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

    Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees

    Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using...

    Rediet Oshone, Mariama Ngom, Feixia Chu, Samira Mansour, Mame Ourèye Sy, Antony Champion and Louis S. Tisa

    BMC Genomics 2017 18:633

    Published on: 18 August 2017

  2. Research article

    Role of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host

    Type VI secretion systems (T6SS) are widespread among Gram-negative bacteria and have a potential role as essential virulence factors or to maintain symbiotic interactions. Three T6SS gene clusters were identi...

    Tim Kamber, Joël F. Pothier, Cosima Pelludat, Fabio Rezzonico, Brion Duffy and Theo H. M. Smits

    BMC Genomics 2017 18:628

    Published on: 17 August 2017

  3. Research article

    Identification of new protein-coding genes with a potential role in the virulence of the plant pathogen Xanthomonas euvesicatoria

    Bacteria of the genus Xanthomonas are economically important plant pathogens. Pathogenicity of Xanthomonas spp. depends on the type III-secretion system and additional virulence determinants. The number of sequen...

    Ulrike Abendroth, Norman Adlung, Andreas Otto, Benjamin Grüneisen, Dörte Becher and Ulla Bonas

    BMC Genomics 2017 18:625

    Published on: 16 August 2017

  4. Research article

    Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences

    Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a...

    Yuan Li, Benjamin J. Metcalf, Sopio Chochua, Zhongya Li, Robert E. Gertz Jr, Hollis Walker, Paulina A. Hawkins, Theresa Tran, Lesley McGee and Bernard W. Beall

    BMC Genomics 2017 18:621

    Published on: 15 August 2017

  5. Research article

    Essential genome of Campylobacter jejuni

    Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in bot...

    Rabindra K. Mandal, Tieshan Jiang and Young Min Kwon

    BMC Genomics 2017 18:616

    Published on: 14 August 2017

  6. Research article

    Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources

    The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition syst...

    Bijay K. Khajanchi, Nur A. Hasan, Seon Young Choi, Jing Han, Shaohua Zhao, Rita R. Colwell, Carl E. Cerniglia and Steven L. Foley

    BMC Genomics 2017 18:570

    Published on: 2 August 2017

  7. Research article

    The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110

    Acarbose is used in the treatment of diabetes mellitus type II and is produced by Actinoplanes sp. SE50/110. Although the biosynthesis of acarbose has been intensively studied, profound knowledge about transcript...

    Timo Wolf, Julian Droste, Tetiana Gren, Vera Ortseifen, Susanne Schneiker-Bekel, Till Zemke, Alfred Pühler and Jörn Kalinowski

    BMC Genomics 2017 18:562

    Published on: 25 July 2017

  8. Methodology Article

    Common and phylogenetically widespread coding for peptides by bacterial small RNAs

    While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often as...

    Robin C. Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A. Mueller, Martina Chovancová, Martin von Bergen and Benno Schwikowski

    BMC Genomics 2017 18:553

    Published on: 21 July 2017

  9. Research article

    Genome analysis of E. coli isolated from Crohn’s disease patients

    Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was cont...

    Daria V. Rakitina, Alexander I. Manolov, Alexandra V. Kanygina, Sofya K. Garushyants, Julia P. Baikova, Dmitry G. Alexeev, Valentina G. Ladygina, Elena S. Kostryukova, Andrei K. Larin, Tatiana A. Semashko, Irina Y. Karpova, Vladislav V. Babenko, Ruzilya K. Ismagilova, Sergei Y. Malanin, Mikhail S. Gelfand, Elena N. Ilina…

    BMC Genomics 2017 18:544

    Published on: 19 July 2017

  10. Research article

    Evolutionary and genetic analysis of the VP2 gene of canine parvovirus

    Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar ...

    Gairu Li, Senlin Ji, Xiaofeng Zhai, Yuxiang Zhang, Jie Liu, Mengyan Zhu, Jiyong Zhou and Shuo Su

    BMC Genomics 2017 18:534

    Published on: 17 July 2017

  11. Research article

    Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery

    Tuberculosis (TB) is caused by Mycobacterium tuberculosis and represents one of the major challenges facing drug discovery initiatives worldwide. The considerable rise in bacterial drug resistance in recent years...

    Amine Namouchi, Mena Cimino, Sandrine Favre-Rochex, Patricia Charles and Brigitte Gicquel

    BMC Genomics 2017 18:530

    Published on: 13 July 2017

  12. Research article

    Plasmid composition in Aeromonas salmonicida subsp. salmonicida 01-B526 unravels unsuspected type three secretion system loss patterns

    Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in i...

    Katherine H. Tanaka, Antony T. Vincent, Jean-Guillaume Emond-Rheault, Marcin Adamczuk, Michel Frenette and Steve J. Charette

    BMC Genomics 2017 18:528

    Published on: 12 July 2017

  13. Research article

    Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts

    A restricted set of aerobic bacteria dominated by the Acinetobacter genus was identified in murine intestinal colonic crypts. The vicinity of such bacteria with intestinal stem cells could indicate that they prot...

    Azadeh Saffarian, Marie Touchon, Céline Mulet, Régis Tournebize, Virginie Passet, Sylvain Brisse, Eduardo P. C. Rocha, Philippe J. Sansonetti and Thierry Pédron

    BMC Genomics 2017 18:525

    Published on: 11 July 2017

  14. Research article

    Assembling metagenomes, one community at a time

    Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes,...

    Andries Johannes van der Walt, Marc Warwick van Goethem, Jean-Baptiste Ramond, Thulani Peter Makhalanyane, Oleg Reva and Don Arthur Cowan

    BMC Genomics 2017 18:521

    Published on: 10 July 2017

  15. Research article

    Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface

    Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute up to 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic sq...

    Henk Bolhuis, Ana Belén Martín-Cuadrado, Riccardo Rosselli, Lejla Pašić and Francisco Rodriguez-Valera

    BMC Genomics 2017 18:510

    Published on: 3 July 2017

  16. Research article

    Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

    Marine phages are spectacularly diverse in nature. Dozens of roseophages infecting members of Roseobacter clade bacteria were isolated and characterized, exhibiting a very high degree of genetic diversity. In the...

    Kai Tang, Dan Lin, Qiang Zheng, Keshao Liu, Yujie Yang, Yu Han and Nianzhi Jiao

    BMC Genomics 2017 18:485

    Published on: 27 June 2017

  17. 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

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