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

    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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. Research article

    The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes

    The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the gen...

    Jon Bohlin, Vegard Eldholm, John H. O. Pettersson, Ola Brynildsrud and Lars Snipen

    BMC Genomics 2017 18:151

    Published on: 10 February 2017

  10. Research article

    Prophages and adaptation of Staphylococcus aureus ST398 to the human clinic

    It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characteri...

    Seydina M. Diene, Anna Rita Corvaglia, Patrice François and Nathalie van der Mee-Marquet

    BMC Genomics 2017 18:133

    Published on: 6 February 2017

  11. Research article

    Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts

    Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium)...

    Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf and Jose-Antonio Munive

    BMC Genomics 2017 18:85

    Published on: 14 January 2017

  12. Research article

    The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions

    Bifidobacteria are among the first anaerobic bacteria colonizing the gut. Bifidobacteria require iron for growth and their iron-sequestration mechanisms are important for their fitness and possibly inhibit ent...

    Pamela Vazquez-Gutierrez, Marc J. A. Stevens, Peter Gehrig, Simon Barkow-Oesterreicher, Christophe Lacroix and Christophe Chassard

    BMC Genomics 2017 18:41

    Published on: 6 January 2017

  13. Research Article

    Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

    Xanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.), X. transluc...

    Lena Hersemann, Daniel Wibberg, Jochen Blom, Alexander Goesmann, Franco Widmer, Frank-Jörg Vorhölter and Roland Kölliker

    BMC Genomics 2017 18:35

    Published on: 5 January 2017

  14. Research article

    Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

    Transmission of Borrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regula...

    Niko Popitsch, Ivana Bilusic, Philipp Rescheneder, Renée Schroeder and Meghan Lybecker

    BMC Genomics 2017 18:28

    Published on: 5 January 2017

  15. Methodology article

    In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria

    Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (...

    Olaa Motwalli, Magbubah Essack, Boris R. Jankovic, Boyang Ji, Xinyao Liu, Hifzur Rahman Ansari, Robert Hoehndorf, Xin Gao, Stefan T. Arold, Katsuhiko Mineta, John A. C. Archer, Takashi Gojobori, Ivan Mijakovic and Vladimir B. Bajic

    BMC Genomics 2017 18:33

    Published on: 5 January 2017

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