Journal of Microbiology

Volume 49(5); October 2011

Research Support, Non-U.S. Gov't

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 PDF: 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.

Research Support, U.S. Gov't, Non-P.H.S.

Carnobacterium maltaromaticum Infections in Feral Oncorhynchus spp. (Family Salmonidae) in Michigan: Thomas P. Loch , Rakesh Kumar , Wei Xu , Mohamed Faisal; J. Microbiol. 2011;49(5):703-713. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-0527-1

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Abstract PDF: Members of the genus Oncorhynchus were introduced from the Pacific Northwest to the Laurentian Great Lakes basin and now constitute one of its most commercially and ecologically valuable fisheries. Recently, infections by a group of Gram-positive atypical lactobacilli belonging to the genus Carnobacterium have been detected in feral and captive Oncorhynchus spp. broodstock, some of which were associated with mortalities. Out of 1564 rainbow and steelhead trout (O. mykiss), coho salmon (O. kisutch), and Chinook salmon (O. tshawytscha) that were bacteriologically examined, 57 Carnobacterium spp. isolates were recovered from the kidneys, spleen, swimbladder, and/or external ulcerations of 51 infected fish. Phenotypic and biochemical characterization, as well as partial 16S rDNA sequencing and phylogenetic analyses of 30 representative isolates identified 29 as Carnobacterium maltaromaticum and 1 as C. divergens, though some phenotypic and genotypic heterogeneity was observed. Infections with C. maltaromaticum were associated with signitures typical of pseudokidney disease, but on occasion were also observed in fish displaying the gross and histopathological changes characteristic of nephrocalcinosis. While C. maltaromaticum infections were found to be widespread in both feral and farmed spawning populations of Oncorhynchus spp. residing within the Great Lakes basin, infection prevalence varied significantly according to fish species and strain, gender, and across time, but not by sampling location according to logistic regression analysis. The findings of this study further underscore the presence of phenotypic variations among Carnobacterium maltaromaticum strains that necessitate genotypic analysis to achieve definitive identification.

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

Ecological Development and Genetic Diversity of Microcystis aeruginosa from Artificial Reservoir in Russia: Nikolay A. Gaevsky , Vladimir I. Kolmakov , Olga I. Belykh , Irina V. Tikhonova , Yochan Joung , Tae Seok Ahn , Valentina A. Nabatova , Anna S. Gladkikh; J. Microbiol. 2011;49(5):714-720. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-0523-5

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Microcystis aeruginosa is a well-known Cyanobacterium responsible for the formation of toxic water blooms around the world. Shallow, warm, and eutrophic reservoirs provide the most favourable conditions for M. aeruginosa development. Numerous studies have been devoted to this species, but there still is a necessity to develop additional approaches for the monitoring of cyanobacteria in reservoirs. In this study, M. aeruginosa in the water column of a hypereutrophic Siberian reservoir was investigated by fluorescence, light, and electron microscopy as well as genetic analysis using a mcyE marker. Here, we demonstrate the genetic diversity and features of the fluorescence spectra for different ecotypes of this species. We suggest that a fluorescence approach can be used to identify M. aeruginosa in a natural environment in order to increase the effectiveness of ecological monitoring and water quality evaluation.

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Systematic Review on CyanoHABs in Central Asia and Post-Soviet Countries (2010–2024)
Kakima Kastuganova, Galina Nugumanova, Natasha S. Barteneva
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A case study performed in Küçükçekmece Lagoon channel/Istanbul, Turkey: how the heavy metal contamination and the seasonal variations on phytoplankton composition influence water quality
Nese Yilmaz, Ibrahim Ilker Ozyigit, Ilhan Dogan, Goksel Demir, Ibrahim Ertugrul Yalcin
Desalination and Water Treatment.2021; 239: 126. CrossRef
Microcystis Chemotype Diversity in the Alimentary Tract of Bigheaded Carp
Milán Riba, Attila Kiss-Szikszai, Sándor Gonda, Gergely Boros, Zoltán Vitál, Andrea Kériné Borsodi, Gergely Krett, Gábor Borics, Andrea Zsuzsanna Ujvárosi, Gábor Vasas
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Everything is not everywhere: a tale on the biogeography of cyanobacteria
Karine Felix Ribeiro, Leandro Duarte, Luciane Oliveira Crossetti
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Phycogeography of freshwater phytoplankton: traditional knowledge and new molecular tools
Judit Padisák, Gábor Vasas, Gábor Borics
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Dynamic variation of toxic and non-toxic Microcystis proportion in the eutrophic Daechung Reservoir in Korea
Seung-Hyun Joung, Hee-Mock Oh, Kyung-A You
Journal of Microbiology.2016; 54(8): 543. CrossRef
Determination of phytoplankton density, and study of the variation of nutrients and heavy metals in the surface water of Riva Stream; one of the water sources of Istanbul, Turkey
Nese Yilmaz, Ibrahim Ilker Ozyigit, Goksel Demir, Ibrahim Ertugrul Yalcin
Desalination and Water Treatment.2015; 55(3): 810. CrossRef
African Origin and Europe-Mediated Global Dispersal of The Cyanobacterium Microcystis aeruginosa
Cristiana Moreira, Charles Spillane, Afef Fathalli, Vitor Vasconcelos, Agostinho Antunes
Current Microbiology.2014; 69(5): 628. CrossRef
Role of Microcystis aeruginosa passing through the digestive tracts of filter-feeding animals in eutrophic water reservoirs (review)
V. I. Kolmakov
Contemporary Problems of Ecology.2014; 7(4): 455. CrossRef
Genetic diversity of Microcystis cyanophages in two different freshwater environments
Ginji Nakamura, Shigeko Kimura, Yoshihiko Sako, Takashi Yoshida
Archives of Microbiology.2014; 196(6): 401. CrossRef
Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins
Cristiana Moreira, Vitor Vasconcelos, Agostinho Antunes
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Identification of toxigenic Cyanobacteria of the genus Microcystis in the Curonian Lagoon (Baltic Sea)
O. I. Belykh, O. A. Dmitrieva, A. S. Gladkikh, E. G. Sorokovikova
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Safety Evaluation In Vitro of Enterococcus durans from Tibetan Traditional Fermented Yak Milk: Jing Li , Fazheng Ren , Huiyong Gu , Xiaopeng Li , Bozhong Gan; J. Microbiol. 2011;49(5):721-728. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1062-9

