Advertisement
Research Article

Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis

  • Mathieu Picardeau equal contributor,

    equal contributor Contributed equally to this work with: Mathieu Picardeau, Dieter M. Bulach

    Affiliation: Unité de Biologie des Spirochètes, Institut Pasteur, Paris, France

    X
  • Dieter M. Bulach equal contributor,

    equal contributor Contributed equally to this work with: Mathieu Picardeau, Dieter M. Bulach

    Affiliations: Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia, Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia

    X
  • Christiane Bouchier,

    Affiliation: Plate-forme Génomique, Institut Pasteur, Paris, France

    X
  • Richard L. Zuerner,

    Affiliation: Bacterial Diseases of Livestock Research Unit, National Animal Disease Center (NADC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, Iowa, United States of America

    X
  • Nora Zidane,

    Affiliation: Plate-forme Génomique, Institut Pasteur, Paris, France

    X
  • Peter J. Wilson,

    Affiliation: Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia

    X
  • Sophie Creno,

    Affiliation: Plate-forme Génomique, Institut Pasteur, Paris, France

    X
  • Elizabeth S. Kuczek,

    Affiliation: Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia

    X
  • Simona Bommezzadri,

    Affiliation: Unité de Biologie des Spirochètes, Institut Pasteur, Paris, France

    X
  • John C. Davis,

    Affiliation: Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia

    X
  • Annette McGrath,

    Affiliation: Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia

    X
  • Matthew J. Johnson,

    Affiliation: Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia

    X
  • Caroline Boursaux-Eude,

    Affiliation: Plate-forme Intégration et Analyse génomique, Institut Pasteur, Paris, France

    X
  • Torsten Seemann,

    Affiliation: Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia

    X
  • Zoé Rouy,

    Affiliation: Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Laboratoire de Génomique Comparative, Institut de Génomique, Genoscope, Evry, France

    X
  • Ross L. Coppel,

    Affiliations: Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia

    X
  • Julian I. Rood,

    Affiliations: Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia, Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia

    X
  • Aurélie Lajus,

    Affiliation: Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Laboratoire de Génomique Comparative, Institut de Génomique, Genoscope, Evry, France

    X
  • John K. Davies,

    Affiliations: Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia, Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia

    X
  • Claudine Médigue,

    Affiliations: Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Laboratoire de Génomique Comparative, Institut de Génomique, Genoscope, Evry, France, Centre National de la Recherche Scientifique (CNRS) UMR8030, Génomique Métabolique, Evry, France

    X
  • Ben Adler mail

    *E-mail: Ben.Adler@med.monash.edu.au

    Affiliations: Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia, Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia

    X
  • Published: February 13, 2008
  • DOI: 10.1371/journal.pone.0001607
  • Published in PLOS ONE

Reader Comments (2)

Post a new comment on this article

Referee comments: Referee 1

Posted by PLoS_ONE_Group on 18 Feb 2008 at 18:21 GMT

Referee 1's review:

It's a good paper and a welcome initiative. The L. biflexa genome was long awaited. It's a well written manuscript. However, I think the following issues need to be remedied before the manuscript can be accepted:

Authors have taken a short-cut approach to compile methods section. There is no dearth of space in PLoS ONE, so please don't feel shy of expanding on this (follow the style of ... Herron-Olson L, Fitzgerald JR, Musser JM, Kapur V. Molecular Correlates of Host Specialization in Staphylococcus aureus. PLoS ONE. 2007 Oct 31;2(10):e1120). Also please enlighten the readers on how the gaps (both physical and sequencing gaps) were encountered in the assemblies and how they were closed. This is the point where many genome sequencing labs get trouble and the experience of the authors in this area will be greatly helpful to the readers who would like to follow their work.

I think this paper could have been developed as a marvelous treatise in the light of all the spirochete genomes that have been sequenced till date. For the genus Leptospira alone, L. interrogans (2 strains), L. borgpetersenii (2 strains) and L. biflexa (2 strains) have been sequenced and the data in public domain is overwhelming. Given this scenario, are we going to witness a 'metagenomic' era in spirochete biology wherein the wisdom gained from all the six leptospiral genomes can be harnessed? The authors discuss 'leptospiral core genome' as a sub topic; why not they also discuss 'leptospiral metagenome' as a separate issue? (follow the style of .... Beres S and Musser JM Contribution of exogenous genetic elements to the group A Streptococcus metagenome. PLoS ONE. 2007 Aug 29;2(8):e800). This tells me of yet another short-cut that the authors seemingly adopted (to have merged results and discussion section). Are they falling short of story to discuss? Perhaps this is the reason they cite just 37 references. Is this kind of 'extra terseness' sufficient to gauge current state of the art and the exact dimensions of the findings?

Finally, I am happy that the authors considered publish their paper under the open access (OA) charter. However, the manuscript is not written and developed keeping in mind the flexibility of the OA system. From the manuscript formatting I can guess that authors may have initially considered print journals (like PNAS etc.) for their paper, before opting for PLoSONE, and at the end they did not take pains to rebuild everything in an OA format. OA journals, (especially PLoS ONE) have no page length restriction; it is therefore, inappropriate to have sequestered much of the essential data in the supplemental files. Many readers, more often tend to rely on main pdf file only and forget to consult supplemental data. Therefore, I would like to see all the supplemental material to be rebuilt with the main manuscript, except may be the excel file. This may please be followed scrupulously.

**********
N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.