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

    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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Research article

    Quorum sensing of Streptococcus mutans is activated by Aggregatibacter actinomycetemcomitans and by the periodontal microbiome

    The oral cavity is inhabited by complex microbial communities forming biofilms that can cause caries and periodontitis. Cell-cell communication might play an important role in modulating the physiologies of in...

    Szymon P. Szafrański, Zhi-Luo Deng, Jürgen Tomasch, Michael Jarek, Sabin Bhuju, Manfred Rohde, Helena Sztajer and Irene Wagner-Döbler

    BMC Genomics 2017 18:238

    Published on: 20 March 2017

  12. Research article

    Genome analysis following a national increase in Scarlet Fever in England 2014

    During a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with compari...

    Victoria Chalker, Aleksey Jironkin, Juliana Coelho, Ali Al-Shahib, Steve Platt, Georgia Kapatai, Roger Daniel, Chenchal Dhami, Marisa Laranjeira, Timothy Chambers, Rebecca Guy, Theresa Lamagni, Timothy Harrison, Meera Chand, Alan P. Johnson and Anthony Underwood

    BMC Genomics 2017 18:224

    Published on: 10 March 2017

  13. Research article

    Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

    Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicate...

    Joseph Crispell, Ruth N. Zadoks, Simon R. Harris, Brent Paterson, Desmond M. Collins, Geoffrey W. de-Lisle, Paul Livingstone, Mark A. Neill, Roman Biek, Samantha J. Lycett, Rowland R. Kao and Marian Price-Carter

    BMC Genomics 2017 18:180

    Published on: 16 February 2017

  14. Research article

    Plasmid diversity and phylogenetic consistency in the Lyme disease agent Borrelia burgdorferi

    Bacteria from the genus Borrelia are known to harbor numerous linear and circular plasmids. We report here a comparative analysis of the nucleotide sequences of 236 plasmids present in fourteen independent isolat...

    Sherwood R. Casjens, Eddie B. Gilcrease, Marija Vujadinovic, Emmanuel F. Mongodin, Benjamin J. Luft, Steven E. Schutzer, Claire M. Fraser and Wei-Gang Qiu

    BMC Genomics 2017 18:165

    Published on: 15 February 2017

  15. Research article

    Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains

    CRISPR and CRISPR-flanking genomic regions are important for molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) strains, and potentially for adaptive immunity to phage and plasmid DNA, and endoge...

    Paul Jeffrey Freidlin, Israel Nissan, Anna Luria, Drora Goldblatt, Lana Schaffer, Hasia Kaidar-Shwartz, Daniel Chemtob, Zeev Dveyrin, Steven Robert Head and Efrat Rorman

    BMC Genomics 2017 18:168

    Published on: 15 February 2017

  16. Research article

    Genetic and functional characterisation of the lactococcal P335 phage-host interactions

    Despite continuous research efforts, bacterio(phages) infecting Lactococcus lactis starter strains persist as a major threat to dairy fermentations. The lactococcal P335 phages, which are currently classified int...

    Jennifer Mahony, Joana Oliveira, Barry Collins, Laurens Hanemaaijer, Gabriele Andrea Lugli, Horst Neve, Marco Ventura, Thijs R. Kouwen, Christian Cambillau and Douwe van Sinderen

    BMC Genomics 2017 18:146

    Published on: 10 February 2017

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