• Asian-Australasian Journal of Animal Sciences
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• v.30 no.1
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• pp.100-110
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• 2017

Objective: The gastrointestinal tract of sheep contain complex microbial communities that influence numerous aspects of the sheep's health and development. The objective of this study was to analyze the composition and diversity of the microbiota in the gastrointestinal tract sections (rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum) of sheep. Methods: This analysis was performed by 454 pyrosequencing using the V3-V6 region of the 16S rRNA genes. Samples were collected from five healthy, small tailed Han sheep aged 10 months, obtained at market. The bacterial composition of sheep gastrointestinal microbiota was investigated at the phylum, class, order, family, genus, and species levels. Results: The dominant bacterial phyla in the entire gastrointestinal sections were Firmicutes, Bacteroidetes, and Proteobacteria. In the stomach, the three most dominant genera in the sheep were Prevotella, unclassified Lachnospiraceae, and Butyrivibrio. In the small intestine, the three most dominant genera in the sheep were Escherichia, unclassified Lachnospiraceae, and Ruminococcus. In the large intestine, the three most dominant genera in the sheep were Ruminococcus, unclassified Ruminococcaceae, and Prevotella. R. flavefaciens, B. fibrisolvens, and S. ruminantium were three most dominant species in the sheep gastrointestinal tract. Principal Coordinates Analysis showed that the microbial communities from each gastrointestinal section could be separated into three groups according to similarity of community composition: stomach (rumen, reticulum, omasum, and abomasum), small intestine (duodenum, jejunum, and ileum), and large intestine (cecum, colon, and rectum). Conclusion: This is the first study to characterize the entire gastrointestinal microbiota in sheep by use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the gastrointestinal bacterial community of sheep.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.169-178
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• 2010

The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis. Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthrobacter koreensis and $\beta$-Proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic-contaminated soils. The majority of the As-resistant isolates were Gramnegative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. The PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using the Pearson product-moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. Although many isolates were genetically diverse, others were clonal in nature. Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.

• Journal of Microbiology and Biotechnology
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• v.30 no.8
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• pp.1195-1206
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• 2020

Beringraja pulchra, Cham-hong-eo in Korean, is a mottled skate which is belonging to the cartilaginous fish. Although this species is economically valuable in South Korea as an alkaline-fermented food, there are few microbial studies on such fermentation. Here, we analyzed microbial changes and pH before, during, and after fermentation and examined the effect of inoculation by a skin microbiota mixture on the skate fermentation (control vs. treatment). To analyze microbial community, the V4 regions of bacterial 16S rRNA genes from the skates were amplified, sequenced and analyzed. During the skate fermentation, pH and total number of marine bacteria increased in both groups, while microbial diversity decreased after fermentation. Pseudomonas, which was predominant in the initial skate, declined by fermentation (Day 0: 11.39 ± 5.52%; Day 20: 0.61 ± 0.9%), while the abundance of Pseudoalteromonas increased dramatically (Day 0: 1.42 ± 0.41%; Day 20: 64.92 ± 24.15%). From our co-occurrence analysis, the Pseudoalteromonas was positively correlated with Aerococcaceae (r = 0.638) and Moraxella (r = 0.474), which also increased with fermentation, and negatively correlated with Pseudomonas (r = -0.847) during fermentation. There are no critically significant differences between control and treatment. These results revealed that the alkaline fermentation of skates dramatically changed the microbiota, but the initial inoculation by a skin microbiota mixture didn't show critical changes in the final microbial community. Our results extended understanding of microbial interactions and provided the new insights of microbial changes during alkaline fermentation.

• Microbiology and Biotechnology Letters
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• v.46 no.2
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• pp.162-170
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• 2018

Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012-2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of "gold standard typing method era" for routine works in genome study is being set.

• Journal of Microbiology and Biotechnology
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• v.26 no.7
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• pp.1303-1310
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• 2016

Although many studies on the effects of genetically modified (GM) crops on soil microorganisms have been carried out over the past decades, they have provided contradictory information, even for the same GM crop, owing to the diversity of the soil environments in which they were conducted. This inconsistency in results suggests that the effects of GM crops on soil microorganisms should be considered from many aspects. In this study, we investigated the effects of the GM drought-tolerant rice MSRB2-Bar-8, which expresses the CaMSRB2 gene, on soil microorganisms based on the culture-dependent and culture-independent methods. To this end, rhizosphere soils of GM and non-GM (IM) rice were analyzed for soil chemistry, population densities of soil microorganisms, and microbial community structure (using pyrosequencing technology) at three growth stages (seedling, tillering, and maturity). There was no significant difference in the soil chemistry between GM and non-GM rice. The microbial densities of the GM soils were found to be within the range of those of the non-GM rice. In the pyrosequencing analyses, Proteobacteria and Chloroflexi were dominant at the seedling stage, while Chloroflexi showed dominance over Proteobacteria at the maturity stage in both the GM and non-GM soils. An UPGMA dendrogram showed that the soil microbial communities were clustered by growth stage. Taken together, the results from this study suggest that the effects of MSRB2-Bar-8 cultivation on soil microorganisms are not significant.

