Journal of Microbiology

Research Support, Non-U.S. Gov'ts

Molecular Detection and Genotyping of Fusarium oxysporum f. sp. psidii Isolates from Different Agro-Ecological Regions of India: Rupesh Kumar Mishra , Brajesh Kumar Pandey , Vijai Singh , Amita John Mathew , Neelam Pathak , Mohammad Zeeshan; J. Microbiol. 2013;51(4):405-412. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2638-3

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Abstract: Twenty one isolates of Fusarium oxysporum f. sp. psidii (Fop), causing a vascular wilt in guava (Psidium guajava L.), were collected from different agro-ecological regions of India. The pathogenicity test was performed in guava seedlings, where the Fop isolates were found to be highly pathogenic. All 21 isolates were confirmed as F. oxysporum f. sp. psidii by a newly developed, species-specific primer against the conserved regions of 28S rDNA and the intergenic spacer region. RAPD and PCR-RFLP were used for genotyping the isolates to determine their genetic relationships. Fifteen RAPD primers were tested, of which five primers produced prominent, polymorphic, and reproducible bands. RAPD yielded an average of 6.5 polymorphic bands per primer, with the amplified DNA fragments ranging from 200–2,000 bp in size. A dendrogram constructed from these data indicated a 22–74% level of homology. In RFLP analysis, two major bands (350 and 220 bp) were commonly present in all isolates of F. oxysporum. These findings provide new insight for rapid, specific, and sensitive disease diagnosis. However, genotyping could be useful in strain-level discrimination of isolates from different agro-ecological regions of India.

Morphological and Genetic Characteristics of Newly Crossbred Cauliflower Mushroom (Sparassis latifolia): Hong-Duck Sou , Rhim Ryoo , Sung-Ryul Ryu , Kang-Hyeon Ka , Hyun Park , Sung-Hyun Joo; J. Microbiol. 2013;51(5):552-557. Published online June 25, 2013; DOI: https://doi.org/10.1007/s12275-013-2666-z

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Cauliflower mushroom (Sparassis latifolia or S. crispa) is popular for food and medicine. Importance of new varieties of Sparassis was raised and studied widely by protection system of UPOV. In this study, 10 crossbred strains of Sparassis latifolia that specifically expressed distinctive features during basidiocarp formation and mycelium growth were applied to sawdust medium inoculated with S. latifolia mycelia. The 10 crossbred strains were divided into 3 groups on the basis of morphological (size of marginal wave and basidiocarp color) and genetic characteristics. Each phenotype of the parent and crossbred strains represented 3 marginal wave-sizes (large, medium, and small) and 3 color notations (NN155D, 163C, and 8D). Our result suggests that morphological characteristics of cauliflower mushroom can be affected by various environmental and genetic stimuli under artificial conditions such as crossbreed. Also this research showed genetic differences among breeding isolates and their morphological characteristics were correlated with the molecular data within parent and crossed strain.

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Neuroprotective Effects of Sparassis crispa Ethanol Extract through the AKT/NRF2 and ERK/CREB Pathway in Mouse Hippocampal Cells
Malk Eun Pak, Wei Li
Journal of Fungi.2023; 9(9): 910. CrossRef
Breeding of a high-yield strain for commercial cultivation by crossing Pholiota adiposa
Chengbo Rong, Shuang Song, Li Yang, Xuejiao Pan, Yu Liu, Shouxian Wang
Ciência e Agrotecnologia.2021;[Epub] CrossRef
Elicitor-induced β-glucan contents in fruit body of cauliflower mushroom (Sparassis latifolia)
Rhim Ryoo, Hong-Duck Sou, Kang-Hyeon Ka, Hyun Park
Forest Science and Technology.2018; 14(3): 119. CrossRef
Development of a highly productive strain of Pleurotus tuoliensis for commercial cultivation by crossbreeding
Shouxian Wang, Shuang Zhao, Zhenxing Huang, Limin Yin, Jie Hu, Jianghong Li, Yu Liu, Chengbo Rong
Scientia Horticulturae.2018; 234: 110. CrossRef
Effects of Sparassis crispa in Medical Therapeutics: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Le Thi Nhu Ngoc, You-Kwan Oh, Young-Jong Lee, Young-Chul Lee
International Journal of Molecular Sciences.2018; 19(5): 1487. CrossRef
The mycelial growth and ligninolytic enzyme activity of cauliflower mushroom (Sparassis latifolia)
Hong-Duck Sou, Rhim Ryoo, Kang-Hyeon Ka, Hyun Park
Forest Science and Technology.2017; 13(4): 158. CrossRef

