• Animal cells and systems
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• v.16 no.6
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• pp.488-497
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• 2012

A DNA barcode based on 648 bp of cytochrome c oxidase I (COI) gene aims to build species-specific libraries for animal groups. However, it is hard to recover full-length (648 bp) barcode gene from environmental fecal samples due to DNA degradation. In this study, we designed a new primer set (K_Bird), which amplifies a 226 bp fragment targeted an inner position of full-length COI barcode based on 102 species of Korean birds to improve amplification success, and we attempted to identify bird species from 39 avian fecal samples collected during 4 months from Jinan, South Korea. Simultaneously, we conducted a dietary analysis using a universal DNA mini-barcode (Uni_Minibar) from same fecal samples. In silico analysis on newly designed mini-barcode represented that genetic distances were 0.5% in species and 9.1% in genera. Intraspecific variations of 149 species out of 174 species (86%) between Korea and North America were within the threshold (5.3% threshold in this study). From environmental fecal samples collected in Jinan, we identified seven avian species, which have high similarity (99-100%) with registered COI sequences in GenBank. Eight kinds of prey species, such as moth, spider, fly, and dragonfly, were identified in dietary analysis. We suppose that our strategy applying mini-barcode for environmental fecal samples, might be a useful and convenient tool for species identification and dietary analysis for birds.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.812-822
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• 2014

Metagenomic analysis of the human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of the lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new long-range 16S rRNA universal PCR primer set targeting the V6 to V9 regions with a 580 bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for the highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.

• Journal of Veterinary Clinics
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• v.19 no.3
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• pp.295-298
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• 2002

This study was conducted to develope noninvasive fecal PCR assay for detecting the Helicobacter species in dogs. From the DNA isolated from fecal samples, and a region of the 16S rRNA gene conserved among Helicobacter spp. was amplified In comparison with gastric biopsy test, the fecal PCR assay showed high specificity(100%) and sensitivity(96%). The prevalence of Helicobacter spp. infection in privately owned pet dogs in Korea detemined by the fecal PCR assay was 72.1%. the fecal PCR assay determined in this study can a new noninvasive test detecting Helicobacter spp. infection in dogs.

• Korean Journal of Veterinary Research
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• v.54 no.1
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• pp.55-57
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• 2014

Paratuberculosis caused by Mycobacterium avium subsp. paratuberculosis (MAP) has extended latent periods of infection. Due to this property, difficulties in the detection of fecal shedder have been raised. A newly designed method for DNA extraction from fecal specimens, mGITC/SC was evaluated in terms of diagnostic efficiency. The detection limit of IS900 real-time PCR was about 50 MAP (1.5 cfu) in 250 mg of feces (6 cfu per g). Also, this DNA extraction method was faster and cheaper than that using commercial kit or other methods. Consequently, the mGITC/SC is an economical DNA extraction method that could be a useful tool for detecting MAP from fecal specimens.

• Journal of Microbiology and Biotechnology
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• v.15 no.2
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• pp.310-320
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• 2005

A membrane-based oligonucleotide array was used to detect predominant bacterial species in human fecal samples. Digoxygenin-labeled 16S rDNA probes were generated by PCR from DNA that had been extracted from fecal samples or slurries. These probes were hybridized to an array of 120 oligonucleotides with sequences specific for 40 different bacterial species commonly found in human feces, followed by color development using an alkaline phosphatase-conjugated antibody and NBT /BCIP. Twenty of the species were detected by this method, but E. coli, which was present at $\~$1 $\times 10$^5$ CFU per gram feces, was not detected. To improve the sensitivity of this assay, reverse transcriptase-PCR was used to generate probes from RNA extracted from fecal cultures. Coupled with a chemiluminescence detection method, this approach lowered the detection limit for E. coli from $\~1$ $\times 10$^6$ to ${\leq}$ 1 $\times 10$^5$ These results indicate that the membrane-array method with reverse transcriptase-PCR and chemiluminescence detection can simultaneously identify bacterial species present in fecal samples at cell concentrations as low as${\leq}$ 1 $\times 10$^5$ CFU per gram.

• Parasites, Hosts and Diseases
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• v.47 no.4
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• pp.417-420
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• 2009

Neospora caninum is an important cause of abortion in dairy cattle worldwide. Dog is the definitive host for N. caninum and can infect dairy cattle. The aim of this study is to determine the prevalence of Neospora oocysts in feces of dogs from dairy farms. A total of 174 fecal samples was collected from 89 farm dogs and 85 household dogs during 2006 and 2008. Fecal samples of dogs were microscopically examined for detecting Hammondia Neospora-like oocysts (HNLO) by Mini $Parasep^{(R)}SF$ fecal parasite concentrator. HNLO were microscopically detected in 4 fecal samples (2.2%). The fecal samples with HNLO were examined by N. caninum-specific PCR. Two of the samples were positive for N. caninum. The 2 positive fecal samples were selected for inoculation to calves. Two inoculated calves were seronegative by ELISA for 4 months post-infection. This is the first report of finding N. caninum DNA in feces of farm dogs in Mashhad area, Iran.

