Surveillance and Elimination of Bacteriophage Contamination in an Industrial Fermentation Process

Commercial fermentation processes are often vulnerable to bacteriophage due to the lack of genetic diversity and use of high cell density cultures. Bacteriophage infections in these fermentations can have adverse impacts on operability of the production facility and product quality and prevent recovery of valuable bioproducts in the downstream process. Prevention strategies have been developed and optimized through feedback from bacteriophage diagnostic tests, which inform improvements to process design for elimination of entry points, as well as modification of the biocatalyst to reduce or eliminate bacteriophage virulence. In this chapter, we provide case studies for successful elimination of bacteriophage virulence via host modifications, including bacteriophage binding-site modifications on the outer membrane of an Escherichia coli production host, used for commercial manufacture of 1,3-propanediol, as well as application of CRISPR-associated protein 9 (Cas9) for bacteriophage immunity. Finally, we report application of bacteriophage diagnostic methods to fully characterize and eliminate bacteriophage entry points in a commercial fermentation process.