Genetic Diversity and Population Structure of Escherichia coli from Neighboring Small-Scale Dairy Farms: Jesús Andrei Rosales-Castillo , Ma. Soledad Vázquez-Garcidueñas , Hugo Álvarez-Hernández , Omar Chassin-Noria , Alba Irene Varela-Murillo , María Guadalupe Zavala-Páramo , Horacio Cano-Camacho , Gerardo Vázquez-Marrufo; J. Microbiol. 2011;49(5):693-702. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-0461-2

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Abstract: The genetic diversity and population structure of Escherichia coli isolates from small-scale dairy farms were used to assess the ability of E. coli to spread within the farm environment and between neighboring farms. A total of 164 E. coli isolates were obtained from bovine feces, bedding, cow teats and milk from 6 small-scale dairy farms. Ward’s clustering grouped the isolates into 54 different random amplified polymorphic DNA (RAPD) types at 95% similarity, regardless of either the sample type or the farm of isolation. This suggests that RAPD types are shared between bovine feces, bedding, cow teats, and milk. In addition, transmission of RAPD types between the studied farms was suggested by the Ward grouping pattern of the isolates, Nei’s and AMOVA population analyses, and genetic landscape shape analysis. For the first time, the latter analytical tool was used to assess the ability of E. coli to disseminate between small-scale dairy farms within the same producing region. Although a number of dispersal mechanisms could exist between farms, the genetic landscape shape analysis associated the flow of E. coli RAPD types with the movement of forage and milking staff between farms. This study will aid in planning disease prevention strategies and optimizing husbandry practices.

Genetic Relationships among Penicillium Species by Characterizing RAPD Markers: Yoon, Cheol Sik , Bae, Kyung Sook; J. Microbiol. 1995;33(3):171-177.

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Abstract: Random amplified polymorphic DAN markers were characterized for three taxonomically problematic Penicillium species : P. aurantiogriseum var. Aurantiogriseum, P. verrucosum and P. puberulum, as well as for 25 species of mono, bi-, and terverticillate Penicillia. The relationships among mono, bi-, and terverticillate Penicillium species were determined from these RAPD markers. Eight species from mono-, eight from bi-, and nine from terverticilate Penicillia were examined. With 14 randomly chosen 10-mer primes, a 310 character by 25 species matrix was generated. Phenetic analysis separated the 25 species into three genetically distinct groups that correspond to the different arrangements of penicilli (mono-, bi-, and terverticillate). The results of this study suggest that P. aurantiogriseum var. aurantiogriseum, P. VERRUCOSUM, AND P. puberulum represent genetically distinct species, and that P. vulpinum should be included in terverticilate Penicillia. Phenogram branching patterns indicated that biverticillate species are genetically more similar to monoverticilate species than they are to terverticillate species.

Fast genetic variation among coliphage quasispecies revealed by a random amplified polymorphic DNA (RAPD) analysis: Kwon, Oh Sik , Lee, Jae Yung; J. Microbiol. 1996;34(2):166-171.

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Abstract: Genetic analysis was conducted on newly isolated coliphages form soil by using a RAPD assay. From the initial result, the coliphages were turned out to be different form one another but were closely related to φλ due to the fact that they shared the same RAPD maker in which other T phage testing failed to show. By using the primers EC01 or EC02, a fast genetic mutation of φC1 was found by producing specific RAPD markers on the phages from the first filial progeny to the second filial progeny. When we made a RAPD assay with combined primers (EC01, EC05 and EC08), the genetic mutation was again confirmed in φC1. The assay detection showed mutations in other coliphages such as φC2 and φC3 by revealing specific RAPD bands among different progeny phages, where genetic instability of the coliphages in implied.

Differentiation of Salmonella typhimurium from Gram-negative Intestinal Microbes by Randomly Amplified Polymorphic DNA (RAPD) Fingerprinting: Un-Ho Jin , Tae-Wook Chung , June-Ki Kim , Kyung-Soo Nam , Sang-Do Ha , Cheorl-Ho Kim; J. Microbiol. 2000;38(1):8-10.

