Prokaryote microbial genomics

Section edited by Theo Smits

This section covers the structure and function of the genomes of prokaryotic and archaea microorganisms.

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  1. Research article

    Genome analysis of the thermoacidophilic archaeon Acidianus copahuensis focusing on the metabolisms associated to biomining activities

    Several archaeal species from the order Sulfolobales are interesting from the biotechnological point of view due to their biomining capacities. Within this group, the genus Acidianus contains four biomining speci...

    María Sofía Urbieta, Nicolás Rascovan, Martín P. Vázquez and Edgardo Donati

    BMC Genomics 2017 18:445

    Published on: 6 June 2017

  2. Research article

    Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival

    Vibrio parahaemolyticus causes serious seafood-borne gastroenteritis and death in humans. Raw seafood is often subjected to post-harvest processing and low-temperature storage. To date...

    Chunhua Zhu, Boyi Sun, Taigang Liu, Huajun Zheng, Wenyi Gu, Wei He, Fengjiao Sun, Yaping Wang, Meicheng Yang, Weicheng Bei, Xu Peng, Qunxin She, Lu Xie and Lanming Chen

    BMC Genomics 2017 18:436

    Published on: 5 June 2017

  3. Research article

    Defining the ABC of gene essentiality in streptococci

    Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant lib...

    Amelia R. L. Charbonneau, Oliver P. Forman, Amy K. Cain, Graham Newland, Carl Robinson, Mike Boursnell, Julian Parkhill, James A. Leigh, Duncan J. Maskell and Andrew S. Waller

    BMC Genomics 2017 18:426

    Published on: 31 May 2017

  4. Research article

    Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia

    Meningococcal colonization is a prerequisite for transmission and disease, but the bacterium only very infrequently causes disease while asymptomatic carriage is common. Carriage is highly dynamic, showing a g...

    Guro K. Bårnes, Ola Brønstad Brynildsrud, Bente Børud, Bereket Workalemahu, Paul A. Kristiansen, Demissew Beyene, Abraham Aseffa and Dominique A. Caugant

    BMC Genomics 2017 18:407

    Published on: 25 May 2017

  5. Research article

    Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad

    Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an “accidental pathogen”; however, the transiti...

    Kanny Diallo, Kadija Gamougam, Doumagoum M. Daugla, Odile B. Harrison, James E. Bray, Dominique A. Caugant, Jay Lucidarme, Caroline L. Trotter, Musa Hassan-King, James M. Stuart, Olivier Manigart, Brian M. Greenwood and Martin C. J. Maiden

    BMC Genomics 2017 18:398

    Published on: 22 May 2017

  6. Research article

    Complete sequence and comparative genomic analysis of eight native Pseudomonas syringae plasmids belonging to the pPT23A family

    The pPT23A family of plasmids appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related specie...

    José A. Gutiérrez-Barranquero, Francisco M. Cazorla, Antonio de Vicente and George W. Sundin

    BMC Genomics 2017 18:365

    Published on: 10 May 2017

  7. Research article

    No evidence for a bovine mastitis Escherichia coli pathotype

    Escherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result ...

    Andreas Leimbach, Anja Poehlein, John Vollmers, Dennis Görlich, Rolf Daniel and Ulrich Dobrindt

    BMC Genomics 2017 18:359

    Published on: 8 May 2017

  8. Research article

    European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

    Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in hum...

    H. M. B. Seth-Smith, Leonor Sánchez Busó, M. Livingstone, M. Sait, S. R. Harris, K. D. Aitchison, Evangelia Vretou, V. I. Siarkou, K. Laroucau, K. Sachse, D. Longbottom and N. R. Thomson

    BMC Genomics 2017 18:344

    Published on: 4 May 2017

  9. Research article

    Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data

    Most tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends.

    Cheng-Han Chung, Michael H. Walter, Luobin Yang, Shu-Chuan (Grace) Chen, Vern Winston and Michael A. Thomas

    BMC Genomics 2017 18:350

    Published on: 4 May 2017

  10. Research article

    Detecting RNA-RNA interactions in E. coli using a modified CLASH method

    Bacterial small regulatory RNAs (sRNAs) play important roles in sensing environment changes through sRNA-target mRNA interactions. However, the current strategy for detecting sRNA-mRNA interactions usually com...

    Tao Liu, Kaiyu Zhang, Song Xu, Zheng Wang, Hanjiang Fu, Baolei Tian, Xiaofei Zheng and Wuju Li

    BMC Genomics 2017 18:343

    Published on: 3 May 2017

  11. Research article

    A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes

    Examination of complex biological systems has long been achieved through methodical investigation of the system’s individual components. While informative, this strategy often leads to inappropriate conclusion...

    Sarah L. Grady, Stephanie A. Malfatti, Thusitha S. Gunasekera, Brian K. Dalley, Matt G. Lyman, Richard C. Striebich, Michael B. Mayhew, Carol L. Zhou, Oscar N. Ruiz and Larry C. Dugan

    BMC Genomics 2017 18:334

    Published on: 28 April 2017

  12. Research article

    Genome adaptive evolution of Lactobacillus casei under long-term antibiotic selection pressures

    The extensive use of antibiotics in medicine has raised serious concerns about biosafety. However, the effect of antibiotic application on the adaptive evolution of microorganisms, especially to probiotic bact...

    Jicheng Wang, Xiao Dong, Yuyu Shao, Huiling Guo, Lin Pan, Wenyan Hui, Lai-Yu Kwok, Heping Zhang and Wenyi Zhang

    BMC Genomics 2017 18:320

    Published on: 24 April 2017

  13. Research article

    Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

    Metagenomics is the study of the microbial genomes isolated from communities found on our bodies or in our environment. By correctly determining the relation between human health and the human associated micro...

    William W. Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J. Craig Venter, Chad Garner, Karen E. Nelson and Weizhong Li

    BMC Genomics 2017 18:296

    Published on: 13 April 2017

  14. Research article

    Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

    Commensal bacteria like Neisseria meningitidis sometimes cause serious disease. However, genomic comparison of hyperinvasive and apathogenic lineages did not reveal unambiguous hints towards indispensable virulen...

    Biju Joseph Ampattu, Laura Hagmann, Chunguang Liang, Marcus Dittrich, Andreas Schlüter, Jochen Blom, Elizaveta Krol, Alexander Goesmann, Anke Becker, Thomas Dandekar, Tobias Müller and Christoph Schoen

    BMC Genomics 2017 18:282

    Published on: 7 April 2017

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The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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