• Journal of Life Science
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• v.32 no.10
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• pp.803-811
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• 2022

Despite the importance of traditional Korean fermented foods, little is known about the microbial communities and diversity of fermented soy products. To gain insight into the unexplored microbial communities of both Doenjang (DJ) and Ganjang (GJ) that may contribute to the fermentation in Korean traditional foods, we carried out next-generation sequencing (NGS) based on the V3-V4 region of 16S rDNA gene analysis. The alpha diversity analysis results revealed that both the Shannon and Simpson diversity indices were significantly different between the two groups, whereas the richness indices, including ACE, CHAO, and Jackknife, were not significant. Firmicutes were the most dominant phylum in both groups, but several taxa were found to be more abundant in DJ than in GJ. The proportions of Bacillus, Kroppenstedtia, Clostridium, and Pseudomonas and most halophiles and halotolerant bacteria, such as Tetragenococcus, Chromohalobacter, Lentibacillus, and Psychrobacter, were lower in DJ than in GJ. Linear discriminant effect size (LEfSe) analysis was carried out to discover discriminative functional biomarkers. Biomarker discovery results showed that Bacillus and Tetragenococcus were identified as the most important features for the classification of subjects to DJ and GJ. Paired-permutational multivariate analysis of variance (PERMANOVA) further revealed that the bacterial community structure between the two groups was statistically different (p=0.001).

• Journal of Marine Life Science
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• v.7 no.1
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• pp.15-20
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• 2022

Glioblastoma is one of the highly aggressive central nervous system tumors and it is difficult to treat owing its anatomical location. Peptides are novel class of drugs which has the potential to cross the blood brain barrier and exerts its anti-tumor activity. Here, we discovered a novel peptide from abalone (Haliotis discus hannai) next generation sequencing (NGS) data and tested its anticancer effect on glioblastoma cell line SNU-489. The anticancer activity was measured using a cytotoxicity assay in a time and dose-dependent manner. A concentration and time dependent increase in the cytotoxicity was seen in cells treated with the novel peptide. The highest cytotoxicity rate of about 67% was observed in SNU-489 cells treated with 200 µM peptide for 48 hrs. However, the cytotoxic effect was not or less observed in a normal skin cell line HaCaT at similar concentration, thus, evident of peptide's cell specific anticancer activity. In addition, the gene expression level of necroptosis-related genes was analyzed by qRT-PCR to elucidate the anticancer mechanism of the novel peptide. RIPK3 expression was significantly increased by 9.6-fold in 200 µM of novel peptide treatment group, and MLKL expression level was significantly elevated by 2-fold in 100 µM treated group compared to the control group. Therefore, this study confirmed that the novel abalone-derived peptide has anticancer potency, and it causes cancer cell death through the necroptosis mechanism. Collectively, these results suggest that the novel peptide could be candidate anticancer agent for the treatment of glioblastoma in the future.

• Journal of Marine Life Science
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• v.6 no.2
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• pp.47-57
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• 2021

In the fishery industry, global aquaculture production has stagnated due to overfishing of aquatic products, restrictions between countries, and climate change. The aquaculture suggests the possibility of a blue revolution that can be expanded in a new way. The aquaculture industry now accounts for more than half of the fishery products from the sea as a raw material for seafood for human consumption. Various latest biological research methods are being applied for the development of a sustainable aquaculture industry. Genomics has made significant progress in recent years. Since the genome sequence of Atlantic cod was sequenced in 2011, the genomes of more species have been sequenced. The genome information is providing a more robust and productive knowledge base for the aquaculture industry, including breeding and breeding of superior traits, improving disease resistance quality, and optimizing aquaculture feed and feed methods. This review looked at the status of genome analysis technology and the current status of genome research of aquaculture species. The development of genome research technology and massive genomic information is important in solving the challenges of the aquaculture industry and will help sustainable fisheries and aquaculture.

