A consortium of human commensals protects against middle ear colonization by otopathogens

A year-long sequencing analysis of bacterial commensals sampled from infants during periods in which they were healthy or suffering recurrent ear infections [otitis media (OM)] identified several species of bacterial commensals that correlate with health and absence of ear infections. Here we consider and test the possibility of a causal relationship between a group of commensals and periods of health. We assemble a set of five health-associated bacterial species into a nasopharyngeal commensal consortium (NPCC) and test whether these organisms can effectively colonize the respiratory tracts of mice so that their effects on invading pathogens could be evaluated. We observed that NPCC efficiently colonize mice and that they provide substantial protection against the otopathogens, Streptococcus pneumoniae and Bordetella pertussis, reducing numbers of each in the middle ears by 99 to 99.9%. The NPCC also affected colonization/growth of these pathogens within the lower respiratory tract, suggesting complexity in these interactions. Together these data demonstrate a profound effect of commensals on invading otopathogens and describe a powerful experimental system in which the important interactions between the healthy infant microbiota and invading pathogens can be studied mechanistically.