• Login
    About WHOAS
    View Item 
    •   WHOAS Home
    • Marine Biological Laboratory
    • Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
    • View Item
    •   WHOAS Home
    • Marine Biological Laboratory
    • Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of WHOASCommunities & CollectionsBy Issue DateAuthorsTitlesKeywordsThis CollectionBy Issue DateAuthorsTitlesKeywords

    My Account

    LoginRegister

    Statistics

    View Usage Statistics

    Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at the genus level

    Thumbnail
    View/Open
    Author's manuscript (969.6Kb)
    Supplementary figure and tables (637.7Kb)
    Date
    2011-04-27
    Author
    Rodrigues, Jorge L. M.  Concept link
    Serres, Margrethe H.  Concept link
    Tiedje, James M.  Concept link
    Metadata
    Show full item record
    Citable URI
    https://hdl.handle.net/1912/4734
    As published
    https://doi.org/10.1128/AEM.00097-11
    Abstract
    The use of comparative genomics among different microbiological species has increased substantially as sequence technologies become more affordable. However, efforts to fully link a genotype to its phenotype remain limited to the development of one mutant at the time. In this study, we provide a high throughput alternative to this limiting step by coupling comparative genomics to phenotype arrays for five sequenced Shewanella strains. Positive phenotypes were obtained for 441 nutrients (C, N, P, and S sources), with N-based compounds being the most utilized for all strains. Many genes and pathways predicted by genome analyses were confirmed with the comparative phenotype assay, and three degradation pathways believed to be missing in Shewanella were confirmed. A number of previously unknown gene products were predicted to be part of pathways or to have a function, expanding the number of gene targets for future genetic analyses. Ecologically, the comparative high throughput phenotype analysis provided insights into niche specialization within the five different strains. For example, Shewanella amazonensis strain SB2B, isolated from the Amazon River delta, was capable of utilizing 60 C compounds, whereas Shewanella sp. strain W3-18-1, from the deep marine sediment, utilized only 25 of them. In spite of the large number of nutrient sources yielding positive results, our study indicated that except for the N-sources they were not sufficiently informative to predict growth phenotypes from increasing evolutionary distances. Our results indicate the importance of phenotypic evaluation for confirming genome predictions. This strategy will accelerate the functional discovery of genes and provide an ecological framework for microbial genome sequencing projects.
    Description
    Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 77 (2011): 5352-5360, doi:10.1128/AEM.00097-11.
    Collections
    • Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
    Suggested Citation
    Preprint: Rodrigues, Jorge L. M., Serres, Margrethe H., Tiedje, James M., "Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at the genus level", 2011-04-27, https://doi.org/10.1128/AEM.00097-11, https://hdl.handle.net/1912/4734
     
    All Items in WHOAS are protected by original copyright, with all rights reserved, unless otherwise indicated. WHOAS also supports the use of the Creative Commons licenses for original content.
    A service of the MBLWHOI Library | About WHOAS
    Contact Us | Send Feedback | Privacy Policy
    Core Trust Logo