Inflammatory Bowel Disease (IBD) is an autoimmune disorder characterized by inflammation of the intestinal tract. Imbalance in the bacterial or viral microbiome has been associated with IBD and multiple studies have demonstrated bacteriophages can exacerbate intestinal inflammation. Bacteriophages in the gut can be produced when bacteriophages integrated into bacterial genomes, or prophages, are induced to excise from the bacterial genome and produce viruses. Determinants of prophage induction remain unknown. Using an IBD-associated E. coli pathotype, Adherent Invasive Escherichia coli (AIEC), we sought to characterize excision of three identified prophages in mouse models of intestinal colonization and colitis.
We utilized polymerase chain reaction (PCR) to screen bacterial colonies for integration and excision of prophages identified in the NC101 AIEC genome: Myoviridae (MV), Siphoviridae (SV), and Inoviridae (Ino). Colonies were screened from fecal and tissue samples from (i) germ-free mice competitively colonized with GFP and RFP strains and (ii) specific pathogen-free mice colonized with AIEC strains followed by induced colitis. To improve quantitative assessment of prophage induction, quantitative polymerase chain reaction (qPCR) primers were designed.
Following colonization, 5-10% of colonies demonstrated spontaneous loss of the SV prophage. There were no significant differences between colonies screened during colonization versus colitis. To address PCR limitations due to integration of two Ino copies, and to quantitatively assess prophage induction, we designed a qPCR strategy to quantify bacterial genomes with integrated, excised, and recirculated phage genomes for the Ino and MV phages, design of SV phage qPCRs is ongoing.
We described spontaneous loss of the Siphovirus prophage from an AIEC strain during in vivo gut colonization. Future directions characterizing AIEC prophage dynamics will use qPCR to quantitatively assess prophage induction following macrophage infection in vitro and in other sample types.