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Abstract PDF: Despite its ubiquity in fermented dairy products, the safety of lactic acid enterococcal bacteria remains controversial. In this study, five Enterococcus durans strains – A1, A2, B1, B2, and C1 – were isolated from traditional fermented yak milk from Tibet. To evaluate the strains’ safety, biogenic amine production, antibiotic resistance and presence of known virulence determinants were investigated. Strain A1 can produce biogenic amines for histamine, spermine, and spermidine (mean values: 8.64, 8.31, and 0.30 mg/L, respectively). Polymerase chain reaction amplification for Strain A1 found genes involved in expression of gelatinase (gleE), cytolysin (cylA, cylB, and cylM), sex pheromones (ccf and cpd) and cell wall adhesion (efaA). Strain A2 showed sensitivity or intermediate resistance to all tested antibiotics, and no virulence determinants except gelE and ccf, but did produce tyramine at a relatively high level (912.02 mg/L). Both strains B1 and B2 could produce histamine (10.43 and 10.56 mg/L, respectively), and showed vancomycin resistance; B1 also produced tyramine (504.02 mg/L). Strain C1 could produce all five biogenic amines tested in the study – putrescine, histamine, tyramine, spermine, and spermidine; concentrations were 6.51, 9.59, 205.85, 5.55, and 5.39 mg/L, respectively. All E. durans strains found in Tibetan traditional fermented yak milk thus offer potential risk.

Comparative Approach to Capture Bacterial Diversity of Coastal Waters: Hyunsoo Na , Ok-Sun Kim , Seok-Hwan Yoon , Yunmin Kim , Jongsik Chun; J. Microbiol. 2011;49(5):729-740. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1205-z

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Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1% of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.

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Insights into Bacterial Community Structure and Metabolic Diversity of Mercury-Contaminated Sediments from Hyeongsan River, Pohang, South Korea
Dhiraj Kumar Chaudhary, Kyung Hee Kim, Mikyung Lee, Hwansuk Kim, Yongseok Hong
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Microbial community niches on microplastics and prioritized environmental factors under various urban riverine conditions
Hien Thi Nguyen, Woodan Choi, Eun-Ju Kim, Kyungjin Cho
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Abundance, community structure and diversity of nitrifying bacterial enrichments from low and high saline brackishwater environments
P.K. Patil, V. Baskaran, T.‐N. Vinay, S. Avunje, M. Leo‐Antony, M.S. Shekhar, S.V. Alavandi, K.K. Vijayan
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Fei Sjöberg, Intawat Nookaew, Shora Yazdanshenas, Monica Gio-Batta, Ingegerd Adlerberth, Agnes E. Wold
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Andrew M Boddicker, Annika C Mosier
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International Journal of Systematic and Evolutionary Microbiology.2015; 65(Pt_10): 3591. CrossRef
Nitrotoga-like bacteria are previously unrecognized key nitrite oxidizers in full-scale wastewater treatment plants
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Edward Alain B. Pajarillo, Jong Pyo Chae, Marilen P. Balolong, Hyeun Bum Kim, Kang-Seok Seo, Dae-Kyung Kang
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Christiane Brack, Annett Mikolasch, Rüdiger Pukall, Peter Schumann, Marion Köster, Frieder Schauer
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Jay Vornhagen, Michael Stevens, David W. McCormick, Scot E. Dowd, Joseph N.S. Eisenberg, Blaise R. Boles, Alexander H. Rickard
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Journal of Life Science.2013; 23(6): 770. CrossRef
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Detection of Viruses in Farmed Rainbow Trout (Oncorhynchus mykiss) in Korea by RT-LAMP Assay: Rungkarn Suebsing , Jeong-Ho Kim , Seok Ryel Kim , Myung-Ae Park , Myung-Joo Oh; J. Microbiol. 2011;49(5):741-746. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1209-8

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Abstract PDF: The viral diseases have been the serious problem in salmonid farming, and rainbow trout is not an exception. In this study, routine surveys were conducted for detecting of viruses in farmed rainbow trout (Oncorhynchus mykiss) in Korea during 2009-2010. Head kidneys from individual fish were employed for virus detection by using a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. Infectious pancreatic necrosis virus (IPNV), infectious hematopoietic necrosis virus (IHNV), and viral hemorrhagic septicemia virus (VHSV) were the target viruses in this study. 53.5% (46/86) were found to be IPNV-positive, while IHNV and VHSV showed RT-LAMP negative during examination for 2 years. Ten IPNV-positive samples were randomly selected for viral isolation and the cells showing CPEs were subjected to RT-LAMP, RT-PCR, and direct sequencing. Phylogenetic analysis showed that the rainbow trout isolate has high similarity homologies with the VR-299 strain, as previously described.