• Journal of Dairy Science and Biotechnology
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• v.41 no.1
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• pp.9-25
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• 2023

Yogurt fermentation is known to be beneficial because it provides a low pH and harsh environment for foodborne pathogens and improves organoleptic properties. Additionally, organic acids produced through fermentation have a good effect on the viscosity and gelling properties of yogurt. Several potential health benefits of probiotic and generally recognized as safe strains have been suggested. Yogurt is the preferred vehicle for delivering probiotics to health-conscious consumers. Therefore, manufacturers of probiotic beverages must comply with the relevant regulations. The development of probiotic yogurt begins with the selection of strains with safety and functional properties of probiotics. The selected probiotic strain should be technically suitable for viability and improve organoleptic quality while maintaining the number of bacteria above the standard value during processing and storage conditions. In addition, the efficacy of probiotic strains contained in yogurt should be investigated, confirmed, and approved according to well-designed clinical trials. Although various methods are used to detect probiotic strains, the recently widely used next generation sequencing method can be actively utilized. In the future, more research should be conducted with the latest methods to identify probiotic functions and accurately detect probiotic strains.

• Journal of Life Science
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• v.33 no.1
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• pp.25-33
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• 2023

The fermentation process of kimchi, which is a traditional Korean food, influences the resulting compo- sition of microorganisms, such as the genera Leuconostoc, Weissella, and Lactobacillus. In addition, several factors, including the type of kimchi, fermentation conditions, materials, and ingredients, can influence the distribution of the kimchi microbial community. In this study, next-generation sequencing (NGS) of kimchi samples obtained from central (Gangwon-do and Gyeonggi-do) and southern (Jeolla-do and Gyeongsang-do) regions in Korea was performed, and the microbial communities in samples from the two regions were compared. Good's coverage prediction for all samples was higher than 99%, indicating that there was sufficient reliability for comparative analysis. However, in a α -diversity analysis, there was no significant difference in species richness and diversity between samples. The Firmicutes phylum was common in both regions. At the species level, Weissella kandleri dominated in central (46.5%) and southern (30.8%) regions. Linear discriminant analysis effect size (LEfSe) analysis was performed to identify biomarkers representing the microbial community in each region. The LEfSe results pointed to statistically significant differences between the two regions in community composition, with Leuconostocaceae (71.4%) dominating in the central region and Lactobacillaceae (61.0%) dominating in the southern region. Based on these results, it can be concluded that the microbial communities of kimchi are significantly influenced by regional properties and that it can provide more useful scientific data to study the relationship between regional characteristics of kimchi and their microbial distribution.

• Journal of Life Science
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• v.33 no.8
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• pp.623-631
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• 2023

This study was conducted to develop microsatellite markers in Parapristipoma trilineatum using next-generation sequencing. A total of 402,244,934 reads were generated on the Illumina Hiseq X Ten System, yielding 60,738,985,034 bp of sequences. The de novo assembly resulted in 1,320,995 contigs. A total of 952,326 contigs (0.016%) including 151 microsatellite loci were derived from the 1,320,995 contigs longer than 640 bp. A total of 34 primer sets were designed from the 151 microsatellite loci. As a result, 15 microsatellite loci were chosen and used for assuming population genetic parameters in the wild and farmed populations. The mean number of effective alleles was 12, ranging from 6 to 25. The observed heterozygosity (H_O) and the expected heterozygosity (H_E) ranged between 0.530 and 0.873, with an average of 0.750, and from 0.647 to 0.895, with an average of 0.793, respectively. According to these results, the developed set of 15 microsatellite markers is expected to be useful for the analysis of genetic characteristics in the population of P. trilineatum in Korea. There are requirements now for further genetic information, fishery resource management, breeding guidelines, support with the selection of breeds and studies on the effects of release, all of which will improve species conservation, and through future research, we aim to offer genetic foundational data with that goal.

• Korean Journal of Plant Resources
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• v.36 no.4
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• pp.290-298
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• 2023

Several members of the genus Broussonetia are woody plants with high-quality cellulose fibers and are used to make a traditional type of Korean paper known as Hanji. Three of these species, Broussonetia kazinoki, Broussonetia monoica, and Broussonetia papyrifera, are found in the Korean Peninsula. Because it is challenging to distinguish different Broussonetia species based on morphology alone, we have developed a set of insertion/deletion (InDel) markers for genetic identification of these species. From twenty-two Broussonetia samples collected throughout Korea, we selected six for next-generation sequencing analysis. InDel marker candidates were identified by comparing this sequence information with the B. kazinoki chloroplast genome sequence. The marker candidates were used to screen the genomes of the twenty-two Broussonetia plants, and five useful chloroplast-based InDel markers were identified. Detailed genotyping using these five markers showed that the twenty-two plants of the genus Broussonetia could be clustered into five groups, verifying that the markers developed here can be used for breeding, identification, and analysis of species in the genus Broussonetia.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.30-30
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• 2022

