Interactions among members of polymicrobial infections or between pathogens and the commensal flora may determine disease outcomes. Pseudomonas aeruginosa and Staphylococcus aureus are important opportunistic human pathogens and are both part of the polymicrobial infection communities in human hosts. In this study, we analyzed the in vitro interaction between S. aureus and a collection of P. aeruginosa isolates representing different evolutionary steps of a dominant lineage, DK2, that have evolved through decades of growth in chronically infected patients. While the early adapted P. aeruginosa DK2 strains outcompeted S. aureus during coculture on agar plates, we found that later P. aeruginosa DK2 strains showed a commensal-like interaction, where S. aureus was not inhibited by P. aeruginosa and the growth activity of P. aeruginosa was enhanced in the presence of S. aureus. This effect is mediated by one or more extracellular S. aureus proteins greater than 10 kDa, which also suppressed P. aeruginosa autolysis and prevented killing by clinically relevant antibiotics through promoting small-colony variant (SCV) formation. The commensal interaction was abolished with S. aureus strains mutated in the agr quorum sensing system or in the SarA transcriptional virulence regulator, as well as with strains lacking the proteolytic subunit, ClpP, of the Clp protease. Our results show that during evolution of a dominant cystic fibrosis lineage of P. aeruginosa, a commensal interaction potential with S. aureus has developed. M ost microbial species are embedded within mixed-species communities where mutualistic, antagonistic, and neutral interactions within the community control behaviors and activities of the individual species. In relation to microbial infections, it is becoming clear that interactions between bacterial pathogens and other microbial species present at the infection site (either coinfecting pathogens or commensal bacteria) can result in altered pathogen behaviors such as enhanced virulence (1, 2), biofilm formation (3), and antibiotic tolerance (4), which may influence disease progression and clinical outcome of the infection. Despite advances in elucidating the molecular details underlying microbial interactive processes, the extent to which evolutionary processes remodel interspecies interactions during the course of infection and therapy is currently not understood. Thus, studies of interaction patterns between species and the evolution within polymicrobial infections are a critical first step toward developing novel interference strategies against such infections.Chronic cystic fibrosis (CF) airway infections caused by the bacterium Pseudomonas aeruginosa offer optimal opportunities to study evolutionary dynamics within a natural environment because of systematic routine sampling of the ecosystem over extended time periods (years) and because of the well-characterized ecological properties of the system (5). We have recently determined the genetic basis of adaptation in a highly successful P. aeruginosa ...