Epidemiological Investigation of eaeA-Positive Escherichia coli and Escherichia albertii Strains Isolated from Healthy Wild Birds: Jae-Young Oh , Min-Su Kang , Hee-Tae Hwang , Byung-Ki An , Jun-Hun Kwon , Yong-Kuk Kwon; J. Microbiol. 2011;49(5):747-752. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1133-y

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Escherichia coli has commonly been associated with diarrheal illness in humans and animals. Recently, E. albertii has been reported to be a potential pathogen of humans and animals and to be carried by wild birds. In the present study, the prevalence and genetic characteristics of intimin-producing E. coli and E. albertii strains were evaluated in wild birds in Korea. Thirty one of 790 Enterobacteriaceae strains from healthy wild birds were positive for the intimin gene (eaeA) and twenty two of the 31 strains were identified as atypical enteropathogenic E. coli (aEPEC) that did not possess both EAF and bfpA genes. A total of nine lactose non-fermenting coliform bacterial strains were identified as E. albertii by PCR and sequence analysis of housekeeping genes. A total of 28 (90.3%) eaeA-positive strains were isolated from waterfowl. Fifteen aEPEC (68.2%) and two E. albertii (22.2%) strains had a β-intimin subtype and 14 aEPEC strains harboring β-intimin belonged to phylogenetic group B2. All eaeA-positive E. albertii and 3 aEPEC strains possessed the cytolethal distending toxin gene (cdtB). The eaeA-positive E. coli and E. albertii strains isolated from healthy wild birds need to be recognized as a potential pathogroup that may pose a potential threat to human and animal health. These findings indicate that eaeA-positive E. coli as well as E. albertii can be carried by wild birds, posing a potential threat to human and animal health.

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Diagnostic Microbiology and Infectious Disease.2013; 77(2): 91. CrossRef
Molecular detection of enteropathogenic Escherichia coli in asymptomatic captive psittacines
André Becker Saidenberg, Rodrigo Hidalgo F. Teixeira, Neiva Maria R. Guedes, Mariangela da Costa Allgayer, Priscilla Anne Melville, Nilson Roberti Benites
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Prevalence and characteristics of intimin-producing Escherichia coli strains isolated from healthy chickens in Korea
J.-Y. Oh, M.-S. Kang, B.-K. An, E.-G. Shin, M.-J. Kim, Y.-J. Kim, Y.-K. Kwon
Poultry Science.2012; 91(10): 2438. CrossRef

Production of Cephalosporin C Using Crude Glycerol in Fed-Batch Culture of Acremonium chrysogenum M35: Hyun Yong Shin , Jin Young Lee , Han Suk Choi , Ja Hyun Lee , Seung Wook Kim; J. Microbiol. 2011;49(5):753-758. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1155-5

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Abstract PDF: In this study, cephalosporin C production by Acremonium chrysogenum M35 cultured with crude glycerol instead of rice oil and methionine was investigated. The addition of crude glycerol increased cephalosporin C production by 6-fold in shake-flask culture, and also the amount of cysteine. In fed-batch culture without methionine, crude glycerol resulted only in overall improvement in cephalosporin C production (about 700%). In addition, A. chrysogenum M35 became highly differentiated in fed-batch culture with crude glycerol, compared with the differentiation in batch culture. The results presented here suggest that crude glycerol can replace methionine and plant oil as cysteine and carbon sources during cephalosporin C production by A. chrysogenum M35.

Deciphering the Biodiversity of Listeria monocytogenes Lineage III Strains by Polyphasic Approaches: Hanxin Zhao , Jianshun Chen , Chun Fang , Ye Xia , Changyong Cheng , Lingli Jiang , Weihuan Fang; J. Microbiol. 2011;49(5):759-767. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1006-4

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Listeria monocytogenes is a foodborne pathogen of humans and animals. The majority of human listeriosis cases are caused by strains of lineages I and II, while lineage III strains are rare and seldom implicated in human listeriosis. We revealed by 16S rRNA sequencing the special evolutionary status of L. monocytogenes lineage III, which falls between lineages I and II strains of L. monocytogenes and the non-pathogenic species L. innocua and L. marthii in the dendrogram. Thirteen lineage III strains were then characterized by polyphasic approaches. Biochemical reactions demonstrated 8 biotypes, internalin profiling identified 10 internalin types clustered in 4 groups, and multilocus sequence typing differentiated 12 sequence types. These typing schemes show that lineage III strains represent the most diverse population of L. monocytogenes, and comprise at least four subpopulations IIIA-1, IIIA-2, IIIB, and IIIC. The in vitro and in vivo virulence assessments showed that two lineage IIIA-2 strains had reduced pathogenicity, while the other lineage III strains had comparable virulence to lineages I and II. The IIIB strains are phylogenetically distinct from other subpopulations, providing additional evidence that this sublineage represents a novel lineage. The two biochemical reactions L-rhamnose and L-lactate alkalinization, and 10 internalins were identified as potential markers for lineage III subpopulations. This study provides new insights into the biodiversity and population structure of lineage III strains, which are important for understanding the evolution of the L. monocytogenes-L. innocua clade.

