• Journal of Life Science
• /
• v.28 no.12
• /
• pp.1529-1535
• /
• 2018

The number of antibiotic-resistant bacteria is increasing rapidly while the discovery rate of new antibiotics is in decline. A systematic study is therefore necessary to investigate which bacteria are resistant to medically important antibiotics and how high that resistance is. To that end, this study aimed to analyze which bacteria demonstrated resistance to ampicillin, one of the currently most-widely used medical antibiotics. Water samples were collected from the Changwon-Cheon that runs through Changwon City and from the pond in front of the dormitory building at Changwon University. Hundreds of ampicillin-resistant colonies were obtained and 22 morphologically distinct examples were chosen for further study. These bacteria were identified by amplifying their 16S rRNA genes and comparing those sequences with data in GenBank. The bacteria was identified as belonging to 10 families, 12 genera, and 17 species, and all were able to grow in the presence of $50{\mu}g/ml$ ampicillin while seven showed growth at ampicillin concentrations as high as 1.5 mg/ml.

• Journal of Microbiology
• /
• v.44 no.4
• /
• pp.409-416
• /
• 2006

Clarithromycin resistance in Helicobacter pylori is a principal cause of failure of eradication therapies, and its prevalence varies geographically. The IceA gene is a virulence factor associated with clinical outcomes. The objective of this study was to determine the current state of clarithromycin resistance prevalence, and to investigate the role of iceA genotypes in 87 Turkish adult patients (65 with functional dyspepsia and 22 with duodenal ulcer). A2143G and A2144G point mutations were tested by PCR-RFLP for clarithromycin resistance. Among the patients in the study, 28 patients were tested by agar dilution as well. Allelic variants of the iceA gene were identified by PCR. A total of 24 (27.6%) strains evidenced one of the mutations, either A2143G or A2144G. IceA1 was found to be positive in 28 of the strains (32.2 %), iceA2 was positive in 12 (13.8 %) and, both iceA1 and iceA2 were positive in 22 (25.3 %) strains. In conclusion, we discovered no relationships between iceA genotypes and functional dyspepsia or duodenal ulcer, nor between clarithromycin resistance and iceA genotypes. clarithromycin resistance appears to be more prevalent in Turkish patients.

• The Plant Pathology Journal
• /
• v.25 no.3
• /
• pp.247-255
• /
• 2009

Root-knot nematode species, such as Meloidogyne hapla, M. incognita, M. arenaria, and M. javanica are the most economically notorious nematode pests, causing serious damage to a variety of crops throughout the world. In this study, DNA sequence analyses were performed on the D3 expansion segment of the 28S gene in the ribosomal DNA in an effort to characterize genetic variations in the three Meloidogyne species obtained from Korea and four species from the United States. Further, PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism), SCAR (Sequence Characterized Amplified Region) PCR and RAPD (Randomly Amplified Polymorphic DNA) were also utilized to develop methods for the accurate and rapid species identification of the root-knot nematode species. In the sequence analysis of the D3 expansion segment, only a few nucleotide sequence variations were detected among M. incognita, M. arenaria, and M, javanica, but not M. hapla. As a result of our haplotype analysis, haplotype 5 was shown to be common in M. arenaria, M. incognita, M. javanica, but not in the facultatively parthenogenetic species, M. hapla. PCR-RFLP analysis involving the amplification of the mitochondrial COII and large ribosomal RNA (lrRNA) regions yielded one distinct amplicon for M. hapla at 500 bp, thereby enabling us to distinguish M. hapla from M. incognita, M. arenaria, and M. javanica reproduced via obligate mitotic parthenogenesis. SCAR markers were used to successfully identify the four tested root-knot nematode species. Furthermore, newly attempted RAPD primers for some available root-knot nematodes also provided some species-specific amplification patterns that could also be used to distinguish among root-knot nematode species for quarantine purposes.

• Microbiology and Biotechnology Letters
• /
• v.39 no.2
• /
• pp.133-139
• /
• 2011

In this study, we determined the changes in microbial numbers in solar salts according to the manufacturing process and storage duration. The salt samples were harvested from salt farms in Shinan (area 2) and Yeonggwang (area 1). They were serially diluted ten-fold and then placed on 4 kinds of cultivable media (mannitol salt agar, eosin methylene blue, plate count agar, and trypticase soy agar). After incubation, we obtained 62 halophilic isolates from the salt samples. Coliform and general bacteria were not detected in all salt samples. By 16S rRNA sequencing analysis, we found 12 kinds of halophilic bacteria belonging to the genera Halobacillus, Halomonas, Bacillus, Idiomarina, Marinobacter, Pseudoalteromonas, Vibrio, Salinivibrio, Virgibacillus, Alteromonas, Staphylococcus and some un-known stains. In our study, we discovered two novel species that have a 16S rDNA sequence similarity below 97%.

