Prophages and antiphage defence systems in genomes of gut commensal Enterobacteriaceae

Millions of years of co-evolution gave rise to a delicately balanced yet intricately diverse and complex microbial community that inhabits the gastrointestinal tract of animals, collectively known as the gut microbiota. This collection of microorganisms is dominated by bacteria and viruses, with bacteriophages (phages) composing the lion`s share of the viral component of the microbiota (the virome). Our research focuses on bacterial- phage interactions in the gut.

We isolated murine commensal Enterobacteriaceae strains from faeces of healthy adult animals, and analysed them using 16s rRNA sequencing. We found these strains to belong to four major genuses of Enterobacteriaceae commonly found in the large intestine: Escherichia coli, Klebsiella, Enterobacter, and Proteus. We then conducted whole genome sequencing on selected isolates and analysed the genomes for the presence of prophage. We found each of the isolates to contain several prophages, partial phages and putative phages. Exposure of live cultures to a DNA-damaging agent resulted in a significant increase in the ratio of phage to bacteria DNA copies, indicating prophage induction and production of phage DNA.

Additionally, we found that the commensal gut strains encode various antiphage defence systems including restriction modification systems, CRISPR-cas and AVAST.

Our data suggest a high prevalence of active prophage and antiphage defence systems in the genomes of commensal bacteria. Thus, we propose that phages and antiphage defence systems contribute to colonisation of commensal gut bacteria and in this way they can contribute to shaping the composition of the endogenous gut-associated microbial community.