Philippines is the second world supplier of coconut by-products. As its first major genomics project, the Philippine Genome Center program for Agriculture (PGC-Agriculture) took the challenge to sequence and assemble the whole coconut genome. The project aims to provide advance genetics tools for our collaborating coconut researchers while taking the opportunity to initiate local capacity. Combination of different NGS platforms was explored and the Philippine 'Catigan Green Dwarf' (CATD) variety was selected with the breeders to be the crop's reference genome. A high quality genome assembly of CATD was generated and used to characterize important genes of coconut towards the development of resilient and outstanding varieties especially for added high-value traits. The talk will present the significant results of the project as published in various papers including the first report of whole genome sequence of a dwarf coconut variety. Updates will include the challenges hurdled and specific applications such as gene mining for host insect resistance and screening for least damaged coconuts (thus potentially insect resistant varieties). Genome-wide DNA markers as published and genes related to coconut oil qualitative/quantitative traits will also be presented, including initial molecular/biochemical studies that support nutritional and medicinal claims. A web-based genome database is currently built for ease access and wider utility of these genomics tools. Indeed, a major milestone accomplished by the coconut genomics research team, which was facilitated with the all-out government support and strong collaboration among multidisciplinary experts and partnership with advance research institutes.

• Journal of Marine Life Science
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• v.8 no.2
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• pp.93-103
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• 2023

eDNA, an abbreviation for environmental DNA, means DNA derived from organisms inhabiting in a specific environment. The utilization of eDNA extracted from environmental samples allows for efficient and accurate monitoring of organisms inhabiting the respective environment. Specifically, eDNA obtained from seawater samples can be used to analyze marine biodiversity. After collecting seawater samples and extracting eDNA, metagenome analysis enables the taxonomic and diversity analysis among marine organisms inhabiting the sampled area. This review proposed an overall process of marine biodiversity analysis by utilizing eDNA from seawater. Currently, the application of eDNA for analyzing marine biodiversity in domestic setting is not yet widespread. This review can contribute to establishment of marine eDNA research methods in Korea, providing valuable assistance in standardizing the use of eDNA in marine biodiversity studies.

• Fisheries and Aquatic Sciences
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• v.27 no.3
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• pp.180-194
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• 2024

Mass mortalities of mud crab Scylla spp. larvae due to pathogenic Vibrio spp. outbreaks have frequently occurred in hatcheries. To overcome this problem, probiotics containing Bacillus subtilis bacteria are applied to inhibit pathogenic ones. We tested different doses of probiotic-containing B. subtilis (10⁸ CFU/g) on the Scylla tranquebarica larvae and investigated the microbiota population, including Vibrio. Water quality, larvae development, and crablet production were also monitored. The recently hatched larvae were grown in twelve conical fiber tanks filled with 200 L sterile seawater, with a salinity of 30 ppt at a stocking density of 80 ind/L. Four different doses of probiotics were applied in the larvae rearing, namely, A = 2.5 mg/L, B = 5 mg/L, C = 7.5 mg/L, and D = 0 mg/L, with three replicates. Next-generation sequencing analysis was used to obtain the abundance of microbes in the whole body of megalopa and the water media for larvae rearing after applying probiotics. Sixteen Raw Deoxyribonucleic Acid samples (eight from a whole body of megalopa extraction from four treatments of probiotics defined as A, B, C, D, and eight from water media extraction from four treatments of probiotic defined as E, F, G, H) were prepared. Then, they were sent to the Genetics Science Laboratory for NGS analysis. Ammonia, nitrite, total organic matter (TOM), larvae, and crablet production were monitored. Based on the Next-generation sequencing analysis data, the Vibrio spp. decreased significantly (p < 0.05) than control test (D) in megalopa-applied probiotics at the doses of 2.5 mg/L (A) and 7.5 mg/L (C) and in the water media for megalopa rearing treated with probiotics at the dosage of 5.0 mg/L (F). Ammonia in the zoea stage in B treatment and TOM in the zoea and megalopa stage in B and C treatments were decreased significantly (p < 0.05). It impacts the higher number of zoea survival in treatments B and C. Finally, it results in a significantly high crablet production in treatments B and C. Therefore, the dosage of 5 mg/L to 7.5 mg/L improves crablet S. tranquebarica production significantly.