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Listeria monocytogenes, Salmonella spp., and Staphylococcus aureus: Threats to the Food Industry and Public Health
Vinicius B. Mantovam, David F. dos Santos, Luis C. Giola Junior, Mariza Landgraf, Uelinton M. Pinto, Svetoslav D. Todorov
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Phillip Brown, Sangmi Lee, Driss Elhanafi, Wilhelm Tham, Marie-Louise Danielsson-Tham, Gloria Lopez-Valladares, Yi Chen, Mirena Ivanova, Pimlapas Leekitcharoenphon, Sophia Kathariou
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Dongyou Liu
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Genetic diversity of internalin genes in the ascB‐dapE locus among Listeria monocytogenes lineages III and IV strains
Jianshun Chen, Changyong Cheng, Yonghui Lv, Weihuan Fang
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Jianshun Chen, Chun Fang, Tianlun Zheng, Ningyu Zhu, Yijiang Bei, Weihuan Fang
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A Genome-Wide Identification of Genes Potentially Associated with Host Specificity of Brucella Species: Kyung Mo Kim , Kyu-Won Kim , Samsun Sung , Heebal Kim; J. Microbiol. 2011;49(5):768-775. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1084-3

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Brucella species are facultative intracellular pathogenic α-Proteobacteria that can cause brucellosis in humans and domestic animals. The clinical and veterinary importance of the bacteria has led to well established studies on the molecular mechanisms of Brucella infection of host organisms. However, to date, no genome-wide study has scanned for genes related to the host specificity of Brucella spp. The majority of bacterial genes related to specific environmental adaptations such as host specificity are well-known to have evolved under positive selection pressure. We thus detected signals of positive selection for individual orthologous genes among Brucella genomes and identified genes related to host specificity. We first determined orthologous sets from seven completely sequenced Brucella genomes using the Reciprocal Best Hits (RBH). A maximum likelihood analysis based on the branch-site test was accomplished to examine the presence of positive selection signals, which was subsequently confirmed by phylogenetic analysis. Consequently, 12 out of 2,033 orthologous genes were positively selected by specific Brucella lineages, each of which belongs to a particular animal host. Extensive literature reviews revealed that half of these computationally identified genes are indeed involved in Brucella host specificity. We expect that this genome-wide approach based on positive selection may be reliably used to screen for genes related to environmental adaptation of a particular species and that it will provide a set of appropriate candidate genes.

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Udayakumar S. Vishnu, Jagadesan Sankarasubramanian, Jayavel Sridhar, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
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Bacillus kyonggiensis sp. nov., Isolated from Soil of a Lettuce Field: Ke Dong , Sangseob Lee; J. Microbiol. 2011;49(5):776-781. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1218-7

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A Gram-positive, rod-shaped, motile, endospore-forming bacterial strain, designated NB22T, was isolated from soil of a lettuce field in Kyonggi province, South Korea, and was characterized by using a polyphasic taxonomic approach. This novel isolate grew optimally at 30-37°C and pH 8-9. It grew in the presence of 0-4% NaCl (optimum, 1-2%). Comparative 16S rRNA gene sequence analysis showed that strain NB22T was closely related to members of the genus Bacillus and fell within a coherent cluster comprising B. siralis 171544T (98.1%) and B. korlensis ZLC-26T (97.3%). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.4%. Strain NB22T had a genomic DNA G+C content of 36.3 mol% and the predominant respiratory quinone was MK-7. The peptidoglycan contained meso-diaminopimelic acid. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, C14:0, and C16:0. These chemotaxonomic results supported the affiliation of strain NB22T to the genus Bacillus, and the low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain NB22T from recognized Bacillus species. On the basis of the evidence presented, strain NB22T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus kyonggiensis sp. nov. is proposed. The type strain is NB22T (=KEMB 5401-267T =JCM 17569T).

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Use of rpoB Sequences and rep-PCR for Phylogenetic Study of Anoxybacillus Species: Kadriye Inan , Yusuf Bektas , Sabriye Canakci , Ali Osman Belduz; J. Microbiol. 2011;49(5):782-790. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1136-8

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This study was conducted to investigate the applicability of rpoB, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA gene sequence similarity analysis in the thermophilic genus Anoxybacillus. Partial rpoB sequences were generated for the 14 type strains of Anoxybacillus species and 6 other strains of four Anoxybacillus species. The sequences and the phylogenetic tree of rpoB were compared with those obtained from 16S rRNA gene analysis. The rpoB gene was found to provide a better resolution for Anoxybacillus species, with lower interspecies sequence similarities. The rpoB sequence similarity analysis permitted a more accurate discrimination of the species within the Anoxybacillus genus than the more commonly used 16S rRNA gene. Furthermore, rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP-, ERIC-, and BOX-PCR) were employed for the specimens of genus Anoxybacillus. Through comparison of the three methods, it was found that the BOX-PCR method generated more informative results than REP-PCR for the studied strains; BOX-PCR profiles were more distinct for the different strains, including a higher number of bands. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (rep-PCR) constitute a suitable molecular approach for the validation and maintenance of taxonomy within the Anoxybacillus genus. The results of this study show that rpoB and rep-PCR provide rapid and reliable methods for molecular typing of Anoxybacillus species.

