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Microbial genetics, genomics and proteomics

This section aims to publish studies relating to all aspects of microbial genomics, transcriptomics, proteomics, metabolomics and microbial genome editing.

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  1. Streptomyces species are widely distributed in natural habitats, such as soils, lakes, plants and some extreme environments. Replication loci of several Streptomyces theta-type plasmids have been reported, but ar...

    Authors: Tao Wang, Zhenhua Chen, Qiuxiang Cheng, Min Zhou, Xinli Tian, Pengfei Xie, Li Zhong, Meijuan Shen and Zhongjun Qin

    Citation: BMC Microbiology 2012 12:253

    Content type: Research article

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  2. Burkholderia pseudomallei is the etiological agent of melioidosis and a CDC category B select agent with no available effective vaccine. Previous immunizations in mice have utilized the lipopolysaccharide (LPS) a...

    Authors: Joshua K Stone, Mark Mayo, Stephanie A Grasso, Jennifer L Ginther, Stephanie D Warrington, Christopher J Allender, Adina Doyle, Shalamar Georgia, Mirjam Kaestli, Stacey M Broomall, Mark A Karavis, Joseph M Insalaco, Kyle S Hubbard, Lauren A McNew, Henry S Gibbons, Bart J Currie…

    Citation: BMC Microbiology 2012 12:250

    Content type: Research article

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  3. FK506 (Tacrolimus) is an important immunosuppressant, produced by industrial biosynthetic processes using various Streptomyces species. Considering the complex structure of FK506, it is reasonable to expect compl...

    Authors: Dušan Goranovič, Marko Blažič, Vasilka Magdevska, Jaka Horvat, Enej Kuščer, Tomaž Polak, Javier Santos-Aberturas, Miriam Martínez-Castro, Carlos Barreiro, Peter Mrak, Gregor Kopitar, Gregor Kosec, Štefan Fujs, Juan F Martín and Hrvoje Petković

    Citation: BMC Microbiology 2012 12:238

    Content type: Research article

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  4. Glutamyl queuosine-tRNAAsp synthetase (GluQ-RS) is a paralog of the catalytic domain of glutamyl-tRNA synthetase and catalyzes the formation of glutamyl-queuosine on the wobble position of tRNAAsp. Here we analyz...

    Authors: Valeria C Caballero, Viviana P Toledo, Cristian Maturana, Carolyn R Fisher, Shelley M Payne and Juan Carlos Salazar

    Citation: BMC Microbiology 2012 12:226

    Content type: Research article

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  5. Clostridium thermocellum produces H2 and ethanol, as well as CO2, acetate, formate, and lactate, directly from cellulosic biomass. It is therefore an attractive model for biofuel production via consolidated biopr...

    Authors: Thomas Rydzak, Peter D McQueen, Oleg V Krokhin, Vic Spicer, Peyman Ezzati, Ravi C Dwivedi, Dmitry Shamshurin, David B Levin, John A Wilkins and Richard Sparling

    Citation: BMC Microbiology 2012 12:214

    Content type: Research article

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  6. O-glycosylation of secretory proteins has been found to be an important factor in fungal biology and virulence. It consists in the addition of short glycosidic chains to Ser or Thr residues in the protein backb.....

    Authors: Mario González, Nélida Brito and Celedonio González

    Citation: BMC Microbiology 2012 12:213

    Content type: Research article

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  7. Streptococcus gordonii is one of several species that can initiate the formation of oral biofilms that develop into the complex multispecies microbial communities referred to as dental plaque. It is in the contex...

    Authors: Erik L Hendrickson, Tiansong Wang, Brittany C Dickinson, Sarah E Whitmore, Christopher J Wright, Richard J Lamont and Murray Hackett

    Citation: BMC Microbiology 2012 12:211

    Content type: Research article

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  8. Y. enterocolitica biotype (BT) 1A strains are often isolated from human clinical samples but their contribution to disease has remained a controversial topic. Variation and the population structure among the clin...

    Authors: Leila M Sihvonen, Kaisa Jalkanen, Elisa Huovinen, Susanna Toivonen, Jukka Corander, Markku Kuusi, Mikael Skurnik, Anja Siitonen and Kaisa Haukka

    Citation: BMC Microbiology 2012 12:208

    Content type: Research article

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  9. Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no in...

    Authors: Chao-Dong Qian, Tian-Zhe Liu, Shuang-Lin Zhou, Rui Ding, Wen-Peng Zhao, Ou Li and Xue-Chang Wu

    Citation: BMC Microbiology 2012 12:197

    Content type: Research article

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  10. The central role of Type III secretion systems (T3SS) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. Some Pseudomonas syringae

    Authors: Anastasia D Gazi, Panagiotis F Sarris, Vasiliki E Fadouloglou, Spyridoula N Charova, Nikolaos Mathioudakis, Nicholas J Panopoulos and Michael Kokkinidis

    Citation: BMC Microbiology 2012 12:188

    Content type: Research article

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  11. In this study mass spectrometry was used for evaluating extracted leptospiral protein samples and results were compared with molecular typing methods. For this, an extraction protocol for Leptospira spp. was inde...