• Korean Journal of Environmental Biology
• /
• v.29 no.3
• /
• pp.126-137
• /
• 2011

Although Sumunmulbangdui wetland at the Halla Mountain in Jeju Island, a kind of montane wetlands, has been considered to bear high biodiversity, no study has been reported on the bacterial diversity. In this study, soil and water samples were collected from the wetland in order to isolate novel bacterial species. Bacterial strains belonging to the phyla Bacteroidetes, Firmicutes, and Actinobacteria were isolated after spreading soil and water samples onto solid agar media. The 16S rRNA gene sequences of the strains assigned to the three phyla were compared to those of type strains of the species in the phyla. The strains that showed less than 98.7% 16S rRNA gene sequence similarity to the validly published species were considered to be novel species candidates. A total of 32 strains were regarded as novel species candidates in the phyla Bacteroidetes, Firmicutes, and Actinobacteria. Diversity of novel species candidates was very low; the candidates were confined to only few genera. In the Bacteroidetes, 13 novel candidate species were affiliated with the genera Mucilaginibacter, Sphingobacterium, Pedobacter, Flavobacterium, and Chryseobacterium. A total of 13 novel candidate species that assigned to the genera Paenibacillus Lysinibacillus, and Bacillus were identified in the phylum Firmicutes. Only two candidate species that belonged to the genera Mycobacterium and Nocardia were excavated in the Actinobacteria. Cultural, physiological, and chemotaxonomic characteristics have been determined for the novel species candidates, and the characteristics are described in this study.

• Journal of Naturopathy
• /
• v.7 no.2
• /
• pp.27-38
• /
• 2018

Purpose: The purpose of this study was to investigate whether intestinal proliferation is promoted in beneficial intestinal bacteria or decreased in harmful bacteria before and after ingesting Bacillus fermentation broth (ENM) for 8 weeks in the 16 subjects. Method: Intestinal bacteria were identified by PCR amplification using specific 16S rRNA primers. Results: The Bifidobacterium gene index(%)(gi%) increased to 58.92% in the control group and 69.53% in the test group after the ingestion of ENM, but there was no significant difference. Lactobacillus gi% increased significantly (49.37% in the control and 66.43% in the test) (p<.029). Clostridium gi% was significantly decreased after treatment (83.16% in the control and 67.76% in the test) (p<.077). Bacteroides gi% increased significantly (12.58% in the control and 20.87% in the test) after ingesting (p<.095). Prevotella gi% increased significantly (7.55% in the control and 17.28% in the test) after ingesting (p<.005). After ingesting, the median bacteria increased significantly in the control (20.06%) and the test (35.88%) (p<.001). Conclusions: After ingestion of the ENM, the number of beneficial bacteria increased and the number of harmful bacteria Clostridium tended to decrease. This suggests that ingestion of the Bacillus fermented beverage ENM has an effect on the proliferation of intestinal bacteria.

• Journal of Animal Science and Technology
• /
• v.66 no.2
• /
• pp.353-365
• /
• 2024

Rumen cannulation is a surgical technique used to collect rumen contents from ruminants. However, rumen cannulation surgery may potentially impact the composition of the rumen microbiota. This study aimed to examine the longitudinal alterations in the rumen microbiota composition of Hanwoo steers after cannulation surgery. In this study, eight Hanwoo steers were used; four steers underwent rumen cannulation surgery (cannulation group), while the remaining four were left intact (control group). Rumen samples were collected from all eight steers using the stomach tubing method on the day before surgery (day 0) and on postoperative days 1, 4, 7, 10, 14, 17, 21, 24, and 28, resulting in 80 samples (10 timepoints × 8 animals). The microbiota of all 80 samples were analyzed using 16S rRNA gene amplicon sequencing with Quantitative Insights into Microbial Ecology version 2 (QIIME2). There were no significant differences (p > 0.05) in all major phyla and most major genera representing at least 0.5% of total sequences across all 80 samples between the control and cannulation groups on the preoperative and postoperative days. However, while the alpha diversity indices did not differ (p > 0.05) between the two groups on the preoperative day, they significantly differed (p < 0.05) between the two groups on the postoperative days. Further, the overall microbial distribution based on both unweighted and weighted principal coordinate analysis plots significantly differed (p < 0.05) between the two groups on both the preoperative and postoperative days. Orthogonal polynomial contrasts indicated that major genera and microbial diversity in the cannulation group decreased following surgery but returned to their initial states by postoperative day 28. In conclusion, this study demonstrates that rumen cannulation surgery affects some major taxa and microbial diversity, suggesting that the rumen cannulation method can alter the composition of rumen microbiota in Hanwoo steers.