• Journal of Microbiology and Biotechnology
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• v.26 no.7
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• pp.1320-1332
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• 2016

Light hydrocarbons accumulated in subsurface soil by long-term microseepage could favor the anomalous growth of indigenous hydrocarbon-oxidizing microorganisms, which could be crucial indicators of underlying petroleum reservoirs. Here, Illumina MiSeq sequencing of the 16S rRNA gene was conducted to determine the bacterial community structures in soil samples collected from three typical oil and gas fields at different locations in China. Incubation with n-butane at the laboratory scale was performed to confirm the presence of "universal microbes" in light-hydrocarbon microseepage ecosystems. The results indicated significantly higher bacterial diversity in next-to-well samples compared with background samples at two of the three sites, which were notably different to oil-contaminated environments. Variation partitioning analysis showed that the bacterial community structures above the oil and gas fields at the scale of the present study were shaped mainly by environmental parameters, and geographic location was able to explain only 7.05% of the variation independently. The linear discriminant analysis effect size method revealed that the oil and gas fields significantly favored the growth of Mycobacterium, Flavobacterium, and Pseudomonas, as well as other related bacteria. The relative abundance of Mycobacterium and Pseudomonas increased notably after n-butane cultivation, which highlighted their potential as biomarkers of underlying oil deposits. This work contributes to a broader perspective on the bacterial community structures shaped by long-term light-hydrocarbon microseepage and proposes relatively universal indicators, providing an additional resource for the improvement of microbial prospecting of oil and gas.

• Korean Journal of Plant Taxonomy
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• v.42 no.4
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• pp.267-274
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• 2012

To understand morphological and genetic differentiation between Euphorbia esula and E. maackii we examined 12 morphological characters and 11 isozyme loci from 14 populations of two species. Species of E. esula complex (A = 1.63, P = 44.83, $H_e$ = 0.198) in Korea maintain nearly as high as the genetic diversity reported in East Asian E. jolkinii and E. fauriei while lower than those of E. ebracteolata and E. pekinensis in Korea. Although the ranges of most morphological character variation of the two species overlap, E. esula and E. maackii were well recognized by the combination of the morphological traits, and the result of UPGMA phenogram supports the two distinct species inhibited in Korea. However, isozyme data do not support the recognition of E. esula and E. maackii. The discordance between morphological and allozyme data should be explained by the recent divergence or gene flow via introgressive hybridization between two species.

• Mycobiology
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• v.43 no.1
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• pp.49-56
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• 2015

The present study is the first report on the isolation of Penicillium menonorum from rhizosphere soil in Korea and its identification based on morphological characteristics and internal transcribed spacer gene sequence. The fungal isolate was named KNU-3 and was found to exhibit plant growth-promoting (PGP) activity through indole acetic acid (IAA) and siderophore production, as well as P solubilization. KNU-3 produced 9.7 mg/L IAA and solubilized 408 mg of $Ca_3PO_4/L$, and inoculation with the isolate significantly (p < 0.05) increased the dry biomass of cucumber roots (57%) and shoots (52%). Chlorophyll, starch, protein, and P contents were increased by 16%, 45%, 22%, and 14%, respectively, compared to plants grown in uninoculated soil. The fungus also increased soil dehydrogenase (30%) and acid phosphatase (19%) activities. These results demonstrate that the isolate KNU-3 has potential PGP attributes, and therefore it can be considered as a new fungus to enhance soil fertility and promote plant growth. Moreover, the discovery of PGP ability and traits of this fungus will open new aspects of research and investigations. In this study, plant growth promotion by P. menonorum KNU-3 is reported for the first time in Korea after its original description.

• Journal of Species Research
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• v.6 no.2
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• pp.141-153
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• 2017

During an investigation of the biodiversity of bacterial species in Korea, we discovered many indigenous prokaryotic species. A total of 39 bacterial strains in the class Alphaproteobacteria were isolated from various environmental samples collected from marine organisms, sea water, fresh water, tap water, mud flats, activated sludge, mineral water, tidal flats, soil and decayed plants. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of robust phylogenetic clades with the most closely related species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that any of these 39 Alphaproteobacteria species have been described in Korea. Specifically, 18 species in 11 genera in the order Sphingomonadales, 11 species in 10 genera in the order Rhizobiales, two species in two genera in the order Caulobacterales, six species in six genera in the order Rhodobacterales and two species in two genera in the order Rhodospirillales were found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

• Journal of Species Research
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• v.6 no.2
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• pp.119-128
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• 2017

Within a comprehensive, widescale investigation of indigenous prokaryotic species in Korea, 29 bacterial strains in the phylum Bacteroidetes were isolated from diverse environmental habitats that included soil, plant roots, natural caves, tidal flats, freshwater from lakes, and seawater. Based on their high 16S rRNA gene sequence similarities (>99.1%) and the formation of robust phylogenetic clades with the closest type species, each strain likely belonged to an independent and predefined bacterial species. There are no publications or official reports of the isolation of these 29 species in Korea. Our study provides strong evidence that seven species in three genera in the order Cytophagales, 15 species in 13 genera in the order Flavobacteriales and seven species in five genera in the order Sphingobacteriales, all within the phylum Bacteriodetes, are new reports of bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.