• Journal of Microbiology and Biotechnology
• /
• v.27 no.3
• /
• pp.561-572
• /
• 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.

• Microbiology and Biotechnology Letters
• /
• v.51 no.4
• /
• pp.562-565
• /
• 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.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2019.10a
• /
• pp.73-73
• /
• 2019

Angelica gigas Nakai (Korean danggui), a member of the Umbelliferae family, is a Korean traditional medicinal plant whose roots have been used for treating gynecological diseases. Transcriptomics is the study of the transcriptome, which is the complete set of RNA transcripts that are produced by the genome, using high-throughput methods, such as microarray analysis. In this study, transcriptome analysis of A.gigas Nakai was carried out. Transcriptome sequencing and assembly was carried out by using Illumina Hiseq 2500, Velvet and Oases. A total of 109,591,555 clean reads of A. gigas Nakai was obtained after trimming adaptors. The obtained reads were assembled with an average length of 1,154 bp, a maximum length of 13,166 bp, a minimum length of 200 pb, and N50 of 1,635 bp. Functional annotation and classification was performed using NCBI NR, InterprotScan, KOG, KEGG and GO. Candidate genes for phenylpropanoid biosynthesis were obtanied from A.gigas transcriptome and the genes and its proteins were confirmed through the NCBI homology BLAST searches, revealing high identity with other othologous genes and proteins from various plants pecies. In RNA sequencing analysis using an Illumina Next-Seq2500 sequencer, we identified a total 94,930 transcripts and annotated 71,281 transcripts, which provide basic information for further research in A.gigas Nakai. Our transcriptome data reveal that several differentially expressed genes related to flower color in A.gigas Nakai. The results of this research provide comprehensive information on the A.gigas Nakai genome and enhance our understanding of the flower color related gene pathways in this plant.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.8
• /
• pp.1013-1022
• /
• 2023

Arbuscular mycorrhizal fungi (AMF) are widespread soil endophytic fungi, forming mutualistic relationships with the vast majority of land plants. Biochar (BC) has been reported to improve soil fertility and promote plant growth. However, limited studies are available concerning the combined effects of AMF and BC on soil community structure and plant growth. In this work, a pot experiment was designed to investigate the effects of AMF and BC on the rhizosphere microbial community of Allium fistulosum L. Using Illumina high-throughput sequencing, we showed that inoculation of AMF and BC had a significant impact on soil microbial community composition, diversity, and versatility. Increases were observed in both plant growth (the plant height by 8.6%, shoot fresh weight by 12.1%) and root morphological traits (average diameter by 20.5%). The phylogenetic tree also showed differences in the fungal community composition in A. fistulosum. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that 16 biomarkers were detected in the control (CK) and AMF treatment, while only 3 were detected in the AMF + BC treatment. Molecular ecological network analysis showed that the AMF + BC treatment group had a more complex network of fungal communities, as evidenced by higher average connectivity. The functional composition spectrum showed significant differences in the functional distribution of soil microbial communities among different fungal genera. The structural equation model (SEM) confirmed that AMF could improve the microbial multifunctionality by regulating the rhizosphere fungal diversity and soil properties. Our findings provide new information on the effects of AMF and biochar on plants and soil microbial communities.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.17
• /
• pp.7935-7941
• /
• 2015

The aim of this study was to implement massive parallel sequencing (MPS) technology in clinical genetics testing. We developed and tested an amplicon-based method for resequencing the BRCA1 and BRCA2 genes on an Illumina MiSeq to identify disease-causing mutations in patients with hereditary breast or ovarian cancer (HBOC). The coding regions of BRCA1 and BRCA2 were resequenced in 96 HBOC patient DNA samples obtained from different sample types: peripheral blood leukocytes, whole blood drops dried on paper, and buccal wash epithelia. A total of 16 random DNA samples were characterized using standard Sanger sequencing and applied to optimize the variant calling process and evaluate the accuracy of the MPS-method. The best bioinformatics workflow included the filtration of variants using GATK with the following cut-offs: variant frequency >14%, coverage ($>25{\times}$) and presence in both the forward and reverse reads. The MPS method had 100% sensitivity and 94.4% specificity. Similar accuracy levels were achieved for DNA obtained from the different sample types. The workflow presented herein requires low amounts of DNA samples (170 ng) and is cost-effective due to the elimination of DNA and PCR product normalization steps.

