Illumina MiSeq platform. No statistically significant difference was found in the overall alpha diversity of the rhizosphere bacterial communities, although the species richness and evenness of the bacteria increased in the rhizosphere of N698 compared with that of MD12. Some influence on phylogenetic diversity of the rhizosphere bacterial communities was found between N698 and MD12 by beta diversity analysis based on weighted UniFrac distance. Furthermore, the relative abundances of part rhizosphere bacterial phyla and genera, which included some nitrogen-fixing bacteria, were significantly different between N698 and MD12. Our present results indicate some impact of the glyphosate-tolerant soybean line N698 on the phylogenetic diversity of rhizosphere bacterial communities together with a significant difference in the relative abundances of part rhizosphere bacteria at different classification levels as compared with its control cultivar MD12, when a comparative analysis of surrounding soils between N698 and MD12 was used as a systematic contrast study.

• 미생물학회지
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• 제53권3호
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• pp.163-169
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• 2017

복숭아 수확시기에 낙과한 토양에서 Lactobacillus sp. D4와 D5 균주를 분리하였다. 분리한 Lactobacillus sp. D4와 D5 균주를 동정하기 위하여 형태학적 동정, 생화학적 동정 및 16S rRNA 유전자서열 분석을 수행하였다. 16S rRNA 유전자서열 분석 결과 Lactobacillus sp. D4는 Lactobacillus plantarum subsp. plantarum ATCC $14917^T$과 Lactobacillus pentosus ATCC $40997^T$에 각각 99.05%, 98.98% 일치하였으며, Lactobacillus sp. D5는 Lactobacillus pentosus ATCC $40997^T$, Lactobacillus plantarum subsp. plantarum ATCC $14917^T$에 각각 98.71%, 98.64% 일치하였다. Lactobacillus sp. D4와 D5 균주는 당 이용성 비교에서 Lactobacillus plantarum ATCC $14917^T$과 Lactobacillus pentosus ATCC $8041^T$에 비교하여 다른 결과를 나타내었다. 정확한 동정을 위하여 VITEK MS matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) 분석, multiplex PCR, random amplified polymorphic DNA (RAPD)-PCR을 수행하였다. 이러한 결과에 근거하여 Lactobacillus sp. D4와 D5 균주는 Lactobacillus plantarum으로 동정되었다.

• 미생물학회지
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• 제45권2호
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• pp.148-154
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• 2009

퇴비화 과정은 유기성 폐기물을 비료와 같은 유용한 자원으로 전환하는 생물학적 과정이다. 본 연구에서는 음식 물 쓰레기를 2달 동안 퇴비화시켜 세균군집의 변화를 조사하였다. 온도의 변화를 기준으로 하여 퇴비화 과정은 1단계($2\sim55^{\circ}C$), 2단계($55\sim97^{\circ}C$), 3단계($50\sim89^{\circ}C$)로 나뉘었다. 각 단계별 총세균수는 1단계 $1.66\times10^{11}$ cell/g, 2단계 $0.29\times10^{11}$ cell/g, 3단계 $0.28\times10^{11}$ cell/g으로 관찰되었다. 또한 총세균수에 대한 고온미생물의 비율은 초기에 33% 였으나 2단계 시료에서 최대비율인 89%로 증가하였다. 16S rRNA 유전자를 대상으로 T-RFLP 방법과 염기서열 분석방법을 이용하여 세균군집의 구조가 퇴비화 과정에 따라 변화됨을 확인할 수 있었다. 초고온인 2단계의 세균군집의 발달은 스타터 접종의 영향을 받았으며, Bacillus 및 Pseudomonas와 유연관계가 가까운 세균군집이 퇴비화 과정을 이끄는 주요 미생물임을 확인하였다.

• 환경생물
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• 제29권4호
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• pp.265-273
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• 2011

Bacterial diversity based on the denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene sequences was determined for soil samples from two abandoned mine sites and the corresponding enrichment cultures using soil sample as key inoculum. Sequencing analysis of DGGE bands obtained from both the soil samples matched mostly with sequences of uncultured and newly described organisms, or organisms recently associated with the acid mine drainage environment. However, the enrichment of soil samples in ferrous sulfate and elemental sulfur media yielded sequences that were consistent with well-known iron- and sulfur-oxidizing acidophilic bacteria. Analysis of enrichment cultures of soil samples from Dalsung mine revealed abundant ${\gamma}$-$Proteobacteria$, whereas that of Gubong mine sample displayed acidophilic groups of ${\gamma}$-$Proteobacteria$, ${\alpha}$-$Proteobacteria$, $Actinobacteria$ and $Firmicutes$. Chemical elemental analysis of the mine samples indicated that the Dalsung site contained more iron and sulfate along with other toxic components as compared with those of the Gubong site. Biogeochemistry was believed to be the primary control on the acidophilic bacterial group in the enrichment samples.

• Journal of Microbiology and Biotechnology
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• 제28권3호
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• pp.454-464
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• 2018

Salivary microbiota alterations can correlate with dental caries development in children, and mechanisms mediating this association need to be studied in further detail. Our study explored salivary microbiota shifts in children and their association with the incidence of dental caries with dentine involvement. Salivary samples were collected from children with caries and their subsequently matched caries-free controls before and after caries development. The microbiota was analyzed by 16S rRNA gene-based high-throughput sequencing. The salivary microbiota was more diverse in caries-free subjects than in those with dental caries with dentine involvement (DC). Although both groups exhibited similar shifts in microbiota composition, an association with caries was found by function prediction. Analysis of potential microbiome functions revealed that Granulicatella, Streptococcus, Bulleidia, and Staphylococcus in the DC group could be associated with the bacterial invasion of epithelial cells, phosphotransferase system, and ${\text\tiny{D}}-alanine$ metabolism, whereas Neisseria, Lautropia, and Leptotrichia in caries-free subjects could be associated with bacterial motility protein genes, linoleic acid metabolism, and flavonoid biosynthesis, suggesting that functional differences in the salivary microbiota may be associated with caries formation. These results expand the current understanding of the functional significance of the salivary microbiome in caries development, and may facilitate the identification of novel biomarkers and treatment targets.