• Journal of Interdisciplinary Genomics
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• v.3 no.2
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• pp.41-46
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• 2021

Inherited platelet function disorders (IPFDs) are a disease group of heterogeneous bleeding disorders associated with congenital defects of platelet functions. Normal platelets essential role for primary hemostasis by adhesion, activation, secretion of granules, aggregation, and procoagulant activity of platelets. The accurate diagnosis of IPFDs is challenging due to unavailability of important testing methods, including light transmission aggregometry and flow cytometry, in several medical centers in Korea. Among several IPFDs, Glanzmann thrombasthenia (GT) is a most representative IPFD and is relatively frequently found compare to the other types of rarer IPFDs. GT is an autosomal recessive disorder caused by mutations of ITGA2B or ITGB3. There are quantitative or qualitative defects of the GPIIb/IIIa complex in platelet, which is the binding receptor for fibrinogen, von Willbrand factor, and fibronectin in GT patients. Therefore, patients with GT have normal platelet count and normal platelet morphology, but they have severely decreased platelet aggregation. Thus, GT patients have a very severe hemorrhagic phenotypes that begins at a very early age and persists throughout life. In this article, the general contents about platelet functions and respective IPFDs, the overall contents of GT, and the current status of genetic diagnosis of GT in Korea will be reviewed.

• Genomics & Informatics
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• v.10 no.1
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• pp.33-39
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• 2012

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.

• Journal of Microbiology and Biotechnology
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• v.24 no.2
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• pp.133-143
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• 2014

The development of the gut is controlled and modulated by different interacting mechanisms, such as genetic endowment, intrinsic biological regulatory functions, environment influences and last but no least, the diet influence. In this work, we compared the fecal microbiota of breast-fed (BF), formula-fed (FF), and mixed-fed (MF) infants from Hebei Province, China. By using high-throughput 16S rDNA sequencing analyses, we found some differences in gut microbiota in the three groups. Firmicutes and Proteobacteria were the dominant bacteria at the phylum level in the three groups, where FF infants showed a significant depletion in Bacteroidetes (p < 0.001) and Actinobacteria (p < 0.05). Enterobacteriaceae was the dominant bacteria at the family level in the three groups, but FF infants showed higher Enterobacteriaceae enrichment than BF and MF infants (p < 0.05); the abundance of the Bifidobacteriaceae was only 8.16% in the feces of BF infants, but higher than in MF and FF infants (p < 0.05). The number of genera detected (abundance >0.01%) in BF, MF, and FF infants was only 15, 16, and 13, respectively. This study could provide more accurate and scientific data for the future study of infant intestinal flora.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.1
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• pp.78-84
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• 2017

Objective: The aim of this study was to examine shifts in the composition of the bacterial population in the intestinal tracts (ITs) of weaning piglets by antibiotic treatment using high-throughput sequencing. Methods: Sixty 28-d-old weaning piglets were randomly divided into two treatment groups. The Control group was treated with a basal diet without antibiotics. The Antibiotic group's basal diet contained colistin sulfate at a concentration of 20 g per ton and bacitracin zinc at a concentration of 40 g per ton. All of the pigs were fed for 28 days. Then, three pigs were killed, and the luminal contents of the jejunum, ileum, cecum, and colon were collected for DNA extraction and high-throughput sequencing. Results: The results showed that the average daily weight gain of the antibiotic group was significantly greater (p<0.05), and the incidence of diarrhea lower (p>0.05), than the control group. A total of 812,607 valid reads were generated. Thirty-eight operational taxonomic units (OTUs) that were found in all of the samples were defined as core OTUs. Twenty-one phyla were identified, and approximately 90% of the classifiable sequences belonged to the phylum Firmicutes. Forty-two classes were identified. Of the 232 genera identified, nine genera were identified as the core gut microbiome because they existed in all of the tracts. The proportion of the nine core bacteria varied at the different tract sites. A heat map was used to understand how the numbers of the abundant genera shifted between the two treatment groups. Conclusion: At different tract sites the relative abundance of gut microbiota was different. Antibiotics could cause shifts in the microorganism composition and affect the composition of gut microbiota in the different tracts of weaning piglets.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.995-1004
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• 2017

Culture-dependent methods, such as heterotrophic plate counting (HPC), are usually applied to evaluate the bacteriological quality of hemodialysis water. However, these methods cannot detect the uncultured or viable but non-culturable (VBNC) bacteria, both of which may be quantitatively predominant throughout the hemodialysis water treatment system. Therefore, propidium monoazide (PMA)-qPCR associated with HPC was used together to profile the distribution of the total viable bacteria in such a system. Moreover, high-throughput sequencing of 16S rRNA gene amplicons was utilized to analyze the microbial community structure and diversity. The HPC results indicated that the total bacterial counts conformed to the standards, yet the bacteria amounts were abruptly enhanced after carbon filter treatment. Nevertheless, the bacterial counts detected by PMA-qPCR, with the highest levels of $2.14{\times}10^7copies/100ml$ in softener water, were much higher than the corresponding HPC results, which demonstrated the occurrence of numerous uncultured or VBNC bacteria among the entire system before reverse osmosis (RO). In addition, the microbial community structure was very different and the diversity was enhanced after the carbon filter. Although the diversity was minimized after RO treatment, pathogens such as Escherichia could still be detected in the RO effluent. In general, both the amounts of bacteria and the complexity of microbial community in the hemodialysis water treatment system revealed by molecular approaches were much higher than by traditional method. These results suggested the higher health risk potential for hemodialysis patients from the up-to-standard water. The treatment process could also be optimized, based on the results of this study.

