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].
Highlights
In 2012, the World Health Organization (WHO) announced the beginning of the end of the antibiotic era, and the possible return to a time when even trivial bacterial infections could turn out to be fatal [3]
We developed and benchmarked HostPhinder, a bioinformatics tool for predicting the bacterial host species of phages
HostPhinder relies on a reference database in which Whole Genome Sequences (WGS) data from phages with annotated hosts have been split into k-mers
Summary
In 2012, the World Health Organization (WHO) announced the beginning of the end of the antibiotic era, and the possible return to a time when even trivial bacterial infections could turn out to be fatal [3]. For a number of historical reasons, phage therapy never became general practice in the West, it has been used extensively in countries from the former Eastern bloc [6,7,8,9]. Phages have been suggested for use in the agriculture and food industries [16,17].
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