Abstract
Bacteriophages are the most abundant biological entity on the planet, but at the same time do not account for much of the genetic material isolated from most environments due to their small genome sizes. They also show great genetic diversity and mosaic genomes making it challenging to analyze and understand them. Here we present MetaPhinder, a method to identify assembled genomic fragments (i.e.contigs) of phage origin in metagenomic data sets. The method is based on a comparison to a database of whole genome bacteriophage sequences, integrating hits to multiple genomes to accomodate for the mosaic genome structure of many bacteriophages. The method is demonstrated to out-perform both BLAST methods based on single hits and methods based on k-mer comparisons. MetaPhinder is available as a web service at the Center for Genomic Epidemiology https://cge.cbs.dtu.dk/services/MetaPhinder/, while the source code can be downloaded from https://bitbucket.org/genomicepidemiology/metaphinder or https://github.com/vanessajurtz/MetaPhinder.
Highlights
Bacteriophages, phages in short, are viruses that prey on bacteria
The MetaPhinder method was successfully applied to data sets of prophage genomes and the co-abundance gene groups derived from a metagenomic data set of human gut microbiome samples
All hits are combined into an average nucleotide identity (%ANI) which can be an advantage in the case of mosaic genomes and genome rearrangement
Summary
Bacteriophages, phages in short, are viruses that prey on bacteria. With an estimated total number of 1031 particles [1], they constitute the most abundant biological entity on earth. Even though the phages MS2 and FX174 were the first organisms ever to be sequenced in full [2] [3], this did not spur the scientific interest in phages at the time, beyond their use for deducing several central principles within molecular biology [4] This is currently changing, as an increasing amount of problems with antibiotic resistant bacterial strains are encountered [5]. Phage therapy has been applied as a successful treatment in the states of the former Soviet Union for decades and is being increasingly researched around the world [6,7,8,9] Apart from their therapeutic potential, phages have huge impacts on the environment as catalysts for biogeochemical cycling, affecting the nutrient cycling in the ocean by killing a large part of the bacterial population every day [1].
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