Genetic modification of intractable bacterial clones by heat shock-facilitated phage transduction

Increasing recognition of commensal bacteria as essential for microbiome integrity and pathogen exclusion underscores the urgency of molecularly characterizing commensal interactions. However, many commensals cannot be transformed using available methodologies due to barriers imposed by restriction-modification (RM) systems. We developed a method for introducing plasmid DNA into otherwise intractable non-Staphylococcus aureus (NAS) staphylococci, important commensals of the human nasal and skin microbiomes, via phage transduction. We demonstrate that exposing recipient bacteria to a pulse of elevated temperature prior to phage exposure renders NAS isolates effectively and transiently amenable to transduction. Transduction of NAS mutants lacking RM systems did not respond to heat shock, indicating that transient deactivation of RM enzymes enables transduction. Our method also facilitates the transduction of representatives from other Bacillota and Actinomycetota taxa, suggesting that this approach will support research on diverse bacterial groups across a range of ecosystems.