• Genomics & Informatics
• /
• v.13 no.3
• /
• pp.81-85
• /
• 2015

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (${\sim}72{\times}coverage$) was sequenced with a $2{\times}150bp$ paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.3
• /
• pp.524-534
• /
• 2017

The development and utilization of crop straw biogas resources can effectively alleviate the shortage of energy, environmental pollution, and other issues. This study performed a continuous batch test at $35^{\circ}C$ to assess the methane production potential and volatile organic acid contents using the modified Gompertz equation. Illumina MiSeq platform sequencing, which is a sequencing method based on sequencing-by-synthesis, was used to compare the archaeal community diversity, and denaturing gradient gel electrophoresis (DGGE) was used to analyze the bacterial community diversity in rice straw, dry maize straw, silage maize straw, and tobacco straw. The results showed that cumulative gas production values for silage maize straw, rice straw, dry maize straw, and tobacco straw were 4,870, 4,032.5, 3,907.5, and $3,628.3ml/g{\cdot}VS$, respectively, after 24 days. Maximum daily gas production values of silage maize straw and rice straw were 1,025 and $904.17ml/g{\cdot}VS$, respectively, followed by tobacco straw and dry maize straw. The methane content of all four kinds of straws was > 60%, particularly that of silage maize straw, which peaked at 67.3%. Biogas production from the four kinds of straw was in the order silage maize straw > rice straw > dry maize straw > tobacco straw, and the values were 1,166.7, 1,048.4, 890, and $637.4ml/g{\cdot}VS$, respectively. The microbial community analysis showed that metabolism was mainly carried out by acetate-utilizing methanogens, and that Methanosarcina was the dominant archaeal genus in the four kinds of straw, and the DGGE bands belonged to the phyla Firmicutes, Bacteroidetes, and Chloroflexi. Silage maize is useful for biogas production because it contains four kinds of straw.

• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.34.1-34.10
• /
• 2023

Nosocomial infections, commonly referred to as healthcare-associated infections, are illnesses that patients get while hospitalized and are typically either not yet manifest or may develop. One of the most prevalent nosocomial diseases in hospitalized patients is pneumonia, among the leading causes of mortality and morbidity. Viral, bacterial, and fungal pathogens cause pneumonia. More severe introductions commonly included Staphylococcus aureus, which is at the top of bacterial infections, per World Health Organization reports. The staphylococci, S. aureus, strain RMI-014804, mesophile, on-sporulating, and non-motile bacterium, was isolated from the sputum of a pulmonary patient in Pakistan. Many characteristics of S. aureus strain RMI-014804 have been revealed in this paper, with complete genome sequence and annotation. Our findings indicate that the genome is a single circular 2.82 Mbp long genome with 1,962 protein-coding genes, 15 rRNA, 49 tRNA, 62 pseudogenes, and a GC content of 28.76%. As a result of this genome sequencing analysis, researchers will fully understand the genetic and molecular basis of the virulence of the S. aureus bacteria, which could help prevent the spread of nosocomial infections like pneumonia. Genome analysis of this strain was necessary to identify the specific genes and molecular mechanisms that contribute to its pathogenicity, antibiotic resistance, and genetic diversity, allowing for a more in-depth investigation of its pathogenesis to develop new treatments and preventive measures against infections caused by this bacterium.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.37-37
• /
• 2018

The genus Crepidiastrum (Asteraceae), containing ca. 20 species, is mainly distributed in Asia. Crepidiastrum denticulatum, an edible plant that commonly call "e-go-deulppae-gi" in Korean, distributes in Korea, Japan, and China. The complete chloroplast (cp) genome sequences of C. denticulatum was characterized from MiSeq2000 (Illumina Co.) pair-end sequencing data. The cp genome of C. denticulatum has a total sequence length of 152,689 bp and show a typical quadripartite structure. It consists of the large single copy (LSC: 84,022 bp), small single copy (SSC: 18,519 bp), separated by a pair of inverted repeats (IRs: 25,074 bp) and contains 110 unique genes and 18 genes duplicated in the IR regions. Our comparative analysis identified three cpDNA regions (matK, rbcL, and psbA-trnH) from three Crepidiastrum species, which may be useful for molecular identification of each species, and providing a guideline for its clear confirming about dried medical herb.

• The Journal of Pediatrics of Korean Medicine
• /
• v.34 no.4
• /
• pp.43-58
• /
• 2020

Objectives The purpose of this study is to analyze the effect of various herbal medicin on gut microbiota. Methods Electronic searches were performed using NDSL, OASIS, KISS, KMBASE, K-portal, Pub med, Cochrane, CNKI. Results we analyzed 25 experimental studies on the effect of herbal medicine on microbiota. Diabetes, obesity, inflammatory bowel disease have been frequently studied in micobiota-related disease. The most common experimental animal model used in the studies C57BL/7 mouse. Among the studies wherein single herbal medication were used, Gynostemma pentaphyllum was most commonly studies, and different herbal medications were used in the studies wherein complex herbal medications were studied. Next generation sequencing was performed using Illumina MiSeq system, and gut microbiota analysis was performed using QIIME and Ribosomal Database Project (RDP). In most studies, the herbal medicines exerted regulatory effects on gut microbiota and improved the symptoms of the experimental groups. Conclusions This review provides basic data on the correlation between korean medicine and gut microbiota, as well as information for the development of korean medicine.