    Authors: Anna Rettinger, Inke Krupka, Karola Grünwald, Viktor Dyachenko, Volker Fingerle, Regina Konrad, Heribert Raschel, Ulrich Busch, Andreas Sing, Reinhard K Straubinger and Ingrid Huber

    Citation: BMC Microbiology 2012 12:185

    Content type: Methodology article

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  12. The outcome of an Entamoeba histolytica infection is variable and can result in either asymptomatic carriage, immediate or latent disease (diarrhea/dysentery/amebic liver abscess). An E. histolytica multilocus ge...

    Authors: Carol A Gilchrist, Ibne Karim M Ali, Mamun Kabir, Faisal Alam, Sana Scherbakova, Eric Ferlanti, Gareth D Weedall, Neil Hall, Rashidul Haque, William A Petri Jr and Elisabet Caler

    Citation: BMC Microbiology 2012 12:151

    Content type: Research article

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  13. Hazelnut (Corylus avellana) decline disease in Greece and Italy is caused by the convergent evolution of two distantly related lineages of Pseudomonas syringae pv. avellanae (Pav). We sequenced the genomes of thr...

    Authors: Heath E O’Brien, Shalabh Thakur, Yunchen Gong, Pauline Fung, Jianfeng Zhang, Lijie Yuan, Pauline W Wang, Choseung Yong, Marco Scortichini and David S Guttman

    Citation: BMC Microbiology 2012 12:141

    Content type: Research article

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  14. Ureaplasma urealyticum (UUR) and Ureaplasma parvum (UPA) are sexually transmitted bacteria among humans implicated in a variety of disease states including but not limited to: nongonococcal urethritis, infertilit...

    Authors: Vanya Paralanov, Jin Lu, Lynn B Duffy, Donna M Crabb, Susmita Shrivastava, Barbara A Methé, Jason Inman, Shibu Yooseph, Li Xiao, Gail H Cassell, Ken B Waites and John I Glass

    Citation: BMC Microbiology 2012 12:88

    Content type: Research article

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  15. The tyramine producer Enterococcus durans IPLA655 contains all the necessary genes for tyramine biosynthesis, grouped in the TDC cluster. This cluster includes tyrS, an aminoacyl-tRNA synthetase like gene.

    Authors: Daniel M Linares, Maria Fernández, Beatriz Del-Río, Victor Ladero, Maria Cruz Martin and Miguel A Alvarez

    Citation: BMC Microbiology 2012 12:23

    Content type: Research article

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  16. The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machi...

    Authors: Sang-Hoon Kim, Christina Harzman, John K Davis, Rachel Hutcheson, Joan B Broderick, Terence L Marsh and James M Tiedje

    Citation: BMC Microbiology 2012 12:21

    Content type: Research article

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  17. Huanglongbing (HLB) is a highly destructive disease of citrus production worldwide. 'Candidatus Liberibacter asiaticus', an unculturable alpha proteobacterium, is a putative pathogen of HLB. Information about the...

    Authors: Xuefeng Wang, Changyong Zhou, Xiaoling Deng, Huanan Su and Jianchi Chen

    Citation: BMC Microbiology 2012 12:18

    Content type: Research article

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  18. Pseudomonas aeruginosa is an opportunistic pathogen that is the major cause of morbidity and mortality in patients with cystic fibrosis (CF). While most CF patients are thought to acquire P. aeruginosa from the e...

    Authors: Nathan J Hare, Nestor Solis, Christopher Harmer, N Bishara Marzook, Barbara Rose, Colin Harbour, Ben Crossett, Jim Manos and Stuart J Cordwell

    Citation: BMC Microbiology 2012 12:16

    Content type: Research article

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  19. There has been a rising incidence of invasive aspergillosis (IA) in critically ill patients, even in the absence of an apparent predisposing immunodeficiency. The diagnosis of IA is difficult because clinical ...

    Authors: Li-ning Shi, Fang-qiu Li, Mei Huang, Jing-fen Lu, Xiao-xiang Kong, Shi-qin Wang and Hai-feng Shao

    Citation: BMC Microbiology 2012 12:11

    Content type: Research article

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  20. Mangotoxin is an antimetabolite toxin that is produced by strains of Pseudomonas syringae pv. syringae; mangotoxin-producing strains are primarily isolated from mango tissues with symptoms of bacterial apical nec...

