For patients with lung diseases like cystic fibrosis (CF), morbidity and mortality is often due to polymicrobial infections. A current issue with disease treatment, is that the complexity of the microbial ecosystem is often not considered. It is also unclear what the contribution of other members in the microbiome may play in virulence of known pathogens presumed to drive the disease state. It has previously been shown that lung microbe-pathogen associations can perpetuate, attenuate or have no impact on the virulence of CF pathogens like Pseudomonas aeruginosa. Here we propose that these pathogen-microbe association also exists for other emerging pathogens in CF patients. To address this hypothesis, we isolated emerging and opportunistic pathogens such as Staphlylococcus aureus, Stenotrophomonas maltophilia, Achromobacter spp. and Streptococcus spp. from 20 CF sputum patient samples (Whelan, NatMicro. 2020). We next examined their pathogen-microbe associations using a high throughput Drosophila melanogaster chronic infection model coupled with DIAMonDS, a published computational readout to assess fly survival. This approach generates a large dataset that will enable us to identify unique disease-associated microbial networks, and key genetic elements that contribute to the perpetuation and attenuation of disease to be used in therapeutic interventions against polymicrobial infections. There is an urgent need to understand the mechanisms that influence and promote virulence in pathogens and how their associations with other microbes in their ecosystem drive disease.