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Industrially Significant Extremophiles and Their Unexplored Habitats in Hot Water Springs
Nisha Sharma, Yogesh K. Ahlawat, Sajid Mehmood, Arti Jamwal Sharma, Princy Thakur, Anurag Malik, Monika Sindhu, Maryam Samani, Umang Ahlawat
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Phylogenomic and molecular marker based studies to clarify the evolutionary relationships amongst Anoxybacillus species and demarcation of the family Anoxybacillaceae and some of its constituent genera
Isha Patel, Sarah Bello, Radhey S. Gupta
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Isolation and Screening of Polyhydroxybutyrate (PHB) Producing Bacteria from Soils
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Isolation and Molecular Identification of Xylanase and Glucose-Isomerase Producer Geobacillus and Brevibacillus Strains from Hot Springs in Turkey
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Masanto ., Arif Wibowo, Tri Joko, Siti Subandiyah, Koji Kageyama
Plant Pathology Journal.2020; 19(1): 22. CrossRef
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Sathyanarayana Reddy Gundlapally, Ferran Garcia-Pichel
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Qianying Zhang, Yuju Yuan, Wen Luo, Liyun Zeng, Zhengyun Wu, Wenxue Zhang
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Soniya Mantri, Mohan Rao Chinthalagiri, Sathyanarayana Reddy Gundlapally
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Sisinthy Shivaji, Gundlapally Sathyanarayana Reddy, Vetaikorumagan Raman Sundareswaran, Celia Thomas
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Anoxybacillus kaynarcensis sp. nov., a moderately thermophilic, xylanase producing bacterium
Kadriye Inan, Ali Osman Belduz, Sabriye Canakci
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Kian Mau Goh, Ummirul Mukminin Kahar, Yen Yen Chai, Chun Shiong Chong, Kian Piaw Chai, Velayudhan Ranjani, Rosli Md. Illias, Kok-Gan Chan
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Research Support, Non-U.S. Gov'ts

Rapid Discrimination of Potato Scab-Causing Streptomyces Species Based on the RNase P RNA Gene Sequences: Hang-Yeon Weon , Jaekyeong Song , Byung-Yong Kim , On-Suk Hur , In-Cheol Park , Joo-Won Suh; J. Microbiol. 2011;49(5):791-796. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1279-7

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Abstract PDF: Scab disease significantly damages potatoes and other root crops. Some Streptomyces species have been reported as potato-scab pathogens. Identification of the phytopathogenic Streptomyces is mainly done on the basis of the 16S rRNA gene, but use of this gene has some limitations for discriminating these strains because they share high similarities of 16S rRNA gene sequences. We tested the RNase P RNA (rnpB) gene as a taxonomic marker to clarify the relationship among closely related scab-causing Streptomyces strains. The rnpB genes were analyzed for 41 strains including 9 isolates from Jeju, Korea. There were 4 highly variable regions including nucleotide gaps in the rnpB genes. Interspecies similarity of the rnpB gene in tested Streptomyces strains was lower than about 97%, while the intraspecies similarity was higher than about 98%. Phylogenetic analysis demonstrated that the rnpB tree has similar topology to the 16S rRNA gene tree, but produces a more divergent phyletic lineage. These results revealed that the rnpB gene could be used as a powerful taxonomic tool for rapid differentiation of closely related Streptomyces species. In addition, it was also suggested that the variable regions marked as α, β, γ, and δ in the rnpB gene could be useful markers for the detection of specific Streptomyces species.

Biochemical Properties and Physiological Roles of NADP-Dependent Malic Enzyme in Escherichia coli: Baojuan Wang , Peng Wang , Enxia Zheng , Xiangxian Chen , Hanjun Zhao , Ping Song , Ruirui Su , Xiaoning Li , Guoping Zhu; J. Microbiol. 2011;49(5):797-802. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-0487-5

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Malic enzymes catalyze the reversible oxidative decarboxylation of L-malate using NAD(P)+ as a cofactor. NADP-dependent malic enzyme (MaeB) from Escherichia coli MG1655 was expressed and purified as a fusion protein. The molecular weight of MaeB was about 83 kDa, as determined by SDS-PAGE. The recombinant MaeB showed a maximum activity at pH 7.8 and 46°C. MaeB activity was dependent on the presence of Mn2+ but was strongly inhibited by Zn2+. In order to understand the physiological roles, recombinant E. coli strains (icdNADP/ΔmaeB and icdNAD/ΔmaeB) containing NADP-dependent isocitrate dehydrogenase (IDH), or engineered NAD-dependent IDH with the deletion of the maeB gene, were constructed using homologous recombination. During growth on acetate, icdNAD/ΔmaeB grew poorly, having a growth rate only 60% that of the wild-type strain (icdNADP). Furthermore, icdNADP/ΔmaeB exhibited a 2-fold greater adaptability to acetate than icdNAD/ΔmaeB, which may be explained by more NADPH production for biosynthesis in icdNADP/ΔmaeB due to its NADP-dependent IDH. These results indicated that MaeB was important for NADPH production for bacterial growth on acetate. We also observed that MaeB activity was significantly enhanced (7.83-fold) in icdNAD, which was about 3-fold higher than that in icdNADP, when switching from glucose to acetate. The marked increase of MaeB activity was probably induced by the shortage of NADPH in icdNAD. Evidently, MaeB contributed to the NADPH generation needed for bacterial growth on two carbon compounds.