    Authors: Eva Arrebola, Víctor J Carrión, Francisco M Cazorla, Alejandro Pérez-García, Jesús Murillo and Antonio de Vicente

    Citation: BMC Microbiology 2012 12:10

    Content type: Research article

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  21. Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-eliminat...

    Authors: Alicia Lara-Márquez, María G Zavala-Páramo, Everardo López-Romero, Nancy Calderón-Cortés, Rodolfo López-Gómez, Ulises Conejo-Saucedo and Horacio Cano-Camacho

    Citation: BMC Microbiology 2011 11:260

    Content type: Research article

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  22. Sphingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, s...

    Authors: David R Johnson, Edith Coronado, Silvia K Moreno-Forero, Hermann J Heipieper and Jan Roelof van der Meer

    Citation: BMC Microbiology 2011 11:250

    Content type: Research article

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  23. Two closely related ICEs, ICESt1 and ICESt3, have been identified in the lactic acid bacterium Streptococcus thermophilus. While their conjugation and recombination modules are almost identical (95% nucleotide id...

    Authors: Nicolas Carraro, Virginie Libante, Catherine Morel, Bernard Decaris, Florence Charron-Bourgoin, Pierre Leblond and Gérard Guédon

    Citation: BMC Microbiology 2011 11:238

    Content type: Research article

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  24. The genus Flavivirus encompasses more than 50 distinct species of arthropod-borne viruses, including several major human pathogens, such as West Nile virus, yellow fever virus, Japanese encephalitis virus and the...

    Authors: Marc Le Breton, Laurène Meyniel-Schicklin, Alexandre Deloire, Bruno Coutard, Bruno Canard, Xavier de Lamballerie, Patrice Andre, Chantal Rabourdin-Combe, Vincent Lotteau and Nathalie Davoust

    Citation: BMC Microbiology 2011 11:234

    Content type: Research article

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  25. Clostridium botulinum is the taxonomic designation for at least six diverse species that produce botulinum neurotoxins (BoNTs). There are seven known serotypes of BoNTs (/A through/G), all of which are potent tox...

    Authors: Rebecca R Terilli, Hercules Moura, Adrian R Woolfitt, Jon Rees, David M Schieltz and John R Barr

    Citation: BMC Microbiology 2011 11:232

    Content type: Research article

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  26. Acinetobacter baumannii is an opportunistic pathogen responsible for hospital-acquired infections. A. baumannii epidemics described world-wide were caused by few genotypic clusters of strains. The occurrence of e...

    Authors: Pier Paolo Di Nocera, Francesco Rocco, Maria Giannouli, Maria Triassi and Raffaele Zarrilli

    Citation: BMC Microbiology 2011 11:224

    Content type: Research article

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  27. Streptococcus thermophilus is an important starter strain for the production of yogurt and cheeses. The analysis of sequenced genomes of four strains of S. thermophilus indicates that they contain several genes o...

    Authors: Romain Henry, Emmanuelle Bruneau, Rozenn Gardan, Stéphane Bertin, Betty Fleuchot, Bernard Decaris and Nathalie Leblond-Bourget

    Citation: BMC Microbiology 2011 11:223

    Content type: Research article

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  28. The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genom...

    Authors: Mark Voorhies, Catherine K Foo and Anita Sil

    Citation: BMC Microbiology 2011 11:216

    Content type: Research article

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  29. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) was first reported in remote regions of Western Australia and is now the predominant MRSA isolated in the state. The objective of this st...

    Authors: Geoffrey W Coombs, Stefan Monecke, Julie C Pearson, Hui-leen Tan, Yi-Kong Chew, Lynne Wilson, Ralf Ehricht, Frances G O'Brien and Keryn J Christiansen

    Citation: BMC Microbiology 2011 11:215

    Content type: Research article

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  30. The fungal pathogen Candida albicans is frequently seen in immune suppressed patients, and resistance to one of the most widely used antifungals, fluconazole (FLC), can evolve rapidly. In recent years it has beco...

    Authors: Samantha J Hoot, Xiuzhong Zheng, Catherine J Potenski, Theodore C White and Hannah L Klein

    Citation: BMC Microbiology 2011 11:214

    Content type: Research article

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  31. A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacteria...

    Authors: György Schneider, Ulrich Dobrindt, Barbara Middendorf, Bianca Hochhut, Valéria Szijártó, Levente Emődy and Jörg Hacker

    Citation: BMC Microbiology 2011 11:210

    Content type: Research article

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  32. The glutamate dehydrogenase gene (gdh) is one of the most popular and useful genetic markers for the genotypic analysis of Giardia duodenalis (syn. G. lamblia, G. intestinalis), the protozoan that widely causes e...

