• Korean Journal of Microbiology
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• v.54 no.4
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• pp.428-435
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• 2018

In this study, we isolated and identified bacteria from freshwater and soil collected from Osang reservoir, to screen antimicrobial bacteria against various pathogenic bacteria. 38 strains were isolated and assigned to the class Proteobacteria (22 strains), Actinobacteria (7 strains), Bacteroidets (6 strains), and Firmicutes (3 strains) based on 16S rRNA gene sequence analysis. Among them, strain OS17 showed a good growth inhibition against 5 methicillin-resistant Staphylococcus aureus subsp. aureus strains and Bacillus cereus, Bacillus subtilis, Filobasidium neoformans. As a result of the 16S rRNA gene sequence analysis, strain OS17 show the high similarity with Burkholderia ambifaria $AMMD^T$, B. diffusa $AM747629^T$, B. tettitorii $LK023503^T$ 99.8%, 99.7%, 99.6%, respectively. We investigated cell growth and antimicrobial activity according to commercial culture medium, temperature, pH for culture optimization of strain OS17. Optimal conditions for growth and antimicrobial activity in strain OS17 were found to be: YPD medium, $35^{\circ}C$ and pH 6.5. When the strain was cultured in LB, NB, TSB, R2A media at $20^{\circ}C$ and $25^{\circ}C$, the antimicrobial activity did not show. Culture filtrate of strain OS17 showed antimicrobial activity against 5 MRSA strains, Bacillus cereus, Bacillus subtilis, and Filobasidium neoformans with inhibition zones from 2 to 8 mm. Optimal reaction time was 48 h in YPD medium, 100 rpm and 0.3 vvm in 2 L-scale fed-batch fermentation process for antimicrobial activity. Culture optimization of strain OS17 can be improved on antimicrobial activity. Therefore, the antimicrobial activity of Burkholderia sp. OS17 had potential as antibiotics for pathogens including MRSA.

• Animal Bioscience
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• v.35 no.11
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• pp.1808-1816
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• 2022

Objective: The study of Hanwoo (Korean native cattle) has mainly been focused on meat quality and productivity. Recently the field of microbiome research has increased dramatically. However, the information on the microbiome in Hanwoo is still insufficient, especially relationship between vagina and feces. Therefore, the purpose of this study is to examine the microbial community characteristics by analyzing the 16S rRNA sequencing data of Hanwoo vagina and feces, as well as to confirm the difference and correlation between vaginal and fecal microorganisms. As a result, the goal is to investigate if fecal microbiome can be used to predict vaginal microbiome. Methods: A total of 31 clinically healthy Hanwoo that delivered healthy calves more than once in Cheongju, South Korea were enrolled in this study. During the breeding season, we collected vaginal and fecal samples and sequenced the microbial 16S rRNA genes V3-V4 hypervariable regions from microbial DNA of samples. Results: The results revealed that the phylum-level microorganisms with the largest relative distribution were Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria in the vagina, and Firmicutes, Bacteroidetes, and Spirochaetes in the feces, respectively. In the analysis of alpha, beta diversity, and effect size measurements (LefSe), the results showed significant differences between the vaginal and fecal samples. We also identified the function of these differentially abundant microorganisms by functional annotation analyses. But there is no significant correlation between vaginal and fecal microbiome. Conclusion: There is a significant difference between vaginal and fecal microbiome, but no significant correlation. Therefore, it is difficult to interrelate vaginal microbiome as fecal microbiome in Hanwoo. In a further study, it will be necessary to identify the genetic relationship of the entire microorganism between vagina and feces through the whole metagenome sequencing analysis and meta-transcriptome analysis to figure out their relationship.

• Korean Journal of Environmental Agriculture
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• v.41 no.4
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• pp.335-343
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• 2022

BACKGROUND: Antibiotics used in animal husbandry for disease prevention and treatment have resulted in the rapid progression of antibiotic resistant bacteria which can be introduced into the environment through livestock feces/manure, disseminating antibiotic resistant genes (ARGs). In this study, fecal samples were collected from the livestock farms located in Jeju Island to investigate the relationship between microbial communities and ARGs. METHODS AND RESULTS: Illumina MiSeq sequencing was applied to characterize microbial communities within each fecal sample. Using quantitative PCR (qPCR), ten ARGs encoding tetracycline resistance (tetB, tetM), sulfonamide resistance (sul1, sul2), fluoroquinolone resistance (qnrD, qnrS), fluoroquinolone and aminoglycoside resistance (aac(6')-Ib), beta-lactam resistance (bla_TEM, bla_CTX-M), macrolide resistance (ermC), a class 1 integronsintegrase gene (intI1), and a class 2 integrons-integrase gene (intI2) were quantified. The results showed that Firmicutes and Bacteroidetes were dominant in human, cow, horse, and pig groups, while Firmicutes and Actinobacteria were dominant in chicken group. Among ARGs, tetM was detected with the highest number of copies, followed by sul1 and sul2. Most of the genera belonging to Firmicutes showed positive correlations with ARGs and integron genes. There were 97, 34, 31, 25, and 22 genera in chicken, cow, pig, human, and horse respectively which showed positive correlations with ARGs and integron genes. In network analysis, we identified diversity of microbial communities which correlated with ARGs and integron genes. CONCLUSION(S): In this study, antibiotic resistance patterns in human and livestock fecal samples were identified. The abundance of ARGs and integron genes detected in the samples were associated with the amount of antibiotics commonly used for human and livestocks. We found diverse microbial communities associated with antibiotics resistance genes in different hosts, suggesting that antibiotics resistance can disseminate across environments through various routes. Identifying the routes of ARG dissemination in the environment would be the first step to overcome the challenge of antibiotic resistance in the future.