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Journal Article

A Novel Ribonuclease with Potent HIV-1 Reverse Transcriptase Inhibitory Activity from Cultured Mushroom Schizophyllum commune: Yong-Chang Zhao , Guo-Qing Zhang , Tzi-Bun Ng , He-Xiang Wang; J. Microbiol. 2011;49(5):803-808. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1098-x

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A 20-kDa ribonuclease (RNase) was purified from fresh fruiting bodies of cultured Schizophyllum commune mushrooms. The RNase was not adsorbed on Affi-gel blue gel but adsorbed on DEAE-cellulose and CM-cellulose. It exhibited maximal RNase activity at pH 6.0 and 70°C. It demonstrated the highest ribonucleolytic activity toward poly (U) (379.5 μ/mg), the second highest activity toward poly (C) (244.7 μ/mg), less activity toward poly (A) (167.4 μ/mg), and much weaker activity toward poly (G) (114.5 μ/mg). The RNase inhibited HIV-1 reverse transcriptase with an IC50 of 65 μM. No effect on [3H-methyl]-thymidine uptake by lymphoma MBL2 cells and leukemia L1210 cells was observed at 100 μM concentration of the RNase. A comparison of RNases from S. commune and Volvariella volvacea revealed that they demonstrated some similarities in N-terminal amino acid sequence, optimum pH and polyhomoribonucleotide specificity. However, some differences in chromatographic behavior and molecular mass were observed.

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

Biochemical Properties of an Extracellular Trehalase from Malbranchea pulchella var. Sulfurea: Marita Gimenez Pereira , Luis Henrique Souza Guimarães , Rosa Prazeres Melo Furriel , Maria de Lourdes , Teixeira de Moraes Polizeli , Hector Francisco Terenzi , João Atílio Jorge; J. Microbiol. 2011;49(5):809-815. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-0532-4

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Abstract PDF: The thermophilic fungus Malbranchea pulchella var. sulfurea produced good amounts of extracellular trehalase activity when grown for long periods on starch, maltose or glucose as the main carbon source. Studies with young cultures suggested that the main role of the extracellular acid trehalase is utilizing trehalose as a carbon source. The specific activity of the purified enzyme in the presence of manganese (680 U/mg protein) was comparable to that of other thermophilic fungi enzymes, but many times higher than the values reported for trehalases from other microbial sources. The apparent molecular mass of the native enzyme was estimated to be 104 kDa by gel filtration and 52 kDa by SDS-PAGE, suggesting that the enzyme was composed by two subunits. The carbohydrate content of the purified enzyme was estimated to be 19% and the pI was 3.5. The optimum pH and temperature were 5.0-5.5 and 55°C, respectively. The purified enzyme was stimulated by manganese and inhibited by calcium ions, and insensitive to ATP and ADP, and 1 mM silver ions. The apparent KM values for trehalose hydrolysis by the purified enzyme in the absence and presence of manganese chloride were 2.70±0.29 and 2.58±0.13 mM, respectively. Manganese ions affected only the apparent Vmax, increasing the catalytic efficiency value by 9.2-fold. The results reported herein indicate that Malbranchea pulchella produces a trehalase with mixed biochemical properties, different from the conventional acid and neutral enzymes and also from trehalases from other thermophilic fungi.

Adaptive Stress Response to Menadione-Induced Oxidative Stress in Saccharomyces cerevisiae KNU5377: Il-Sup Kim , Ho-Yong Sohn , Ingnyol Jin; J. Microbiol. 2011;49(5):816-823. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1154-6

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The molecular mechanisms involved in the ability of yeast cells to adapt and respond to oxidative stress are of great interest to the pharmaceutical, medical, food, and fermentation industries. In this study, we investigated the time-dependent, cellular redox homeostasis ability to adapt to menadione-induced oxidative stress, using biochemical and proteomic approaches in Saccharomyces cerevisiae KNU5377. Time-dependent cell viability was inversely proportional to endogenous amounts of ROS measured by a fluorescence assay with 2′,7′-dichlorofluorescin diacetate (DCFHDA), and was hypersensitive when cells were exposed to the compound for 60 min. Morphological changes, protein oxidation and lipid peroxidation were also observed. To overcome the unfavorable conditions due to the presence of menadione, yeast cells activated a variety of cell rescue proteins including antioxidant enzymes, molecular chaperones, energy-generating metabolic enzymes, and antioxidant molecules such as trehalose. Thus, these results show that menadione causes ROS generation and high accumulation of cellular ROS levels, which affects cell viability and cell morphology and there is a correlation between resistance to menadione and the high induction of cell rescue proteins after cells enter into this physiological state, which provides a clue about the complex and dynamic stress response in yeast cells.

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Degradation of Endocrine Disrupting Chemicals by Genetic Transformants with Two Lignin Degrading Enzymes in Phlebia tremellosa: Hyunwoo Kum , Sungsuk Lee , Sunhwa Ryu , Hyoung T. Choi; J. Microbiol. 2011;49(5):824-827. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1230-y

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A white rot fungus Phlebia tremellosa produced lignin degrading enzymes, which showed degrading activity against various recalcitrant compounds. However, manganese peroxidase (MnP) activity, one of lignin degrading enzymes, was very low in this fungus under various culture conditions. An expression vector that carried both the laccase and MnP genes was constructed using laccase genomic DNA of P. tremellosa and MnP cDNA from Polyporus brumalis. P. tremellosa was genetically transformed using the expression vector to obtain fungal transformants showing increased laccase and MnP activity. Many transformants showed highly increased laccase and MnP activity at the same time in liquid medium, and three of them were used to degrade endocrine disrupting chemicals. The transformant not only degraded bisphenol A and nonylphenol more rapidly but also removed the estrogenic activities of the chemicals faster than the wild type strain.