    Authors: Suradej Siripattanapipong, Saovanee Leelayoova, Mathirut Mungthin, RC Andrew Thompson, Parima Boontanom, Wilai Saksirisampant and Peerapan Tan-ariya

    Citation: BMC Microbiology 2011 11:206

    Content type: Research article

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  33. Cronobacter, formerly known as Enterobacter sakazakii, is a food-borne pathogen known to cause neonatal meningitis, septicaemia and death. Current diagnostic tests for identification of Cronobacter do not differe...

    Authors: Stephen E Hamby, Susan Joseph, Stephen J Forsythe and Nadia Chuzhanova

    Citation: BMC Microbiology 2011 11:204

    Content type: Research article

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  34. Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. stra...

    Authors: Derek M Bickhart and David R Benson

    Citation: BMC Microbiology 2011 11:192

    Content type: Research article

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  35. Bacteria employ a variety of adaptation strategies during the course of chronic infections. Understanding bacterial adaptation can facilitate the identification of novel drug targets for better treatment of in...

    Authors: Lei Yang, Martin Holm Rau, Liang Yang, Niels Høiby, Søren Molin and Lars Jelsbak

    Citation: BMC Microbiology 2011 11:184

    Content type: Research article

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  36. repABC operons are present on large, low copy-number plasmids and on some secondary chromosomes in at least 19 α-proteobacterial genera, and are responsible for the replication and segregation properties of these...

    Authors: Ramón Cervantes-Rivera, Francisco Pedraza-López, Gabriela Pérez-Segura and Miguel A Cevallos

    Citation: BMC Microbiology 2011 11:158

    Content type: Research article

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  37. Chlamydia trachomatis is a major cause of sexually transmitted disease in humans. Previous studies in both humans and animal models of chlamydial genital tract infection have suggested that the hormonal status of...

    Authors: Ashkan Amirshahi, Charles Wan, Kenneth Beagley, Joanna Latter, Ian Symonds and Peter Timms

    Citation: BMC Microbiology 2011 11:150

    Content type: Research article

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  38. Bean-nodulating Rhizobium etli originated in Mesoamerica, while soybean-nodulating Sinorhizobium fredii evolved in East Asia. S. fredii strains, such as GR64, have been isolated from bean nodules in Spain, sugges...

    Authors: Laura Cervantes, Patricia Bustos, Lourdes Girard, Rosa Isela Santamaría, Guillermo Dávila, Pablo Vinuesa, David Romero and Susana Brom

    Citation: BMC Microbiology 2011 11:149

    Content type: Research article

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  39. Online spectrophotometric measurements allow monitoring dynamic biological processes with high-time resolution. Contrastingly, numerous other methods require laborious treatment of samples and can only be carr...

    Authors: Dave van Ditmarsch and João B Xavier

    Citation: BMC Microbiology 2011 11:140

    Content type: Methodology article

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  40. Insertion elements (IS) are known to play an important role in the evolution and genomic diversification of Escherichia coli O157:H7 lineages. In particular, IS629 has been found in multiple copies in the E. coli

    Authors: Lydia V Rump, Markus Fischer and Narjol Gonzalez-Escalona

    Citation: BMC Microbiology 2011 11:133

    Content type: Research article

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  41. The ability to differentiate a bioterrorist attack or an accidental release of a research pathogen from a naturally occurring pandemic or disease event is crucial to the safety and security of this nation by e...

    Authors: Shamira J Shallom, Jenni N Weeks, Cristi L Galindo, Lauren McIver, Zhaohui Sun, John McCormick, L Garry Adams and Harold R Garner

    Citation: BMC Microbiology 2011 11:132

    Content type: Research article

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  42. The yeast Xanthophyllomyces dendrorhous is used for the microbiological production of the antioxidant carotenoid astaxanthin. In this study, we established an optimal protocol for protein extraction and performed...

    Authors: Pilar Martinez-Moya, Steven Alexander Watt, Karsten Niehaus, Jennifer Alcaíno, Marcelo Baeza and Víctor Cifuentes

    Citation: BMC Microbiology 2011 11:131

    Content type: Research article

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  43. Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding S...

    Authors: Céline Lucchetti-Miganeh, David Goudenège, David Thybert, Gilles Salbert and Frédérique Barloy-Hubler

    Citation: BMC Microbiology 2011 11:105

    Content type: Database

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  44. Fluconazole (FLC), a triazole antifungal drug, is widely used for the maintenance therapy of cryptococcal meningoencephalitis, the most common opportunistic infection in AIDS patients. In this study, we examin...

    Authors: Ada Rita Florio, Selene Ferrari, Elena De Carolis, Riccardo Torelli, Giovanni Fadda, Maurizio Sanguinetti, Dominique Sanglard and Brunella Posteraro

    Citation: BMC Microbiology 2011 11:97

    Content type: Research article

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