• Journal of Animal Science and Technology
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• v.65 no.1
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• pp.175-182
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• 2023

Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.

• Journal of Animal Science and Technology
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• v.65 no.1
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• pp.57-68
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• 2023

Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.

• Parasites, Hosts and Diseases
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• v.61 no.1
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• pp.42-52
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• 2023

The genus Babesia includes parasites that can induce human and animal babesiosis, which are common in tropical and subtropical regions of the world. The gut microbiota has not been examined in hamsters infected by Babesia duncani. Red blood cells infected with B. duncani were injected into hamsters through intraperitoneal route. To evaluate the changes in gut microbiota, DNAs were extracted from small intestinal contents, acquired from hamsters during disease development. Then, the V4 region of the 16S rRNA gene of bacteria was sequenced using the Illumina sequencing platform. Gut microbiota alternation and composition were assessed according to the sequencing data, which were clustered with >97.0% sequence similarity to create amplicon sequence variants (ASVs). Bacteroidetes and Firmicutes were made up of the major components of the gut microbiota in all samples. The abundance of Bacteroidetes elevated after B. duncani infection than the B. duncani-free group, while Firmicutes and Desulfobacterota declined. Alpha diversity analysis demonstrated that the shown ASVs were substantially decreased in the highest parasitemia group than B. duncani-free and lower parasitemia groups. Potential biomarkers were discovered by Linear discriminant analysis Effect Size (LEfSe) analysis, which demonstrated that several bacterial families (including Muribaculaceae, Desulfovibrionaceae, Oscillospiraceae, Helicobacteraceae, Clostridia UGG014, Desulfovibrionaceae, and Lachnospiraceae) were potential biomarkers in B. duncani-infected hamsters. This research demonstrated that B. duncani infectious can modify the gut microbiota of hamsters.

• Journal of Periodontal and Implant Science
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• v.53 no.1
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• pp.69-84
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• 2023

Purpose: The objective of this study was to analyze the microbial profile of individuals with peri-implantitis (PI) compared to those of periodontally healthy (PH) subjects and periodontitis (PT) subjects using Illumina sequencing. Methods: Buccal, supragingival, and subgingival plaque samples were collected from 109 subjects (PH: 30, PT: 49, and PI: 30). The V3-V4 region of 16S rRNA was sequenced and analyzed to profile the plaque microbiota. Results: Microbial community diversity in the PI group was higher than in the other groups, and the 3 groups showed significantly separated clusters in the buccal samples. The PI group showed different patterns of relative abundance from those in the PH and PT groups depending on the sampling site at both genus and phylum levels. In all samples, some bacterial species presented considerably higher relative abundances in the PI group than in the PH and PT groups, including Anaerotignum lactatifermentans, Bacteroides vulgatus, Faecalibacterium prausnitzii, Olsenella uli, Parasutterella excrementihominis, Prevotella buccae, Pseudoramibacter alactolyticus, Treponema parvum, and Slackia exigua. Network analysis identified that several well-known periodontal pathogens and newly recognized bacteria were closely correlated with each other. Conclusions: The composition of the microbiota was considerably different in PI subjects compared to PH and PT subjects, and these results could shed light on the mechanisms involved in the development of PI.

• Animal Bioscience
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• v.36 no.9
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• pp.1453-1464
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• 2023

Objective: This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. Methods: The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. Results: A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. Conclusion: This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.192-192
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• 2022

Sweetpotato is rich in starch, which is converted to sugar during storage due to enzymatic hydrolysis. The sugar content of sweetpotato is a component related to taste and storability. In this study, the sugar content (fructose, glucose, maltose, sucrose and total sugar content) of 94 genotypes was evaluated and the GWAS (Genome-Wide Association Study) was conducted to search for candidate genes for sugar content. The fructose and glucose content were 0.2 ~ 8.8 and 0.2 ~ 9.4 g/100g, respectively. The maltose, sucrose and total sugar content were 0.2 ~ 9.1,3.2 - 30.0 and 7.9 ~ 40.2 g/100g, respectively. The fructose and glucose showed a positive correlation (0.98). The 94 genotypes were genotyped with genotyping-by-sequencing (GBS) and aligned against the reference genome sequences of sweetpotato. The GBS libraries from 94 genotypes were sequenced on an Illumina HiSeqXten system, and 1,339,892 SNPs (Single Nucleotide Polymorphism) were generated. Filtering for < 60% missing rate and > 0.05 minor allele frequency resulted in a total of 44,255 SNPs used in GWAS. The GAPIT (Genome Association and Prediction Integrated Tool) was used to conduct based on the mean of sugar content with a Bonferroni-corrected chromosome-wide significance threshold with a -logio(P) of 5.95. The significant SNPs were obtained with fructose (seven), glucose (six), maltose (four) and sucrose (nine). There were several genes related to sugar content around the significant SNPs such as sugar transport protein 8-like, probable galactose-1 -phosphate uridyltransferase-like and beta-amylase. These results will contribute to understanding of sugar content and conversion in sweetpotato.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.259-259
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• 2022

