EpiBiome is a Bay Area metagenomics company that is developing phage-based treatments for bacterial diseases

Bacteriophages—viruses that target bacteria—were first investigated for therapeutic applications over 50 years ago, but the high rate at which bacteria become resistant (and the high effectiveness of antibiotics) prevented... [ view full abstract ]

Bacteriophages—viruses that target bacteria—were first investigated for therapeutic applications over 50 years ago, but the high rate at which bacteria become resistant (and the high effectiveness of antibiotics) prevented widespread use. However, we now have access to 1) inexpensive genome sequencing and 2) lab automation robotics.

This technology allows us to sequence phages and their bacterial hosts and to measure phage-host interactions in a high-throughput fashion. The goal is to generate a comprehensive "warehouse" of multiple phages that target specific bacterial strains. This has become an even more crucial due to the increasing threat posed by antibiotic-resistant bacteria.

On the bacterial side of sequencing, we will discuss our process for reducing sequencing error rate in order to accurately characterize the species present in a sample. Additionally, we will discuss our workflow for establishing positive controls, the issues faced in using 16S-specific sequencing, and our methods for assembling phage genomes.