• International Journal of Industrial Entomology and Biomaterials
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• v.28 no.2
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• pp.39-50
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• 2014

In order to understand the diversity and genetic relationships of silkworm strains preserved in Korea, we genotyped 78 Bombyx mori strains (Bombycidae: Lepidoptera) originating from Japan, using eight polymorphic microsatellite loci. We obtained per-locus allele numbers ranging from 5 to 16 (with an average value of 9.1), per-locus observed heterozygosity ranging from 0.13 to 1.00, and per-locus polymorphic information content ranging from 0.36 to 0.77, indicating that some loci are highly variable. Phylogenetic analysis with the eight concatenated microsatellite loci showed no clustering based on known strain characteristics and origin. Nineteen strain-specific apomorphic alleles, which discriminated 16 of the 78 silkworm strains, were obtained from eight loci. These strain-specific alleles can thus be utilized for routine discrimination of strains from Japan, without any further typing of other loci. Homozygotes were also observed at some loci (27 of 118 genotypes), which can also be used to discriminate several strains by typing a few loci. These results showed that eight microsatellite loci described herein were sufficiently variable to discriminate among the 78 silkworm strains we examined, and may be useful for future investigations of this economically important species.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.280-282
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• 2019

We present here a draft genome sequence of Bifidobacterium dentium strain ATCC 15424, originally isolated from pleural fluid of an empyema patient. The genome is 2,625,535 bp in length and has a GC content of 58.5%. The genome includes 2,154 protein-coding genes, 4 rRNAs, and 55 tRNAs. Unlike other B. dentium strains isolated from human dental caries, ATCC 15424 carries 247 strain-specific genes, including prophage remnants and type III/IV secretion system proteins, N-acetylmuramoyl-L-alanine amidase, and PRTRC system protein E. The sequence information will contribute to understanding of the natural variation of B. dentium as well as the genome diversity within the bacterial species.

• Genomics & Informatics
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• v.21 no.3
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• pp.34.1-34.10
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• 2023

Nosocomial infections, commonly referred to as healthcare-associated infections, are illnesses that patients get while hospitalized and are typically either not yet manifest or may develop. One of the most prevalent nosocomial diseases in hospitalized patients is pneumonia, among the leading causes of mortality and morbidity. Viral, bacterial, and fungal pathogens cause pneumonia. More severe introductions commonly included Staphylococcus aureus, which is at the top of bacterial infections, per World Health Organization reports. The staphylococci, S. aureus, strain RMI-014804, mesophile, on-sporulating, and non-motile bacterium, was isolated from the sputum of a pulmonary patient in Pakistan. Many characteristics of S. aureus strain RMI-014804 have been revealed in this paper, with complete genome sequence and annotation. Our findings indicate that the genome is a single circular 2.82 Mbp long genome with 1,962 protein-coding genes, 15 rRNA, 49 tRNA, 62 pseudogenes, and a GC content of 28.76%. As a result of this genome sequencing analysis, researchers will fully understand the genetic and molecular basis of the virulence of the S. aureus bacteria, which could help prevent the spread of nosocomial infections like pneumonia. Genome analysis of this strain was necessary to identify the specific genes and molecular mechanisms that contribute to its pathogenicity, antibiotic resistance, and genetic diversity, allowing for a more in-depth investigation of its pathogenesis to develop new treatments and preventive measures against infections caused by this bacterium.

• The Plant Pathology Journal
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• v.24 no.3
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• pp.357-360
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• 2008

Several pathotypes have been recognized in citrus bacterial canker, which causing serious damage in citrus cultivation area. To control the disease, it is important to understand the pathological diversity and reason of difference in virulence of the causal pathogen. We analyzed 124 strains of Xanthomonas causing citrus bacterial canker by southern hybridization with an internal 3.4-kb BamHI fragment from pthA gene. Assuming each band represented an intact gene, each strain of Xanthomonas was estimated to have approximately 1 to 4 copies of pthA gene. X. a. pv. citri A type had more than 3 copies of pthA gene, and the number of pthA gene in X. a. pv. citri $A^*,\;A^w$, and X. a. pv. aurantifolii B, C were different from 1 to 3 according to the strains. When the pthA gene profile was classified into 13 groups according to the number and size of hybridization bands, most of the A types belong to the 3A group, and 4A and 4B type was dominant when they had 4 bands. However, there was no general pattern of difference between the virulence and pthA gene group in this test.

• Korean Journal of Microbiology
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• v.40 no.4
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• pp.302-306
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• 2004

A total of forty strains of pigment-producing halophilic bacteria were isolated from the solar saltern and coastal seawater in Korea. The diversity of those bacteria were determined on the basis of PCR-RFLP and 16S rDNA sequences. The isolated strains were clssified into nine genera: Pseudoalteromonas, Photobacterium, Vibrio, Halobacillus, Bacillus, Paracoccus, Salinicoccus, Tenacilbaculum, and Flavobacterium. While more than $80\%$ of the pigment-producing halophilic bacteria isolated from the coastal seawater were classified as gram-negative Pseudolateromonas, most of the strains isolated from the solar saltern were classified into gram-positive Halo­bacillus. The other strain was KK7, which may be identified as novel species belonging to the genus, Salini­coccus.