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.566-568
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• 2023

In this report, we present the whole-genome sequence of Bifidobacterium bifidum DS0908 isolated from the human fecal sample. The genome composed of a single circular chromosome is 2,223,317 bp long and the DNA G+C content is 62.65%. No virulence genes were detected in the genomic sequences of B. bifidum DS0908.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.5 no.3
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• pp.71-75
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• 2024

In this review, we compared the success rates of DNA amplification and introduced the efficient non-invasive sampling of fecal samples collected from captive and wild Korean long-tailed gorals (Naemorhedus caudatus) by referring to previous non-invasive studies, including three important references (Kim et al., 2008; Kim, 2021; Kim, 2022). A large difference in PCR success rates in the captive and wild populations was observed for mitochondrial (100 and 70.0%), sex-linked (44.4 and 20.8%), and microsatellite markers (73.9 and 34.8%, respectively). Out of the three types of genetic markers, the mitochondrial maker showed the highest success rate, followed by microsatellite and sex-linked markers. In addition, we estimated two factors that affected the PCR success, including the length of the amplified fragments (long, medium, and short) and the type of primer (universal and specific) in fecal samples from a captive population. The length of the PCR fragment was inversely proportional to the PCR success (5.3, 44.4, and 55.6% for long, medium, and short fragments, respectively), and the specific primer set (100%) was more efficient than the universal primer set (60.0%). This review is fundamental but would be greatly helpful for new non-invasive conservation genetic studies, particularly those that use fecal samples from captive and wild populations of rare endangered species. We recommend beginning conservation genetic experiments using mitochondrial markers and then nuclear markers, such as microsatellite and sex-linked markers, to save time, costs, and labor.

• Korean Journal of Veterinary Service
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• v.30 no.4
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• pp.505-510
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• 2007

This study was conducted to detect ${\beta}$-lactam antibiotic-resistant genes in the 400 E coli isolates from porcine fecal samples in Korea by a DNA chip. The DNA chip contains the specific probe DNAs of the ${\beta}$-lactam antibiotic-resistant genes that had been labeled with a mixture of primer set designed to amplify specific genes (PSE, OXA, FOX, MEN, CMY, TEM, SHV, OXY and AmpC) using a multiplex polymerase chain reaction (PCR). Of 400 isolates 339 contained at least one ${\beta}$-lactamases gene. Resistance to ${\beta}$-lactamases was mediated mainly by AmpC (n = 339, 100%), and followed by TEM (n = 200, 59.0%), CMY (n = 101, 29.8%), PSE (n = 30, 8.9%) and both OXA and SHV genes (n = 20, 5.9%), while the FOX, MEN and OXY genes were not detected. The other sixty-one did not contain any ${\beta}$-lactamase genes even though they were resistant to antimicrobial drugs. In conclusion, the DNA chip system can be used as a rapid and reliable method for detecting of ${\beta}$-lactamases genes, which will help veterinarians select the antibiotics for monitoring and treating of animal diseases.

• Journal of Applied Biological Chemistry
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• v.64 no.4
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• pp.399-405
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• 2021

A number of studies have been conducted to prevent obesity due to the worldwide increasing rate of obesity and its adverse effects on our health. Recently, a relationship between obesity and gut microbiome has been reported. Fecal and cecal microbiota are generally targeted for examining the gut microbiome during dietary interventions. There is, however, no common understanding on which microbiota and how results elucidated from the data would differ. In this study, we conducted dietary induced obesity study and compared fecal and cecal microbiota affected by dietary interventions. Normal Diet and high fat diet were fed to 6 weeks old mice for 12 weeks, and 16 S rRNA genes amplified from fecal and cecal DNA were sequenced using MiSeq. Our results show that the 𝛼-diversity showed significant differences between the dietary interventions as well as cecal and fecal microbiota. The difference in the taxonomic compositions between cecal and fecal microbiota had become clearer at the family and genus level. At the genus level, Faecalibaculum and Lactobacillus were more abundant in the cecal and fecal microbiota, respectively. In general dietary intervention studies, dietary effects are more significant than type difference. However, the microbiota analysis results should be interpreted carefully, considering both diet and samples (feces/caecum).