Respiratory tract infections are a significant contributor to global morbidity and mortality. Consequently there are countless studies that have examined the prevalence and carriage of common respiratory pathogens such as Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, Staphylococcus aureus, rhinovirus, coronavirus, influenzae, parainfluenzae, respiratory syncytial virus and adenovirus. With vaccines being the single most effective intervention against infectious diseases it is for this reason that it is essential to understand better the carriage of these pathogens in populations so that improvements in clinical care can be made through informing vaccine development as well as policies for effective implementation. The Infectious Disease Epidemiology Group, University of Southampton UK are engaged in numerous studies geared towards addressing these gaps in our current understanding of the carriage and prevalence of respiratory tract infectious diseases.  Here we present recent findings from various projects covering the changing epidemiology of pneumococci carried in the nasopharynx amongst children after the introduction of pneumococcal conjugate vaccine and carriage of respiratory microbes within the general population. In addition we will present current research on the analysis of respiratory tract microbiomes in healthy and diseased cohorts.