• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVII)
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• pp.485-485
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• 2005

• The Plant Pathology Journal
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• 제38권1호
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• pp.52-52
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• 2022

• Journal of Microbiology and Biotechnology
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• 제18권10호
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• pp.1634-1640
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• 2008

This study was focused on the screening of valuable genetic resources, such as promoters from metagenome, and describes a promoter trapping system with a bidirectional probe concept, which can select promoters or operons from various biological resources including metagenomic DNA. A pair of reporters, GFP and DsRed, facing the opposite direction without promoters, is an effective system that can function regardless of the direction of inserted promoters. The feasibility of this system was tested for the isolation of constitutively expressed promoters in E. coli from a soil metagenome, resulting in a potential pool of various promoters for practical application. The analyses of structural organization of the trapped genes demonstrated that constitutively expressible promoters in E. coli were broadly distributed within the metagenome, and suggested that some promoters were useful for the construction of expression vectors. Based on these observations, three constitutive promoters were employed in the expression vector system and their potentials for practical application were evaluated in terms of expression level, protein solubility, and effects on host growth.

• Journal of Microbiology and Biotechnology
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• 제15권5호
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• pp.1067-1072
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• 2005

A metagenomic library was constructed using a fosmid vector, and total genomic DNA was extracted directly from soil at Cisolok (hot spring area, Indonesia). This library was composed of 10,214 clones and screened for lipolytic enzyme on tributyrin agar plates. An esterase gene (estMa) was subcloned and sequenced from a positive lipolytic active clone. Esterase EstMa was encoded by a 954-bp open reading frame and showed low ($11-33\%$) amino acid similarity to known esterases. The amino acid sequence analysis demonstrated that the enzyme is a new member of lipolytic enzyme family VI. The estMa gene encodes a preprotein of 317 amino acids with a predicted molecular mass of 34,799 Da. The purified enzyme exhibited optimal activity at $50^{\circ}C$ and pH 6.5. The $K_m,\;and\;V_{max}$ values of EstMa for the hydrolysis of p-nitrophenyl valerate were $45.3\;{\mu}M$ and 4.45 U/mg, respectively.

• Journal of Microbiology and Biotechnology
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• 제19권2호
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• pp.187-193
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• 2009

A metagenomic library of surface-water microbes from the Yangtze River in China was constructed, and a novel esterase, designated as EstY, was isolated and characterized. EstY had 423 amino acids with an estimated molecular mass of 44 kDa and pI of 7.28. It hydrolyzed various p-nitrophenyl esters(acetate, butyrate, caprate, caprylate, laurate, myristate, and palmitate) and its best substrate was p-nitrophenyl caprate(C8). The optimum pH for EstY activity was 9.0 and the optimum temperature was $50^{\circ}C$. Metal ions, such as $Mn^{2+},\;Co^{2+},\;Hg^{2+},\;Zn^{2+},\;and\;Fe^{3+}$, strongly inhibited the activity of EstY, whereas $Mg^{2+}$ was required for maximal activity. Activity remained in the presence of 10% alcohol, acetone, isopropanol, and dimethyl sulfoxide, respectively. An analysis of the amino acid sequence deduced from estY revealed that it had 7 closely related lipolytic enzymes. Moreover, a sequence analysis showed that EstY, like its 7 relatives, did not belong to any known lipolytic enzyme family.

• Journal of Microbiology and Biotechnology
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• 제24권4호
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• pp.447-452
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• 2014

To isolate novel and useful microbial enzymes from uncultured gastrointestinal microorganisms, a fecal microbial metagenomic library of the pygmy loris was constructed. The library was screened for amylolytic activity, and 8 of 50,000 recombinant clones showed amylolytic activity. Subcloning and sequence analysis of a positive clone led to the identification a novel gene (amyPL) coding for ${\alpha}$-amylase. AmyPL was expressed in Escherichia coli BL21 (DE3) and the purified AmyPL was enzymatically characterized. This study is the first to report the molecular and biochemical characterization of a novel ${\alpha}$-amylase from a gastrointestinal metagenomic library.