• Journal of odor and indoor environment
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• v.16 no.1
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• pp.54-63
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• 2017

The Automobile HVAC system is a habitat for odor-associated fungal communities. We investigated the odor-associated fungal community in an automobile HVAC system using a high-throughput DNA sequencing method. The fungal community structure was evaluated via metagenome analysis. At the phylum level, Ascomycota and Basidiomycota were detected, accounting for 43.41% and 56.49% of the fungal community in the HVAC system, respectively. Columnosphaeria (8.31%), Didymella (5.60%), Davidiella (5.50%), Microxyphium (4.24%), unclassified Pleosporales (2.90%), and Cladosporium (2.79%) were abundant at phylum of Ascomycota and Christiansenia (36.72%), Rhodotorula (10.48%), and Sporidiobolus (2.34%) were abundant at phylum of Basidiomycota. A total of 22 genera of fungi were isolated and identified from the evaporators of the HVAC systems which support fungal growth and biofilm formation. Among them, Cladosporium, Penicillium, Aspergillus, and Alternaria are the most representative odor-associated fungi in HVAC systems. They were reported to form biofilm on the surface of HVAC systems with other bacteria by hypha. In addition, they produce various mVOCs such as 3-methyl-1-butanol, acetic acid, butanoic acid, and methyl isobutyl ketone. Our findings may be useful for extending the understanding of odor-associated fungal communities in automobile HVAC systems.

• Animal Bioscience
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• v.35 no.8
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• pp.1162-1173
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• 2022

Objective: This study aimed to investigate the fermentation profiles, bacterial community and predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) during ensiling. Methods: First-cutting Sudangrass was harvested at the vegetative stage and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30, and 60 days of ensiling, respectively. The bacterial communities on day 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional profiles were analyzed according to the Kyoto encyclopedia of genes and genomes using Tax4Fun. Results: The Sudangrass silages showed good fermentation quality, indicated by higher lactic acid contents, and lower pH, butyric acid and ammonia nitrogen contents. The dominant genus Lactococcus on day 3 was replaced by Lactobacillus on day 60. The metabolism of amino acid, energy, cofactors and vitamins was restricted, and metabolism of nucleotide and carbohydrate was promoted after ensiling. The 1-phosphofructokinase and pyruvate kinase of bacterial community seemed to play important roles in stimulating the lactic acid fermentation, and the promotion of arginine deiminase could help lactic acid bacteria to tolerate the acidic environment. Conclusion: High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of Sudangrass ensiling not only for distinct bacterial community but also for specific functional metabolites. The results could provide a comprehensive insight into bacterial community and metabolic characteristics to further improve the silage quality.

• Journal of Environmental Science International
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• v.31 no.12
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• pp.1051-1059
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• 2022

This study investigated microbial communities and their diversity in a full-scale mesophilic anaerobic digester treating sewage sludge. Influent sewage sludge and anaerobic digester samples collected from a wastewater treatment plant in Busan were analyzed using high-throughput sequencing. It was found that the microbial community structure and diversity in the anaerobic digester could be affected by inoculation effect with influent sewage sludge. Nevertheless, distinct microbial communities were identified as the dominant microbial communities in the anaerobic digester. Twelve genera were identified as abundant bacterial communities, which included several groups of syntrophic bacteria communities, such as Candidatus Cloacimonas, Cloacimonadaceae W5, Smithella, which are (potential) syntrophic-propionate-oxidizing bacteria and Mesotoga and Thermovigra, which are (potential) syntrophic-acetate-oxidizing bacteria. Lentimicrobium, the most abundant genus in the anaerobic digester, may contribute to the decomposition of carbohydrates and the production of volatile fatty acids during the anaerobic digestion of sewage sludge. Of the methanogens identified, Methanollinea, Candidatus Methanofastidiosum, Methanospirillum, and Methanoculleus were the dominant hydrogenotrophic methanogens, and Methanosaeta was the dominant aceticlastic methanogens. The findings may be used as a reference for developing microbial indicators to evaluate the process stability and process efficiency of the anaerobic digestion of sewage sludge.

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

• Research in Plant Disease
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• v.30 no.2
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• pp.157-164
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• 2024

Jack bean (Canavalia ensiformis) is one of healthy products for fermented or functional food in Korea and is widely distributed and cultivated worldwide. During August 2022, Jack bean plants showing symptoms of yellow flecks, chlorosis, necrotic spots and mosaic were observed in Jangheung-gun, South Korea. By transmission electron microscopy, flexuous filamentous virus particles of approximately 750×13 nm in size were observed in the symptomatic leaf samples. The infection of a Korean isolate of clover yellow vein virus (ClYVV-Ce-JH) was confirmed using double antibody sandwich enzyme-linked sorbent assay, reverse transcription polymerase chain reaction and high-throughput sequencing. The complete genome sequence of ClYVV-Ce-JH consists of 9,549 nucleotides (nt) excluding the poly (A) tail and encodes 3,072 amino acids (aa), with an AUG start and UAG stop codon, containing one open reading frame that is typical of a potyvirus polyprotein. The polyprotein of ClYVV-Ce-JH was divided into ten proteins and each protein's cleavage sites were determined. The coat protein (CP) and polyprotein of ClYVV-Ce-JH were compared at the nt and aa levels with those of the previously reported 14 ClYVV isolates. ClYVV-Ce-JH shared 92.62% to 99.63% and 93.39% to 98.05% at the CP and polyprotein homology. To our knowledge, this is the first report of a Korean isolate of ClYVV from Jack bean plants and the complete genome sequence of a ClYVV Jack bean isolate in the world.