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Abstract: In order to rapidly identify and differentiate Salmonella typhimurium from the intestinal gram-negative bacteria, randomly amplified polymorphic DNA (RAPD) fingerprinting of Salmonella typhimurium was carried out using random primers designated OPA-13 (5'-CAGCACCCAC-3'), OPB-10 (5'-CGT-CTGGGAC-3'), OPB-18 (5'-CCACAGCAGT-3'), and OPJ-10 (5'-AAGCCCGAGG-3'), and its patterns compared with 6 representive intestinal, gram-negative bacterial strains, Vibrio parahaemolyticus, V. vulnificus, Enterobacter cloacae, Escherichia coli O157:H7, Pseudomonas aeruginosa, and Proteus sp., which are often found in foods. S. typhimurium had unique and distinct fingerprinting patterns. RAPD fingerprinting is thus concluded to be a rapid and sensitive method for the identification of S. typh-imurium compared to conventional culturing procedures or immunoassays.

Characterization of Isolated Lactobacillus spp. and Classification by RAPD-PCR Analysis: Oh-Sik Kwon; J. Microbiol. 2000;38(3):137-144.

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Abstract: The genetic relationships of six Lactobacillus strains and five laboratory isolates from fermented milk were determined by a random amplified polymorphic DNA (RAPD)-Polymease chan reaction (PCR) method. With 42 random primers, the results were analyzed by using the NTSYS-PC software for phenetic analysis. It revealed that all tested bacteria were divided into three distinct clusters. The clusters implied three subgenuses existed for the genus Lactobacillus, which were previously proposed by Rogosa and Sharpe. From the results, it was also possible to determine that the isolated Lactobacillus strains from fermented milk were grouped into L. acidophilus or L. bulgaricus. Interestingly, the three tested L. casei strains were divided into different clusters implying different subgenuses, i.e., Thermobacterium (L. casei YIT 9018) and Strepto-bacterium (L. casei CHR. Hansen and L. casei ATCC 4646). According to the distance matrix generated by an UPGMA program, the isolated bacteria LT01 and LT02 were determined as a subspecies of L. bulgaricus. The HK01, HK02 and HK03 were very closely related to either L. acidophilus or L. casei YIT 9018. Hence, RAPD-PCR appears to be a very practical method to determine the genetic relationships of the Lactobacillus species and to characterize the unknown Lactobacillus strains at the subspecies level.

Selection of RAPD Markers for Phytophthora infestans and PCR Detection of Phytophthora infestans from Potatoes: Kyoung Su Kim , Youn Su Lee; J. Microbiol. 2001;39(2):126-132.

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Abstract: For rapid and secure differentiation of P. infestans from other Phytophthora species, two fragments obtained from randomly amplified polymorphic DNA (RAPD) profiles were selected as markers. Also, primers for in polymerase chain reaction (PCR) to detect P. infestans specifically were developed by analyzing the sequences of ITSII regions in rDNA of Phytophthora species. The primers, PISP-1 and ITS3 amplified a single. Fragment 450 bp of about in P. infestans , but not in other fungal or bacterial isolates. Annealing temperatures and template DNA quantities were varied for the optimization of PCR conditions. From the result of the PCR detection study, species-specific primers were selected under annealing temperatures ranging from 55 C to 61 C, and template DNA levels ranging from 10 pg to 100 ng.

Characterization of Quinolone-Resistant Clinical Isolates of Escherichia coli in Korea: Yoojung Oh , Seohyung Park , Misun Ha , Yeonhee Lee; J. Microbiol. 2002;40(2):98-103.

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Abstract: Twenty-eight clinical isolates of Escherichia coli, composed of thirteen norfloxacin resistant isolates (MIC of >16 ug/ml), one intermediately resistant isolate (MIC of 8 ug/ml), and fourteen susceptible isolates (MIC of <4 ug/ml), were randomly selected to study the norfloxacin resistance mechanism and phylogeny in clinical isolates in Korea. Eleven norfloxacin resistant isolates and one susceptible isolate were multi-drug resistant (MDR). Every norfloxacin resistant isolate with MIC higher than 32 ug/ml had the same three mutations: Ser83->Leu and Asp87->Asn or Tyr in GyrA and Ser80->Ile in ParC. Whereas a resistant isolate with MIC of 16 ug/ml had three mutations but Asp87 in GyrA was replaced with Gly instead of Asn. The intermediately resistant isolate had the same two mutations in GyrA but a different mutation in ParC, Glu84->Lys. Among the susceptible isolates, two isolates with MIC of 4 ug/ml had one mutation: Ser83->Leu in GyrA, and no mutation was found in the susceptible isolates. Resistant isolates showed higher efflux activity than the susceptible ones, with random amplification of polymorphic DNA (RAPD), six susceptible isolates form a separate group from the rest of the isolates.

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