Hijackers: Identifying Putative Satellite Phage in Metagenomic Data

Satellite phages, mobile genetic elements that parasitize other phages, harbor extensive and unique molecular machinery that could offer immense applications for research in synthetic biology. As ubiquitous as they are in the environment - 3.2 x 1026 for marine phage satellites alone - their diversity and function remain largely unexplored and understudied. This project aims to identify and assemble genome sequences of suspected satellite phages from metagenomic data. To this day, there has yet to be a comprehensive search for satellites within metagenomic data. To uncover these elements, paired-end shotgun metagenomic sequencing data were retrieved from the NCBI Sequence Read Archive. The raw sequencing reads were assembled into contiguous sequences (contigs) and then analyzed with a novel protein clustering algorithm, developed by a collaborator, to identify families of suspected satellite phages. Through this process, satellite phages were identified across five distinct satellite phage families. Their open reading frames (ORFs) were further analyzed to detect patterns in hypothetical protein similarity and genomic organization, revealing potential functional relationships and conserved elements within and across families. These findings offer new insights into the genetic landscape of satellite phages, shedding light on their roles in microbial ecosystems and their evolutionary relationships with both viruses and bacteria. Understanding these elements may also have applications in synthetic biology and virology, contributing to broader research on employing synthetic biology systems into real world environments.