Microbial genetics, genomics and proteomics

Section edited by Hirotada Mori

This section aims to publish studies relating to all aspects of microbial genomics, proteomics, metabolomics and systems biology.

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  1. Research article

    Towards diagnostic metagenomics of Campylobacter in fecal samples

    The development of diagnostic metagenomics is driven by the need for universal, culture-independent methods for detection and characterization of pathogens to substitute the time-consuming, organism-specific, ...

    Sandra Christine Andersen, Kristoffer Kiil, Christoffer Bugge Harder, Mathilde Hasseldam Josefsen, Søren Persson, Eva Møller Nielsen and Jeffrey Hoorfar

    BMC Microbiology 2017 17:133

    Published on: 8 June 2017

  2. Research article

    Site-specific His/Asp phosphoproteomic analysis of prokaryotes reveals putative targets for drug resistance

    Phosphorylation of amino acid residues on proteins is an important and common post-translational modification in both eukaryotes and prokaryotes. Most research work has been focused on phosphorylation of serin...

    Shu-Jung Lai, I-Fan Tu, Wan-Ling Wu, Jhih-Tian Yang, Louis Y. P. Luk, Mei-Chin Lai, Yu-Hsuan Tsai and Shih-Hsiung Wu

    BMC Microbiology 2017 17:123

    Published on: 25 May 2017

  3. Research article

    Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment

    Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. How...

    Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor and Romilio T. Espejo

    BMC Microbiology 2017 17:118

    Published on: 19 May 2017

  4. Research article

    Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis

    DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria, and is required for DNA transformation to various extents among bacterial species. However, the interaction of DprA with ...

    Getachew Tesfaye Beyene, Shewit Kalayou, Tahira Riaz and Tone Tonjum

    BMC Microbiology 2017 17:96

    Published on: 21 April 2017

  5. Research article

    Comparative genomics and evolution of the amylase-binding proteins of oral streptococci

    Successful commensal bacteria have evolved to maintain colonization in challenging environments. The oral viridans streptococci are pioneer colonizers of dental plaque biofilm. Some of these bacteria have adap...

    Elaine M. Haase, Yurong Kou, Amarpreet Sabharwal, Yu-Chieh Liao, Tianying Lan, Charlotte Lindqvist and Frank A. Scannapieco

    BMC Microbiology 2017 17:94

    Published on: 20 April 2017

  6. Research article

    The expression of fibronectin is significantly suppressed in macrophages to exert a protective effect against Staphylococcus aureus infection

    Fibronectin (Fn) plays a major role in the attachment of Staphylococcus aureus to host cells by bridging staphylococcal fibronectin-binding proteins (FnBPs) and cell-surface integrins. A previous study demonstrat...

    Hong-Yi Chen, Mei-Hui Lin, Chien-Cheng Chen and Jwu-Ching Shu

    BMC Microbiology 2017 17:92

    Published on: 13 April 2017

  7. Research article

    Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae

    The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular space...

    Min Guo, Ruifu Yang, Chen Huang, Qiwen Liao, Guangyi Fan, Chenghang Sun and Simon Ming-Yuen Lee

    BMC Microbiology 2017 17:86

    Published on: 4 April 2017

  8. Research article

    The ST131 Escherichia coli H22 subclone from human intestinal microbiota: Comparison of genomic and phenotypic traits with those of the globally successful H30 subclone

    In 2006, we found healthy subjects carrying ST131 Escherichia coli in their intestinal microbiota consisting of two populations: a subdominant population of fluoroquinolone-resistant E. coli belonging to subclone...