Soil salinity is a major factor that reduces crop yields. The amount of soil affected by salinity is about 83 million hectares (FAO 2000), which is increasing due to the effects of climate change. In soybean [Glycine max (L.) Merr.], nutritional properties such as protein, starch, and sucrose content together with biomass and yield tends to reduce due to excessive salt. As a result of QTL mapping using the 169 F_2:3 population from the KA-1285 (salt-tolerant) × Daepung (salt-sensitive) in a previous study, two major QTLs (Gm03_39796778 and Gm03_40600088) related to salt tolerance were found on chromosome 3. In this study, the CDS region of the Gmsalt3 gene was analyzed using the ABI 3730x1 DNA Analyzer (Macrogen, Korea). The sequence of Gmsalt3 gene in KA-1285 was compared with Williams 82.a4.vl and PI483463 (Glycine soja). Two transversions were found at exon6 in KA-1285 and PI483463. Currently, whole genome sequencing and variation analysis using the Illumine Novaseq 6000 machine (Illumina, USA) are in progress. The results of this study can provide useful molecular markers for the selection of salt-tolerant soybeans and can be used as basic data for future salt-tolerant gene research.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.261-261
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• 2022

Cowpea [Vigna unguiculata (L.) Walp] is one of the most important grain legumes that enhance soil fertility and is well-adapted to various abiotic stress. Also, it is cultivated worldwide as a tropical annual crop, and the semi-arid regions are known as the main cowpea-produced regions. However, accumulation of soil salinity induced by low rainfall in these regions is reducing crop yields and quality. In general, plants exposed to soil salinity cause an accumulation of high ion chloride, which leads to the degradation of root and leaf proteins. In this study, we identified candidate genes associated with salinity tolerance through an analysis of differentially expressed genes (DEGs) in four cowpea germplasms with contrasting salinity tolerance. A total of 553,776,035 short reads were obtained using the Illumina Novaseq 6000 platform for RNA-Seq, which were subsequently aligned to the reference genome of cowpea Vunguiculata v1.2. A total of9,806 DEGs were identified between NaCl treatment and control of four cowpea germplasms. Among these DEGs, functions related to salt stress such as calcium transporter and cytochrome-450 family were associated with salt stress. In GO analysis and KEGG analysis, these DEGs were enriched in terms such as the "phosphorylation", ''extracellular region", and "ion binding". These RNA-seq results will improve the understanding of the salt tolerance of cowpea and can be used as useful basic data for molecular breeding technology in the future.

• Animal Bioscience
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• v.36 no.11
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• pp.1727-1737
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• 2023

Objective: The poultry industry is a primary source of animal protein worldwide. The gut microbiota of poultry birds, such as chickens and ducks, is critical in maintaining their health, growth, and productivity. This study aimed to identify longitudinal changes in the gut microbiota of laying hens from birth to the pre-laying stage. Methods: From a total of 80 Hy-Line Brown laying hens, birds were selected based on weight at equal intervals to collect feces (n = 20 per growth) and ileal contents (n = 10 per growth) for each growth stage (days 10, 21, 58, and 101). The V4 regions of the 16S rRNA gene were amplified after extracting DNA from feces and ileal contents. Amplicon sequencing was performed using Illumina, followed by analysis. Results: Microbial diversity increased with growth stages, regardless of sampling sites. Microbial community analysis indicated that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in the feces and ileal. The abundance of Lactobacillus was highest on day 10, and that of Escherichia-shigella was higher on day 21 than those at the other stages at the genus level (for the feces and ileal contents; p<0.05). Furthermore, Turicibacter was the most abundant genus after changing feed (for the feces and ileal contents; p<0.05). The fecal Ruminococcus torques and ileal Lysinibacillus were negatively correlated with the body weights of chickens (p<0.05). Conclusion: The gut microbiota of laying hens changes during the four growth stages, and interactions between microbiota and feed may be present. Our findings provide valuable data for understanding the gut microbiota of laying hens at various growth stages and future applied studies.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.08a
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• pp.61-61
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• 2020

본 연구는 우리나라 임상 중에서 침엽수림과 침활혼효림으로 구성된 산양삼 시험포지를 선정하고, 임상별 토양의 토양세균군집을 분석하여 산양삼 생육특성과의 상관관계 구명하고자 수행하였다. 산양삼 시험포지는 침염수림으로 구성된 충주 산양삼 종자공급단지와 침활혼효림으로 구성된 함양 산양삼 종자공급단지를 선정하여 각각 조성하였다. 토양세균군집 분석은 pyrosequencing analysis (Illumina platform)를 이용하였고, 토양세균군집과 생육특성 간의 상관관계는 Pearson's correlation을 이용하여 분석하였다. 임상별 시험포지의 토양세균은 두 시험포지 모두 Acidobacteria가 우점종으로 확인되었다. 주좌표 분석을 통해 임상별 산양삼 시험포지에서 우점하는 토양세균 군집을 확인한 결과, 먼저 토양세균 군집은 임상별 시험포지에 따라 군집화를 이루는 것으로 확인되었고, Pearson's 상관관계 분석 결과, 토양세균 군집의 상대적 빈도수는 수종 비율에 따라 상이한 상관관계를 보이는 것으로 확인되었다. 이 중에서 Proteobacteria, Alphaproteobacteria, Actinobacteria_class, Phycisphaerae는 침엽수의 비율과 유의적인 정의 상관관계를 보였고, Nitrospirae, Chlamydiae, Planctomycetia, Acidobacteria_6는 활엽수의 비율과 유의적인 정의 상관관계를 보이는 것으로 나타났다. 또한 임상별 산양삼 시험포지의 토양세균 군집과 산양삼 생육특성 간의 상관관계를 분석한 결과, Nitrospirae, Chlorobi, Planctomycetia, Acidobacteria_6가 산양삼의 생육과 유의적인 정의 상관관계를 보였다. 본 연구결과를 바탕으로 다양한 산림환경에서 토양세균군집과 산양삼 생육특성 간의 상관관계를 명확하게 구명할 수 있다면 향후 산양삼의 최적 재배지를 선정하는데 있어 도움을 줄 수 있을 것으로 사료된다.