• Journal of Microbiology
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• v.42 no.2
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• pp.87-93
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• 2004

Twelve mecoprop-degrading bacteria were isolated from soil samples, and their genetic and phenotypic characteristics were investigated. Analysis of 16S rDNA sequences indicated that the isolates were related to members of the genus Sphingomonas. Ten different chromosomal DNA patterns were obtained by polymerase-chain-reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences from the 12 isolates. The isolates were found to be able to utilize the chiral herbicide meco-prop as a sole source of carbon and energy. While seven of the isolates were able to degrade both (R)-and (S)-mecoprop, four isolates exhibited enantioselective degradation of the (S)-type and one isolate could degrade only the (R)-enantiomer. All of the isolates were observed to possess plasmid DNAs. When certain plasmids were removed from isolates MPll, MP15, and MP23, those strains could no longer degrade mecoprop. This compelling result suggests that plasmid DNAs, in this case, conferred the ability to degrade the herbicide. The isolates MP13, MP15, and MP24 were identified as the same strain; however, they exhibited different plasmid profiles. This indicates that these isolates acquired dif-ferent mecoprop-degradative plasmids in different soils through natural gene transfer.

• The Korean Journal of Mycology
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• v.49 no.4
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• pp.497-505
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• 2021

Endophytic fungal strains were isolated from leaves, stems, and roots of Angelica gigas. The fungal strains were identified based on their morphological characteristics and molecular analysis of the internal transcribed spacer (ITS). A total 35 species of endophytic fungi were identified. The diversity between the endophytic fungal communities differed depending on the tissues of A. gigas. The isolated endophytic fungi were screened for antifungal activity against a pathogenic fungus, Phoma sp. Y11, using a dual culture method. Fourteen species of endophytic fungi showed the standout inhibition effect against the Y11 strain. The results suggest that the endophytic fungi isolated from A. gigas could be used as a biological control agent against leaf spot disease of A. gigas.

• Mycobiology
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• v.40 no.2
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• pp.138-141
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• 2012

We measured physiological functionalities, including antihypertensive angiotensin I-converting enzyme inhibitory activity and immun-stimulating ${\beta}$-glucan content for sixty kinds of Makgeolli that is commercially available from the market. As a result, we selected R-12 commercial raw Makgeolli, with a high content of immuno-stimulating ${\beta}$-glucan, and R-14 commercial raw Makgeolli, exhibiting high antihypertensive activity. Due to the similarities in their overall physicochemical properties and raw materials used for fermentation, we compared the microbial flora in order to investigate the reason for the differences in their functionalities. Nested PCR and denaturing gradient gel electrophoresis for yeasts and bacteria were performed for analysis of microbial diversity of two different kinds of Makgeolli (i.e., R-12, R-14), which showed immuno-stimulating ${\beta}$-glucan content and exhibited a very high level of antihypertensive activity, respectively. Analysis of the 18S rDNA amplicon revealed a major presence of the yeast strain Pichia burtonii in every Makgeolli sample. Analysis of the 16S rDNA amplicon revealed a predominance of lactic acid bacteria, and the most frequent lactic acid bacteria were Lactobacillus ingluviei, L. fermentum, and L. harbinensis, and Lactobacillus sp. Among these, L. harbinensis was detected only in R-12 and L. ingluviei was found only in R-14. Different functionalities from the individual commercially available Makgeolli may be attributed to actions of different microbial flora during fermentation.

• Journal of Microbiology and Biotechnology
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• v.21 no.10
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• pp.1001-1011
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• 2011

To explore bacterial diversity for elucidating genetic variability in acylhomoserine lactone (AHL) lactonase structure, we screened 800 bacterial strains. It revealed the presence of a quorum quenching (QQ) AHL-lactonase gene (aiiA) in 42 strains. These 42 strains were identified using rrs (16S rDNA) sequencing as Bacillus strains, predominantly B. cereus. An in silico restriction endonuclease (RE) digestion of 22 AHL lactonase gene (aiiA) sequences (from NCBI database) belonging to 9 different genera, along with 42 aiiA gene sequences from different Bacillus spp. (isolated here) with 14 type II REs, revealed distinct patterns of fragments (nucleotide length and order) with four REs; AluI, DpnII, RsaI, and Tru9I. Our study reflects on the biodiversity of aiiA among Bacillus species. Bacillus sp. strain MBG11 with polymorphism (115Alanine > Valine) may confer increased stability to AHL lactonase, and can be a potential candidate for heterologous expression and mass production. Microbes with ability to produce AHL-lactonases degrade quorum sensing signals such as AHL by opening of the lactone ring. The naturally occurring diversity of QQ molecules provides opportunities to use them for preventing bacterial infections, spoilage of food, and bioremediation.

• Parasites, Hosts and Diseases
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• v.53 no.3
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• pp.271-277
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• 2015

The genetic diversity of Schistosoma haematobium remains largely unstudied in comparison to that of Schistosoma mansoni. To characterize the extent of genetic diversity in S. haematobium among its definitive host (humans), we collected S. haematobium eggs from the urine of 73 infected schoolchildren at 5 primary schools in White Nile State, Sudan, and then performed a randomly amplified polymorphic DNA marker ITS2 by PCR-RFLP analysis. Among 73 S. haematobium egg-positive cases, 13 were selected based on the presence of the S. haematobium satellite markers A4 and B2 in their genomic DNA, and used for RFLP analysis. The 13 samples were subjected to an RFLP analysis of the S. haematobium ITS2 region; however, there was no variation in size among the fragments. Compared to the ITS2 sequences obtained for S. haematobium from Kenya, the nucleotide sequences of the ITS2 regions of S. haematobium from 4 areas in Sudan were consistent with those from Kenya (> 99%). In this study, we demonstrate for the first time that most of the S. haematobium population in Sudan consists of a pan-African S. haematobium genotype; however, we also report the discovery of Kenyan strain inflow into White Nile, Sudan.