HostPhinder: A Phage Host Prediction Tool

Julia Villarroel, Kortine Annina Kleinheinz, Vanessa Isabell Jurtz, Henrike Zschach, Ole Lund, Morten Nielsen, Mette Voldby Larsen

    Research output: Contribution to journalJournal articleResearchpeer-review

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    Abstract

    The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2].
    Original languageEnglish
    Article number116
    JournalViruses
    Volume8
    Issue number5
    Number of pages22
    ISSN1999-4915
    DOIs
    Publication statusPublished - 2016

    Bibliographical note

    This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Keywords

    • Prediction
    • Genome
    • K-mers
    • “Host specificity”

    Cite this

    Villarroel, J., Kleinheinz, K. A., Jurtz, V. I., Zschach, H., Lund, O., Nielsen, M., & Larsen, M. V. (2016). HostPhinder: A Phage Host Prediction Tool. Viruses, 8(5), [116]. https://doi.org/10.3390/v8050116
    Villarroel, Julia ; Kleinheinz, Kortine Annina ; Jurtz, Vanessa Isabell ; Zschach, Henrike ; Lund, Ole ; Nielsen, Morten ; Larsen, Mette Voldby. / HostPhinder: A Phage Host Prediction Tool. In: Viruses. 2016 ; Vol. 8, No. 5.
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    Villarroel, J, Kleinheinz, KA, Jurtz, VI, Zschach, H, Lund, O, Nielsen, M & Larsen, MV 2016, 'HostPhinder: A Phage Host Prediction Tool', Viruses, vol. 8, no. 5, 116. https://doi.org/10.3390/v8050116

    HostPhinder: A Phage Host Prediction Tool. / Villarroel, Julia; Kleinheinz, Kortine Annina; Jurtz, Vanessa Isabell; Zschach, Henrike; Lund, Ole; Nielsen, Morten; Larsen, Mette Voldby.

    In: Viruses, Vol. 8, No. 5, 116, 2016.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - HostPhinder: A Phage Host Prediction Tool

    AU - Villarroel, Julia

    AU - Kleinheinz, Kortine Annina

    AU - Jurtz, Vanessa Isabell

    AU - Zschach, Henrike

    AU - Lund, Ole

    AU - Nielsen, Morten

    AU - Larsen, Mette Voldby

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    N2 - The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2].

    AB - The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2].

    KW - Prediction

    KW - Genome

    KW - K-mers

    KW - “Host specificity”

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    DO - 10.3390/v8050116

    M3 - Journal article

    VL - 8

    JO - Viruses

    JF - Viruses

    SN - 1999-4915

    IS - 5

    M1 - 116

    ER -

    Villarroel J, Kleinheinz KA, Jurtz VI, Zschach H, Lund O, Nielsen M et al. HostPhinder: A Phage Host Prediction Tool. Viruses. 2016;8(5). 116. https://doi.org/10.3390/v8050116