PhaMers identifies novel bacteriophage sequences from thermophilic hot springs

Abstract

Metagenomic sequencing approaches have become popular for the purpose of dissecting environmental microbial diversity, leading to the characterization of novel microbial lineages. In addition of bacterial and fungal genomes, metagenomic analysis can also reveal genomes of viruses that infect microbial cells. Because of their small genome size and limited knowledge of phage diversity, discovering novel phage sequences from metagenomic data is often challenging. Here we describe PhaMers (Phage k-Mers). a phage identification tool that uses supervised learning to classify metagenomic contigs as phage or non-phage on the basis of tetranucleotide frequencies. a technique that does not depend on existing gene annotations. PhaMers compares the tetranucleotide frequencies of metagenomic contigs to phage and bacteria references from online databases. resulting in assignments of lower level phage taxonomy based on sequence similarity. Using PhaMers. we identified 103 novel phage sequences from hot spring samples of Yellowstone National Park based on data generated from a microfluidic-based minimetagenomic approach. We analyzed assembled contigs over 5 kbp in length using PhaMers and compared the results with those generated by VirSorter, a publicly available phage identification and annotation package. We analyzed the performance of phage genome prediction and taxonomic classification using PhaMers. and presented putative hosts and taxa for some of the novel phage sequences. Finally. mini-metagenomic occurrence profiles of phage and prokaryotic genomes were used to verify putative hosts.