Abstract: Provided herein are methods and compositions for community-based screening of polymicrobial infections for the selection and administration of antibiotics and antibiotic combinations for treating infections associated with diseases such as cystic fibrosis, chronic obstructive pulmonary disease, and chronic sinus infections. The methods and compositions of this disclosure are advantageous in the sense that antibiotic effectiveness is assessed with respect to a community of microbes rather than a single microbial population, thus reflecting more accurately the in vivo disease environment and enabling the identification of beneficial antimicrobial therapeutics even when the primary bacterial strain shows antibiotic resistance.