• Asian-Australasian Journal of Animal Sciences
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• v.20 no.2
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• pp.283-294
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• 2007

Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.

• The Korean Journal of Mycology
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• v.51 no.4
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• pp.491-504
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• 2023

To explore fungal diversity in orchard soil where fire-blighted apple trees are buried, we collected soil samples from apple orchards in Chungju, Korea. Fungal isolates were obtained from DG18 agar and identified at the species level based on morphological features and phylogenetic analyses. The colony characteristics and microstructures were examined using a light microscope and a scanning electron microscope after culturing on potato dextrose agar (PDA), malt extract agar (MEA), Czapek yeast agar (CYA), and oatmeal agar (OA) The PCR-amplified products of the ITS1-5.8S-ITS2 region and 28S large subunit of the nuclear ribosomal RNA gene, as well as partial sequences of the β-tubulin, calmodulin, and translation elongation factor 1-α genes were sequenced and analyzed phylogenetically. Seven previously unknown fungal species were explored in Korea. All samples, including Aspergillus aureolatus, Botryotrichum atrogriseum, Dactylonectria novozelandica, Fusarium denticulatum, Paecilomyces tabacinus, Sarcopodium tibetense and Talaromyces stollii, had ascomycetes. Herein, we report their descriptions and features.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.4
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• pp.483-489
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• 2005

To understand the molecular mechanisms that regulate intramuscular fat deposition and its release, cDNA clones expressed in adipose tissues of Korean cattle were identified by differential screening from adipose tissue cDNA library. By partial nucleotide sequencing of 486 clones and a search for sequence similarity in NCBI nucleotide databases, 245 clones revealed unique clones. By a functional grouping of the clones, 14% of the clones were categorized to metabolism and enzyme-related group (stearoyl CoA desaturase, lactate dehydrogenase, fatty acid synthase, ATP citrate lyase, lipoprotein lipase, acetyl CoA synthetase, etc), and 6% to signal transduction/cell cycle-related group (C/EBP, cAMP-regulated phosphoprotein, calmodulin, cyclin G1, cyclin H, etc), and 4% to cytoskeleton and extracellular matrix components (vimentin, ankyrin 2, gelosin, syntenin, talin, prefoldin 5). The obtained 245 clones will be useful to study lipid metabolism and signal transduction pathway in adipose tissues and to study obesity in human. Some clones were subjected to full-sequencing containing open reading frame. The cDNA clone of bovine homolog of human prefoldin 5 gene had a total length of 959 nucleotides coding for 139 amino acids. Comparison of the deduced amino acid sequences of bovine prefoldin 5 with those of human and mouse showed over 95% identity. The cDNA clone of bovine homolog of human ubiquitin-like/S30 ribosomal fusion protein gene had a total length of 484 nucleotides coding for 133 amino acids. Comparison of the deduced amino acid sequences of bovine ubiquitin-like/S30 ribosomal fusion protein gene with those of human, rat and mouse showed over 97% identity. The cDNA clone of bovine homolog of human proteolipid protein 2 mRNA had a total length of 928 nucleotides coding for 152 amino acids. Comparison of the deduced amino acid sequences of bovine proteolipid protein 2 with those of human and mouse showed 87.5% similarity. The cDNA clone of bovine homolog of rat thymosin beta 4 had a total length of 602 nucleotides coding for 44 amino acids. Comparison of the deduced amino acid sequences of bovine thymosin beta 4 gene with those of human, mouse and rat showed 93.1% similarity. The cDNA clone of bovine homolog of human myotrophin mRNA had a total length of 790 nucleotides coding for 118 amino acids. Comparison of the deduced amino acid sequences of bovine myotrophin gene with those of human, mouse and rat showed 83.9% similarity. The functional role of these clones in adipose tissues needs to be established.