• Journal of the Korea Organic Resources Recycling Association
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• v.27 no.4
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• pp.15-24
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• 2019

The study was compared for soil chemical and microbial properties as well as growth of the cherry tomato (Lycopersicon esculentum var. cerasiforme) plants environmentally friendly gown for 3 years and 5 years, which had been fertigated with homemade liquid fertilizer (LF) with indigenous microorganism as an additional fertilizer. Treatment included LF with indigenous microorganism for 3 years (3-year IM-LF) and for 5 years (5-year IM-LF), with an effective microorganism for 10 years (EM-LF), which had been applied with 1,000 times of dilution in the farmhouse. IM-LF and EM-LF materials had increased pH pattern for 16 weeks, in particular for increase of 1.2 for EM-LF. IM-LF material contained slightly higher EC but similar level of 0.2 dS/m to EM-LF. For a pot experiment in the greenhouse, IM-LF treatment increased root dry weight of the cherry tomato plants. In the farmhouse experiment, IM-LF treatment increased to 7.5 of soil pH and 8.4 dS/m of EC, indicating high salt accumulation. EM-LF treatment increased to 62 g/kg of soil OM, which would have affected concentrations of macro essential nutrients, including T-N in the soil. However, the optimum soil chemical levels for growth of cherry tomato plants were observed on the IM-LF plots. EM-LF treatment increased number of bacteria and actinobacteria in the soil. EM-LF treatment increased concentrations of macro essential nutrients in the plants, except for P, with similar nutrient concentrations observed between 3-year IM-LF and 5-year IM-LF-treated plants. Leaf SPAD and PS II levels decreased in the plants treated with 3-year IM-LF. EM-LF treatment increased leaf width and length, number of leaves, canopy area, plant height, and stem diameter in the mid-term stage of growth, which were not significantly different between the treatments. EM-LF treated-plants had two times higher leaf dry weight than those of values observed on the IM-LF plants, which was the opposite result observed on the number of fruit.

• Korean Journal of Environmental Agriculture
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• v.39 no.1
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• pp.1-9
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• 2020

BACKGROUND: The aim of this study was to investigate the soil chemical properties and soil bacterial community of the cropping system for Cnidium officinale Makino. METHODS AND RESULTS: The bacterial community was analyzed for the relative abundance and principal coordinated analysis (PCoA analysis) by using by Illumina Miseq sequencing. The correlation analysis between soil chemical properties and soil bacterial community were analyzed by Spearman's rank correlation and DISTLM analysis. Soil bacterial community (phylum and class) showed two distinct clusters consisting of cluster 1 (first cropping) and cluster 2 (continuous cropping) from 2 different cultivation methods of Cnidium officinale Makino. PCoA and DISTLM analyses showed that soil pH and Ca significantly affected soil bacterial community in cultivation area of Cnidium officinale Makino. In addition, Spearman's rank correlation showed significant correlation between relative abundance (Acidobacteria and Actinobacteria) and soil factors (soil pH and Ca). CONCLUSION: The results of this study were considered to be important for determining the correlation between soil properties and soil bacterial community of the cropping method for Cnidium officinale Makino. Furthermore, the results will be helpful to investigate the cause of continuous cropping injury of the Cnidium officinale Makino by examining the changes of soil properties and soil bacterial communities.

• Korean Journal of Organic Agriculture
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• v.27 no.4
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• pp.479-499
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• 2019

This study was conducted to investigate the responses of soil properties and microbial communities to different agricultural management and soil types, including organic management in Andisols (Org-A), organic management in Non-andisols (Org-NA), conventional management in Andisols (Con-A) and conventional management in Non-andisols (Con-NA) by using a pyrosequencing approach of 16S rRNA gene amplicon in Radish farms of volcanic ash soil in Jeju island. The results showed that agricultural management systems had a little influence on the soil chemical properties but had significant influence on microbial communities. In addition, soil types had significant influences on both the soil chemical properties and microbial communities. Organic farming increased the microbial density of bacteria and biomass C compared to conventional farming, regardless of soil types. Additionally, Org-NA had the highest dehydrogenase activity among treatments, whereas no difference was found between Org-A, Con-A and Con-NA and had the highest species richness (Chao 1) and diversity (Phyrogenetic diversity). Particularly, Chao 1 and Phyrogenetic diversity were increased in organic plots by 12% and 20%, compared with conventional plots, respectively. Also, regardless of agricultural management and soil types, Proteobacteria was the most abundant bacterial phylum, accounting for 21.9-25.9% of the bacterial 16S rRNAs. The relative abundance of putative copiotroph such as Firmicutes was highest in Org-NA plot by 21.0%, as follows Con-NA (13.1%), Con-A (6.7%) and Org-A (5.1%.), respectively and those of putative oligotrophs such as Acidobacteria and Planctomycetes were higher in Con-A than those in the other plots. Furthermore, LEfSe indicated that organic system enhanced the abundance of Fumicutes, while conventional system increased the abundance of Acidobacteria, especially in Non-andisols. Correlation analysis showed that total organic carbon (TOC) and nutrient levels (e.g. available P and exchangeable K) were significantly correlated to the structure of the microbial community and microbial activity. Overall, our results showed that the continuous organic farming systems without chemical materials, as well as the soil types made by long-term environmental factors might influence on soil properties and increase microbial abundances and diversity.