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Galit Akerman-Sanchez, Keilor Rojas-Jimenez
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Complete degradation of bisphenol A and nonylphenol by a composite of biogenic manganese oxides and Escherichia coli cells with surface-displayed multicopper oxidase CotA
Zhen Zhang, Zhiyong Ruan, Jin Liu, Chang Liu, Fuming Zhang, Robert J. Linhardt, Lin Li
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Applied Biochemistry and Biotechnology.2013; 171(6): 1525. CrossRef

Functional Analysis of SGR4635-Induced Enhancement of Pigmented Antibiotic Production in Streptomyces lividans: Won-Jae Chi , Soon-Youl Lee , JaeHag Lee; J. Microbiol. 2011;49(5):828-833. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1100-7

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The Gram-positive mycelium-producing bacterium Streptomyces undergoes complex morphological differentiation after autolytic degradation of the vegetative mycelium. Cell-wall breakdown during growth stimulates cell development and secondary metabolite production by Streptomyces. N-acetylglucosamine (GlcNAc) produced by cell-wall lysis acts as a signal molecule, triggering the production of secondary metabolites in S. coelicolor A3(2). Here, we report that introduction of multiple copies of the GlcNAc-internalizing gene (sgr4635, encoding nagE2) of S. griseus activates actinorhodin and undecylprodigiosin production during the late growth of S. lividans in the absence of GlcNAc. Furthermore, the repressor-type transcriptional regulator DasR binds to two operator sites upstream of sgr4635. Our findings indicate that sgr4635 induces DasR-mediated antibiotic production by internalizing the GlcNAc accumulated from cell-wall lysis.

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Identification and Testing of Antidermatophytic Oxaborole-6-Benzene Sulphonamide Derivative (OXBS) from Streptomyces atrovirens KM192347 Isolated from Soil
Seham Abdel-Shafi, Abdul-Raouf Al-Mohammadi, Taghreed N. Almanaa, Ahmed H. Moustafa, Tamer M. M. Saad, Abdel-Rahman Ghonemey, Immacolata Anacarso, Gamal Enan, Nashwa El-Gazzar
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Isolde M. Francis, Samuel Jourdan, Steven Fanara, Rosemary Loria, Sébastien Rigali, Anne K. Vidaver
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Gang Liu, Keith F. Chater, Govind Chandra, Guoqing Niu, Huarong Tan
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Antibiotics produced by Streptomyces
Rudi Emerson de Lima Procópio, Ingrid Reis da Silva, Mayra Kassawara Martins, João Lúcio de Azevedo, Janete Magali de Araújo
The Brazilian Journal of Infectious Diseases.2012; 16(5): 466. CrossRef

Berberine Inhibits HEp-2 Cell Invasion Induced by Chlamydophila pneumoniae Infection: Li Jun Zhang , Li Jun Zhang , Wei Quan , Bei Bei Wang , Bing Ling Shen , Teng Teng Zhang , Yi Kang; J. Microbiol. 2011;49(5):834-840. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1051-z

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This study investigated the inhibitory effects of berberine on Chlamydophila (Chlamydia) pneumoniae infection-induced HEp-2 cell invasion and explored the possible mechanisms involved in this process. C. pneumoniae infection resulted in a significant increase in HEp-2 cell invasion when compared with the control cells (P<0.01) in a Matrigel invasion assay. This enhanced cell invasion was strongly suppressed by berberine (50 μM) (P<0.01). In a cell adhesion assay, the infection-induced HEp-2 cell adhesion to Matrigel was also significantly inhibited by berberine (P<0.01). C. pneumoniae infection was found to promote HEp-2 cell migration remarkably (P<0.01), which was markedly suppressed by berberine (P<0.01) in the cell migration assays. There were no statistically significant differences in the expression of matrix metalloproteinase-1 (MMP-1) and MMP-9 in the infected cells and berberine did not change the expression of MMP-1 and MMP-9. These data suggest that berberine inhibits C. pneumoniae infection-induced HEp-2 cell invasion through suppressing HEp-2 cell adhesion and migration, but not through changing the expression of MMP-1 and MMP-9.

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Xue Yang, Yanfen Wang, Ling Li, Daiyan Tang, Zhong Yan, MingYan Li, Jiayi Jiang, Dongming Bi
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European Journal of Pharmacology.2015; 755: 102. CrossRef
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Ning Sun, Fung-Yi Chan, Yu-Jing Lu, Marco A. C. Neves, Hok-Kiu Lui, Yong Wang, Ka-Yan Chow, Kin-Fai Chan, Siu-Cheong Yan, Yun-Chung Leung, Ruben Abagyan, Tak-Hang Chan, Kwok-Yin Wong, Dirk-Jan Scheffers
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Chlamydia pneumoniae infection induces vascular smooth muscle cell migration via Rac1 activation
Junxia Zhang, Haiwei Wang, Lijun Zhang, Tengteng Zhang, Beibei Wang, Xiankui Li, Junyan Wei, Lijun Zhang
Journal of Medical Microbiology .2014; 63(2): 155. CrossRef
Chlamydia pneumoniae Infection Promotes Vascular Smooth Muscle Cell Migration through a Toll-Like Receptor 2-Related Signaling Pathway
Beibei Wang, Lijun Zhang, Tengteng Zhang, Haiwei Wang, Junxia Zhang, Junyan Wei, Bingling Shen, Xin Liu, Zhelong Xu, Lijun Zhang, R. P. Morrison
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Interaction of Acinetobacter baumannii 19606 and 1656-2 with Acanthamoeba castellanii: Migma Dorji Tamang , Shukho Kim , Sung-Min Kim , Hyun-Hee Kong , Jungmin Kim; J. Microbiol. 2011;49(5):841-846. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1063-8