• Journal of Life Science
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• v.18 no.12
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• pp.1771-1774
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• 2008

Control microbial contamination in pathogens to soy sprouts has always been highly concerned in soybean sprout industries because the soybean sprouts are consumed largely as a nutritious fresh vegetable around the world. However, pathogens in soy sprouts are little known. Here, we isolated a strain of Pseudomonas sp. SN239 that caused severer symptoms in sprouts of many soybean cultivars. In phylogenetic relationships using 16S ribosomal RNA sequences of the Pseudomonas species, the identified Pseudomonas sp. SN239 was grouped with P. putita, P. plecoglossicida, P. monteilii and P. mevalonii. Thus, the bacterial strain SN239 might be a newly identified Pseudomonas species which closely related to P. putida. Furthermore, we found that a Korean indigenous soybean (Glycine max) cultivar YNPCSS3-19 has strong resistance against the Pseudomonas sp. SN239.

• Parasites, Hosts and Diseases
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• v.52 no.3
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• pp.299-304
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• 2014

This study aimed to identify the assemblages (or subassemblages) of Giardia duodenalis by using normal or nested PCR based on 4 genetic loci: glutamate dehydrogenase (gdh), triose phosphate isomerase (tpi), ${\beta}$-giardin (bg), and small subunit ribosomal DNA (18S rRNA) genes. For this work, a total of 216 dogs' fecal samples were collected in Guangdong, China. The phylogenetic trees were constructed with MEGA5.2 by using the neighbor-joining method. Results showed that 9.7% (21/216) samples were found to be positive; moreover, 10 samples were single infection (7 isolates assemblage A, 2 isolates assemblage C, and 1 isolate assemblage D) and 11 samples were mixed infections where assemblage A was predominant, which was potentially zoonotic. These findings showed that most of the dogs in Guangdong were infected or mixed-infected with assemblage A, and multi-locus sequence typing could be the best selection for the genotype analysis of dog-derived Giardia isolates.

• Parasites, Hosts and Diseases
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• v.41 no.4
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• pp.181-188
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• 2003

A new species of Acanthamoeba was isolated from a freshwater fish in Korea and tentatively named Acanthamoeba sp. YM-4 (Korean isolate YM-4). The trophozoites were $11.0-23.0{\;}{\mu\textrm{m}}$ in length and had hyaline filamentous projections. Cysts were similar to those of A. culbertsoni and A. royreba, which were previously designated as Acanthamoeba group III. Acanthamoeba YM-4 can survive at $40^{\circ}C$, and its generation time was 19.6 hr, which was longer than that of A. culbertsoni. In terms of the in vitro cytotoxicity of lysates, Acanthamoeba YM-4 was weaker than A. culbertsoni, but stronger than A. polyphaga. On the basis of the mortality of experimentally infected mice, Acanthamoeba YM-4 was found to be highly virulent. The isoenzymes profile of Acanthamoeba YM-4 was similar to that of A. royreba. An anti-Acanthamoeba YM-4 monoclonal antibody, McAY7, was found to react only with Acanthamoeba YM-4, and not with A. culbertsoni. Random amplified polymorphic DNA marker analysis and RFLP analysis of mitochondrial DNA and of 18S small subunit ribosomal RNA, placed Acanthamoeba YM-4 in a separate cluster on the basis of phylogenetic distances. Thus the Acanthamoeba Korean isolate YM-4 was identified as a new species, and assigned as Acanthamoeba sohi.

• Parasites, Hosts and Diseases
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• v.62 no.1
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• pp.139-144
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• 2024

Acanthamoeba infection is associated with keratitis in humans; however, its association with keratitis in dogs remains unclear. To investigate this possibility, we collected 171 conjunctival swab samples from dogs with eye-related diseases (65 with keratitis and 106 without keratitis) at Chungbuk National University Veterinary Teaching Hospital, Korea, from August 2021 to September 2022. Polymerase chain reaction identified 9 samples (5.3%) as Acanthamoeba positive; of these, 3 were from dogs with keratitis (4.6%) and 6 were from dogs without keratitis (5.7%). Our results indicated no significant association between Acanthamoeba infection and keratitis, season, sex, or age. All Acanthamoeba organisms found in this study had the genotype T4, according to 18S ribosomal RNA analysis. Acanthamoeba infection in dogs might have only a limited association with keratitis.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.69-73
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• 2019

