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 sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

    Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its ...

    Xianfeng Guo, Shenghui Li, Jiachun Zhang, Feifan Wu, Xiangchun Li, Dan Wu, Min Zhang, Zihao Ou, Zhuye Jie, Qiulong Yan, Peng Li, Jiangfeng Yi and Yongzheng Peng

    BMC Genomics 2017 18:800

    Published on: 18 October 2017

  2. Research article

    De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

    Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despi...

    Paulina Deptula, Pia K. Laine, Richard J. Roberts, Olli-Pekka Smolander, Helena Vihinen, Vieno Piironen, Lars Paulin, Eija Jokitalo, Kirsi Savijoki, Petri Auvinen and Pekka Varmanen

    BMC Genomics 2017 18:790

    Published on: 16 October 2017

  3. Research article

    Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events

    Horizontal transfer of mobile genetic elements (MGEs) that carry virulence and antimicrobial resistance genes mediates the evolution of methicillin-resistant Staphylococcus aureus, and the emergence of new MRSA c...

    Dorota Jamrozy, Francesc Coll, Alison E. Mather, Simon R. Harris, Ewan M. Harrison, Alasdair MacGowan, Andreas Karas, Tony Elston, M. Estée Török, Julian Parkhill and Sharon J. Peacock

    BMC Genomics 2017 18:684

    Published on: 4 September 2017

  4. Research article

    Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

    Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range of bacterial infections. Plasmid-mediated qnr genes provide resistance to fluoroquinolones in many bacterial species and are ...

    Fredrik Boulund, Fanny Berglund, Carl-Fredrik Flach, Johan Bengtsson-Palme, Nachiket P. Marathe, DG Joakim Larsson and Erik Kristiansson

    BMC Genomics 2017 18:682

    Published on: 2 September 2017

  5. Methodology article

    Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome

    Thanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose...

    Martyna Marynowska, Xavier Goux, David Sillam-Dussès, Corinne Rouland-Lefèvre, Yves Roisin, Philippe Delfosse and Magdalena Calusinska

    BMC Genomics 2017 18:681

    Published on: 1 September 2017

  6. Research

    Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution

    Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, ...

    Bidhan Ch. Bera, Nitin Virmani, Naveen Kumar, Taruna Anand, S Pavulraj, Adam Rash, Debra Elton, Nicola Rash, Sandeep Bhatia, Richa Sood, Raj Kumar Singh and Bhupendra Nath Tripathi

    BMC Genomics 2017 18:652

    Published on: 23 August 2017

  7. Research article

    Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

    The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to o...

    Sean P. Gilmore, John K. Henske, Jessica A. Sexton, Kevin V. Solomon, Susanna Seppälä, Justin I Yoo, Lauren M. Huyett, Abe Pressman, James Z. Cogan, Veronika Kivenson, Xuefeng Peng, YerPeng Tan, David L. Valentine and Michelle A. O’Malley

    BMC Genomics 2017 18:639

    Published on: 21 August 2017

  8. 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

  9. 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

  10. 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

  11. 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

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