Recurrent acute otitis media (rAOM, recurrent ear infection) is a common childhood disease, for which treatment is not always effective. This thesis describes the use of next-generation sequencing approaches to 1) investigate novel pathogens in rAOM; and 2) identify protective microbes for translation into therapy. Alloiococcus otitidis and Turicella otitidis were dominant organisms in rAOM, but are questionably pathogenic. Corynebacterium pseudodiphtheriticum inhibited the growth of an rAOM pathogen. This thesis also details the methodological challenges in applying metagenomics and metatranscriptomics to rAOM; knowledge which is essential for further 'omics-based studies in the upper respiratory tract.