Transcriptional Profiling and Genetic Analysis of a Cystic Fibrosis Airway-Relevant Model Shows Asymmetric Responses to Growth in a Polymicrobial Community

Bacterial infections in the lungs of persons with cystic fibrosis are typically composed of multispecies communities, which modulate clinically relevant phenotypes that cannot be explained in the context of a single species culture. Most analyses to-date provide a picture of the transcriptional responses of individual pathogens, however, there is relatively little data describing the transcriptional landscapes of clinically-relevant multispecies communities. Harnessing a previously described polymicrobial community consisting of P. aeruginosa, S. aureus, S. sanguinis and P. melaninogenica, we performed an RNA-seq analysis to elucidate the transcriptional profiles of the community grown in artificial sputum medium as compared to monoculture, where applicable, and to the addition of mucin and exposure to tobramycin. We provide evidence that although the transcriptional profile of P. aeruginosa is community agnostic, the transcriptomes of S. aureus and S. sanguinis are community aware. Furthermore, P. aeruginosa and P. melaninogenica are transcriptionally sensitive to the presence of mucin in ASM, whereas S. aureus and S. sanguinis, largely do not alter their transcriptional profiles in the presence or absence of mucin when grown in a community. Only P. aeruginosa shows a robust response to tobramycin. Genetic studies of mutants altered in community-specific growth provide complementary data regarding how these microbes adapt to a community context. We hope this RNA-seq dataset will serve as a resource to other researchers.