    Marie-Hélène Nicolas-Chanoine, Marie Petitjean, Azucena Mora, Noémie Mayer, Jean-Philippe Lavigne, Olivier Boulet, Véronique Leflon-Guibout, Jorge Blanco and Didier Hocquet

    BMC Microbiology 2017 17:71

    Published on: 27 March 2017

  9. Researc article

    A shift in the virulence potential of Corynebacterium pseudotuberculosis biovar ovis after passage in a murine host demonstrated through comparative proteomics

    Corynebacterium pseudotuberculosis biovar ovis, a facultative intracellular pathogen, is the etiologic agent of caseous lymphadenitis in small ruminants. During the infection process,

    Wanderson M. Silva, Fernanda A. Dorella, Siomar C. Soares, Gustavo H. M. F. Souza, Thiago L. P. Castro, Núbia Seyffert, Henrique Figueiredo, Anderson Miyoshi, Yves Le Loir, Artur Silva and Vasco Azevedo

    BMC Microbiology 2017 17:55

    Published on: 22 March 2017

  10. Research article

    Genome-wide analysis of a avirulent and reveal the strain induces pro-tective immunity against challenge with virulent Streptococcus suis Serotype 2

    It was previously reported in China that two recent large-scale outbreaks of Streptococcus suis serotype 2 (S. suis 2) infections in human were caused by two highly virulent S. suis 2 strains, from which a novel ...

    Jing Wang, Youjun Feng, Changjun Wang, Feng Zheng, Bachar Hassan, Liming Zhi, Wenjuan Li, Yi Yao, Elaine He, Shibo Jiang and Jiaqi Tang

    BMC Microbiology 2017 17:67

    Published on: 14 March 2017

  11. Research article

    The altered gut microbiota in adults with cystic fibrosis

    Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transme...

    D.G. Burke, F. Fouhy, M. J. Harrison, M. C. Rea, P. D. Cotter, O. O’Sullivan, C. Stanton, C. Hill, F. Shanahan, B. J. Plant and R. P. Ross

    BMC Microbiology 2017 17:58

    Published on: 9 March 2017

    The Erratum to this article has been published in BMC Microbiology 2017 17:102

  12. Research article

    Comparative genomics of Enterococcus spp. isolated from bovine feces

    Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeut...

    Alicia G. Beukers, Rahat Zaheer, Noriko Goji, Kingsley K. Amoako, Alexandre V. Chaves, Michael P. Ward and Tim A. McAllister

    BMC Microbiology 2017 17:52

    Published on: 8 March 2017

  13. Research article

    Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism

    Escherichia coli O157:H7 (O157) strain 86–24, linked to a 1986 disease outbreak, displays curli- and biofilm-negative phenotypes that are correlated with the lack of Congo red (CR) bin...

    V. K. Sharma, D. O. Bayles, D. P. Alt, T. Looft, B. W. Brunelle and J. A. Stasko

    BMC Microbiology 2017 17:56

    Published on: 8 March 2017

  14. Research article

    Signature-tagged mutagenesis screening revealed a novel smooth-to-rough transition determinant of Salmonella enterica serovar Enteritidis

    Salmonella enterica serovar Enteritidis (S. Enteritidis) has emerged as one of the most important food-borne pathogens for humans. Lipopolysaccharide (LPS), as a component of the outer...

    Yang Jiao, Rongxian Guo, Peipei Tang, Xilong Kang, Junlei Yin, Kaiyue Wu, Shizhong Geng, Qiuchun Li, Jun Sun, Xiulong Xu, Xiaohui Zhou, Junji Gan, Xinan Jiao, Xiufan Liu and Zhiming Pan

    BMC Microbiology 2017 17:48

    Published on: 3 March 2017

  15. Research article

    Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi)

    Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be disco...

    Fernanda Badotti, Francislon Silva de Oliveira, Cleverson Fernando Garcia, Aline Bruna Martins Vaz, Paula Luize Camargos Fonseca, Laila Alves Nahum, Guilherme Oliveira and Aristóteles Góes-Neto

    BMC Microbiology 2017 17:42

    Published on: 23 February 2017

  16. Research article

    Molecular pathways underlying inhibitory effect of antimicrobial peptide Nal-P-113 on bacteria biofilms formation of Porphyromonas gingivalis W83 by DNA microarray

    Wound-related infection remains a major challenge for health professionals. One disadvantage in conventional antibiotics is their inability to penetrate biofilms, the main protective strategy for bacteria to e...

    Hong-yan Wang, Li Lin, Li-si Tan, Hui-Yuan Yu, Jya-Wei Cheng and Ya-ping Pan

    BMC Microbiology 2017 17:37

    Published on: 17 February 2017

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