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Acinetobacter baumannii is virtually avirulent for healthy people but maintains a high virulence among critically ill patients or immuno-compromised individuals. The ability of A. baumannii to adhere to cells and persist on surfaces as biofilms could be central to its pathogenicity. In the present study, we compared the virulence of the A. baumannii 1656-2 clinical strain, which is able to form a thick biofilm, with the virulence of the A. baumannii type strain (ATCC 19606T). Acanthamoeba castellanii, a single-celled organism, was used as the host model system to study the virulence of A. baumannii. Compared to A. baumannii ATCC 19606T, A. baumannii 1656-2 exhibited a higher ability to adhere and invade A. castellanii cells and had a higher killing rate of A. castellanii cells. Furthermore, co-incubation of the amoeba cells and the cell-free supernatant of A. baumannii resulted in the cell death of the amoebae. Heat inactivation or proteinase K treatment of the supernatant did not eliminate its cytotoxicity, suggesting heat stable non-protein factors are responsible for its cytotoxicity to A. castellanii cells. In conclusion, this study for the first time has revealed the capacity of the A. baumannii strain and/or its metabolic products to induce cytotoxicity in A. castellanii cells.

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Bacteria-Based In Vivo Peptide Library Screening Using Biopanning Approach: Ji-Hyeon Choi , Sang-Hyun Park; J. Microbiol. 2011;49(5):847-851. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1405-6

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Abstract PDF: Traditionally, library screening has been performed to identify biologically active agents including small molecules or peptides that inhibit target proteins or molecules with therapeutic interests. Due to its chemical nature, library screening is usually performed under in vitro environments using purified proteins and molecules. However, active agents identified from in vitro screenings often fail to exhibit biological activities in cells. To overcome this inherent limitation, we have developed an in vivo peptide library screening system that allows for the identification of dissociative inhibitors of protein interactions of interest. The screening is based on the reconstitution of the cI repressor from bacteriophage lambda with high-density expression peptide library and is entirely performed in bacteria cells. Furthermore, to enhance the efficacy and sensitivity of the screening, a multiple-round biopanning approach was employed for amplification and enrichment of positive peptides. Overall, this in vivo screening should provide a fast and efficient tool for identification of biologically active peptide molecules against target protein assembly.

NOTE] Microbacterium suwonense sp. nov., Isolated from Cow Dung: Rangasamy Anandham , Tomohiko Tamura , Moriyuki Hamada , Hang-Yeon Weon , Soo-Jin Kim , Yi-Seul Kim , Ken-ichiro Suzuki , Soon-Wo Kwon; J. Microbiol. 2011;49(5):852-856. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1036-y

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An actinomycete strain, designated M1T8B9T, was isolated from cow dung in Suwon, Republic of Korea. The isolate was a Gram-positive, nonmotile, and non-spore-forming bacterium. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the genus Microbacterium, with its closest neighbors being Microbacterium soli DCY17T (98.2%) and Microbacterium esteraromaticum DSM 8609T (98.0%). The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, and one unknown glycolipid. Strain M1T8B9T contained the major fatty acids C15:0 anteiso, C16:0 iso, C17:0 anteiso, and C15:0 iso, and the cell-wall peptidoglycan was of type B2β. According to DNA-DNA hybridization studies, strain M1T8B9T showed 42% and 26% relatedness with M. soli DCY17T and M. esteraromaticum DSM 8609T, respectively. On the basis of the data presented, strain M1T8B9T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium suwonense sp. nov. is proposed. The type strain is M1T8B9T (=KACC 14058T =NBRC 106310T).

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NOTE] Pigmentiphaga soli sp. nov., a Bacterium Isolated from Soil: Jae-Jin Lee , Sathiyaraj Srinivasan , Myung Kyum Kim; J. Microbiol. 2011;49(5):857-861. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1375-8

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Abstract PDF: Strain BS12T, a Gram-negative motile bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain belonged to the family Alcaligenaceae in the class Betaproteobacteria. The highest degree of sequence similarities of strain BS12T were found with Pigmentiphaga litoralis JSM 061001T (98.3%), Pigmentiphaga daeguensis K110T (98.2%), and Pigmentiphaga kullae K24T (98.1%). Chemotaxonomic data revealed that strain BS12T possessed ubiquinone-8, which is common in the family Alcaligenaceae, and the predominant fatty acids were C16:0, C17:0 cyclo, summed feature 3 (C16:1 ω6c/ω7c), and summed feature 8 (C18:1 ω6c/ω7c). The major polar lipids of strain BS12T were phosphatidylethanolamine and phosphatidylglycerol. Based on these data, BS12T (=KCTC 23577T =JCM 17666T =KEMB 9004-082T) should be classified as a type strain of a novel species, for which the name Pigmentiphaga soli sp. nov. is proposed.

Journal Article

NOTE] Sawadaea koelreuteriae comb. nov., a Powdery Mildew of Koelreuteria paniculata: Hyeon-Dong Shin , Mi-Jeong Park; J. Microbiol. 2011;49(5):862-866. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1479-1

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Abstract PDF: A powdery mildew parasitizing Koelreuteria spp. was first described under the name Uncinula koelreuteriae Miyake and later transferred to the genus Typhulochaeta. Based on morphological and molecular data of several herbarium specimens collected from Korea, the generic placement of Typhulochaeta is discussed and T. koelreuteriae is combined in the genus Sawadaea. Redescription and epitypification of this species is provided hereby.

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