Bacteria have developed a wide range of defence systems in response to the intense pressure from bacteriophages (or phages) to combat phage infections. Among these defence systems, restriction-modification (RM) systems are the most abundant and widespread. RM systems operate by modifying DNA to either prevent or allow DNA restriction, serving as a prime example of the critical role of methylation in the ongoing arms race between bacteria and phage. Interestingly, many recently discovered defence systems have DNA binding and cleavage capacities. Novel systems like Dnd, Ssp, DISARM and BREX harbour methyltransferases and distinguish self from non-self DNA through methylation, similar to RM systems. Other systems like Gabija and Druantia provide varying levels of protection against phages with different methylation patterns, even though no methylation-related genes are predicted within their operons. To systematically investigate the role of methylation on phage infection, we used long-read sequencing to determine the methylation patterns in the Escherichia coli Reference Collection (ECOR) and phages produced using hosts with diverse methylation backgrounds. By examining the shift in the phage host range between different methylation backgrounds and its correlation with bacterial defence systems, we shed light on the role of methylation in phage infections, and gain valuable insights into the selection of suitable production hosts for phage therapy applications.