• Journal of Microbiology and Biotechnology
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• 제24권1호
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• pp.80-86
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• 2014

Tannase (Tan410) from a soil metagenomic library was immobilized on different supports, including mesoporous silica SBA-15, chitosan, calcium alginate, and amberlite IRC 50. Entrapment in calcium alginate beads was comparatively found to be the best method and was further characterized. The optimum pH of the immobilized Tan410 was shifted toward neutrality compared with the free enzyme (from pH 6.4 to pH 7.0). The optimum temperature was determined to be $45^{\circ}C$ for the immobilized enzyme and $30^{\circ}C$ for the free enzyme, respectively. The immobilized enzyme had no loss of activity after 10 cycles, and retained more than 90% of its original activity after storage for 30 days. After immobilization, the enzyme activity was only slightly affected by $Hg^{2+}$, which completely inhibited the activity of the free enzyme. The immobilized tannase was used to remove 80% of tannins from a green tea infusion on the first treatment. The beads were used for six successive runs resulting in overall hydrolysis of 56% of the tannins.

• Journal of Microbiology and Biotechnology
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• 제29권8호
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• pp.1255-1265
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• 2019

To investigate the diversity of gastrointestinal microflora and lignocellulose-degrading enzymes in wild Asian elephants, three of these animals living in the same group were selected for study from the Wild Elephant Valley in the Xishuangbanna Nature Reserve of Yunnan Province, China. Fresh fecal samples from the three wild Asian elephants were analyzed by metagenomic sequencing to study the diversity of their gastrointestinal microbes and cellulolytic enzymes. There were a high abundance of Firmicutes and a higher abundance of hemicellulose-degrading hydrolases than cellulose-degrading hydrolases in the wild Asian elephants. Furthermore, there were a high abundance and a rich diversity of carbohydrate active enzymes (CAZymes) obtained from the gene set annotation of the three samples, with the majority of them showing low identity with the CAZy database entry. About half of the CAZymes had no species source at the phylum or genus level. These indicated that the wild Asian elephants might possess greater ability to digest hemicellulose than cellulose to provide energy, and moreover, the gastrointestinal tracts of these pachyderms might be a potential source of novel efficient lignocellulose-degrading enzymes. Therefore, the exploitation and utilization of these enzyme resources could help us to alleviate the current energy crisis and ensure food security.

• 한국축산식품학회지
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• 제43권3호
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• pp.441-453
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• 2023

The objective of this study was to investigate the physicochemical and microbiological characteristics of round of Hanwoo by vacuum packaging film materials, polyvinylidene chloride (PVDC) and ethylene vinyl alcohol (EVOH). The packaged beef samples were stored in refrigerated conditions (2±1℃) for 12 weeks. Physicochemical analysis with pH, surface color, thiobarbituric acid reactive substances (TBARS) values, and volatile basic nitrogen (VBN) values and microbiological analysis with aerobic plate count (APC) and metagenomic analysis of packaged beef samples were performed. The pH and surface color did not change substantially during the 12 weeks and EVOH-packaged beef tended to be lower than those of PVDC-packaged beef. PVDC- and EVOH-packaged samples showed low TBARS and VBN values below standard limits. APC did not exceed 7 Log CFU/g for both samples during storage. In metagenomic analysis, Firmicutes and Lactobacillaceae were dominant phylum and family of the PVDC- and EVOH-packaged beef. In both packaged samples, Dellaglioa algida was the dominant species during storage, with the notable difference being the presence of Lactococcus piscium. Therefore, this study provided the information on the quality of vacuum-packaged beef according to different vacuum films for long-term refrigerated storage.

• Genomics & Informatics
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• 제21권4호
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• pp.49.1-49.11
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• 2023

Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for both platforms and further evaluated by using different taxonomic classifiers, reference databases, and assemblers. Normalized BGISEQ-500 sequences retained more reads and base counts after preprocessing, while a slightly higher fraction of HiSeq3000 sequences were taxonomically classified. Kaiju classified a higher percentage of reads relative to Kraken2 for both platforms, and comparison of reference database for taxonomic classification showed that MAR database outperformed RefSeq. Assembly using MEGAHIT produced longer assemblies and higher total contigs count in majority of HiSeq3000 samples than using metaSPAdes, but the assembly statistics notably improved with unprocessed or normalized reads. Our results indicate that both platforms perform comparably in terms of the percentage of taxonomically classified reads and assembled contig statistics for metagenomics samples. This study provides valuable insights for researchers in selecting an appropriate sequencing platform and bioinformatics pipeline for their metagenomics studies.