• ALGAE
• /
• v.28 no.2
• /
• pp.185-192
• /
• 2013

A new cold-adapted Arctic strain of Haematococcus pluvialis from Blomstrandhalv${\o}$ya Island (Svalbard) is described. This strain is predominantly always in non-motile palmelloid stage. Transmission electron microscopy showed the presence of very thick cell wall and abundant lipid vesicles in the palmelloids, including red and green cells. The external morphology of the non-motile palmelloid and motile bi-flagellated cells of our strain is similar to H. pluvialis; however it differs from H. pluvialis in physiology. Our strain is adapted to live and produce astaxanthin in the low temperature ($4-10^{\circ}C$), whilst the usual growth temperature for H. pluvialis is between $20-27^{\circ}C$. Phylogenetic analysis based on 18S rRNA gene data showed that our strain nested within the Haematococcus group, forming a sister relationship to H. lacustris and H. pluvialis, which are considered synonymous. Therefore, we identified our Arctic strain as H. pluvialis.

• Journal of Microbiology and Biotechnology
• /
• v.22 no.9
• /
• pp.1301-1306
• /
• 2012

We combined real-time RT-PCR and real-time PCR (R/P) assays using a hydrolysis probe to detect Mycobacterium tuberculosis complex (MTBC)-specific 16S rRNA and its rRNA gene (rDNA). The assay was applied to 28 non-respiratory and 207 respiratory specimens from 218 patients. Total nucleic acids (including RNA and DNA) were extracted from samples, and results were considered positive if the repeat RT-PCR threshold cycle was ${\leq}35$ and the ratio of real-time RT-PCR and real-time PCR load was ${\geq}1.51$. The results were compared with those from existing methods, including smear, culture, and real-time PCR. Following resolution of the discrepant results between R/P assay and culture, the overall sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV) of all samples (including non-respiratory and respiratory specimens) were 98.2%, 97.2%, 91.7%, and 99.4%, respectively, for R/P assay, and 83.9%, 89.9%, 72.3%, and 94.7%, respectively, for real-time PCR. Furthermore, the R/P assay of four patient samples showed a higher ratio before treatment than after several days of treatment. We conclude that the R/P assay is a rapid and accurate method for direct detection of MTBC, which can distinguish viable and nonviable MTBC, and thus may guide patient therapy and public health decisions.

• Korean Journal of Clinical Laboratory Science
• /
• v.51 no.3
• /
• pp.294-300
• /
• 2019

To investigate the inhibition effect on pathogenic microbes and the antimicrobial resistance of probiotics, a total of 140 probiotics were isolated from 35 kinds of Korean commercially available Kimchi. Of those, L. plantarum was identified from 53 strains (37.9%), E. faecium from 27 strains (19.3%), and L. rhamnosus from 7 strains (5.0%) using 16S rRNA gene sequencing. Sixty nine strains (49.3%) showed overall antimicrobial activity against pathogenic microbes, namely S. Typhi, S. Enteritidis, E. coli O157:H7, S. flexneri, NAG Vibrio, Listeria monocytogenesis, Y. enterocolitica, S. aureus, S. pyogenes, G. vaginalis, C. albicans, and P. acne. The proportions of L. plantarum, E. faecium, and L. rhamnosus strains to pathogenic microbes were 75.5%, 40.7%, and 28.6%, respectively. In addition, a resistance test with 18 antimicrobial agents using a disk diffusion assay revealed a resistance incidence of 98.6% for nalidixic acid, 83.6% for streptomycin, 75.7% for gentamicin 73.6% for vancomycin, 72.1% for norfloxacin, and 67.9% for ciprofloxacin. In conclusion, L. plantarum, L. sakei, and E. faecium strains with various antimicrobial activities and broad antibiotic resistance are useful for treating diarrhea in long-term inpatients and for the alternative use for treating Candida species female vaginitis.