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

    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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Research Article

    Spread of avian pathogenic Escherichia coli ST117 O78:H4 in Nordic broiler production

    Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colib...

    Troels Ronco, Marc Stegger, Rikke Heidemann Olsen, Camilla Sekse, Anne Bang Nordstoga, Tarja Pohjanvirta, Berit Lilje, Ulrike Lyhs, Paal Skytt Andersen and Karl Pedersen

    BMC Genomics 2017 18:13

    Published on: 3 January 2017

  15. Research article

    Identification of genes affecting alginate biosynthesis in Pseudomonas fluorescens by screening a transposon insertion library

    Polysaccharides often are necessary components of bacterial biofilms and capsules. Production of these biopolymers constitutes a drain on key components in the central carbon metabolism, but so far little is k...

    Helga Ertesvåg, Håvard Sletta, Mona Senneset, Yi-Qian Sun, Geir Klinkenberg, Therese Aursand Konradsen, Trond E. Ellingsen and Svein Valla

    BMC Genomics 2017 18:11

    Published on: 3 January 2017

  16. Research article

    Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomes

    Many gram-negative bacteria use type III secretion systems (T3SSs) to translocate effector proteins into host cells. T3SS effectors can give some bacteria a competitive edge over others within the same environ...

    Christopher K. Hobbs, Vanessa L. Porter, Maxwell L. S. Stow, Bupe A. Siame, Herbert H. Tsang and Ka Yin Leung

    BMC Genomics 2016 17:1048

    Published on: 19 December 2016

  17. Research article

    Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078

    How the pathogen Clostridium difficile might survive, evolve and be transferred between reservoirs within the natural environment is poorly understood. Some ribotypes are found both in clinical and environmental ...

    Katherine R. Hargreaves, Anisha M. Thanki, Bethany R. Jose, Marco R. Oggioni and Martha R. J. Clokie

    BMC Genomics 2016 17:1020

    Published on: 13 December 2016

  18. Research article

    Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage

    Propionibacterium freudenreichii is an Actinobacterium widely used in the dairy industry as a ripening culture for Swiss-type cheeses, for vitamin B12 production and some strains displ...

    Flavia Figueira Aburjaile, Marine Rohmer, Hugues Parrinello, Marie-Bernadette Maillard, Eric Beaucher, Gwénaële Henry, Aurélie Nicolas, Marie-Noëlle Madec, Anne Thierry, Sandrine Parayre, Stéphanie-Marie Deutsch, Muriel Cocaign-Bousquet, Anderson Miyoshi, Vasco Azevedo, Yves Le Loir and Hélène Falentin

    BMC Genomics 2016 17:1007

    Published on: 8 December 2016

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