During screening of microbes for compounds having cosmetic benefits, we isolated Marinobacter salarius HL2708#2 from lava seawater on Jeju Island, Republic of Korea. The complete genome sequence was determined. Strain HL27080#2 features a circular chromosome of 4,304,603 bp with 57.21% G+C content and a 244,163 bp plasmid with 53.14% G+C. There were 4,180 protein coding sequences identified, along with 49 transfer RNA and 18 ribosomal RNA noncoding genes. The genome harbored genes for the utilization of alcohol, maltose/starch, and monosaccharide as sole carbon sources. Genes responsible for halophilic characteristics and heavy metal resistance could be annotated, as well as aromatic and alkane hydrocarbons. Contrary to the prior report that M. salarius is negative for nitrate and nitrite reduction, nitrate/nitrite reductase along with nitrate/nitrate transporters and nitronate monooxygenase were evident, suggesting that strain HL2708#2 may be able to denitrify extracellular nitroalkenes to ammonia.

• Journal of Veterinary Clinics
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• v.31 no.3
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• pp.194-198
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• 2014

Methicillin-resistant staphylococci (MRS) are emerging as important pathogens in humans and animals worldwide. The aim of this study was to investigate the prevalence of MRS in the racehorse population and in horse-related personnel in Korea. A total of 195 horses and 18 humans (eight veterinarians, three veterinary hospital staff, and seven horse-handlers) from racehorse farms in Korea were included in the study. The samples were collected from nasal cavities using bacterial transport medium and were cultivated on tryptic soy agar with 5% sheep blood for 3 days at $37^{\circ}C$ to confirm the presence of Staphylococcus spp. Presumptive Staphylococcus spp. isolates were identified by 16S ribosomal RNA gene analysis. The coagulase test and oxacillin susceptibility tests were performed using the tube dilution and disk diffusion methods, respectively. The presence of the mecA gene was determined using a polymerase chain reaction assay. Of the 195 horses, 29 (15.6%) yielded 29 MRS isolates. Twelve (66.7%) of the 18 horse-related personnel yielded 12 MRS isolates. All of the MRS isolates from horses or horse-related personnel were identified as methicillin-resistant coagulase-negative staphylococci (MRCNS). The result of this study suggest that the prevalence of MRS increased with the duration of antibiotic use (p = 0.002). This study also provides evidence for the zoonotic transmission of MRCNS between horses and humans, although further investigations are needed.

• Parasites, Hosts and Diseases
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• v.53 no.1
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• pp.119-124
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• 2015

The objective of this study was to genetically characterize isolates of Giardia duodenalis and to determine if zoonotic potential of G. duodenalis could be found in stray cats from urban and suburban environments in Guangzhou, China. Among 102 fresh fecal samples of stray cats, 30 samples were collected in Baiyun district (urban) and 72 in Conghua district (suburban). G. duodenalis specimens were examined using light microscopy, then the positive specimens were subjected to PCR amplification and subsequent sequencing at 4 loci such as glutamate dehydrogenase (gdh), triose phosphate isomerase (tpi), ${\beta}$-giardin (bg), and small subunit ribosomal RNA (18S rRNA) genes. The phylogenetic trees were constructed using obtained sequences by MEGA5.2 software. Results show that 9.8% (10/102) feline fecal samples were found to be positive by microscopy, 10% (3/30) in Baiyun district and 9.7% (7/72) in Conghua district. Among the 10 positive samples, 9 were single infection (8 isolates, assemblage A; 1 isolate, assemblage F) and 1 sample was mixed infection with assemblages A and C. Based on tpi, gdh, and bg genes, all sequences of assemblage A showed complete homology with AI except for 1 isolate (CHC83). These findings not only confirmed the occurrence of G. duodenalis in stray cats, but also showed that zoonotic assemblage A was found for the first time in stray cats living in urban and suburban environments in China.