The human nose and throat contain distinct, though connected, niches that are important sites of colonization by pathogenic bacteria.  For many of these pathogens colonization increases the risk of infection.  For this reason, and perhaps also due to the limitations of using cultivation to characterize complex polymicrobial communities, most research on the microbiota of nose and throat habitats has focused on carriage of one or a few pathogens.  We hypothesized that increased knowledge of the composition of the complex bacterial communities in which these pathogens reside would provide new insights into why some individuals become colonized with pathogens, while others do not.  We examined the bacterial microbiota of the nostril and posterior wall of the oropharynx from seven healthy adults using two culture-independent methods, a 16S rRNA gene microarray (PhyloChip) and 16S rRNA gene clone libraries.

Results/Conclusions

The bacterial microbiota of the oropharynx was richer than that of the nostril, but there was less interpersonal variation across individuals.  A few phyla accounted for the majority of the bacteria detected in each site:  Firmicutes and Actinobacteria in the nostril and Firmicutes, Proteobacteria and Bacteroidetes in the oropharynx.  Compared to culture-independent surveys of microbiota from other body sites, the nostril and oropharynx showed distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites.  In the nostril, the distribution of Actinobacteria and Firmicutes was reminiscent of skin, though, Proteobacteria were much less prevalent.  The distribution of Firmicutes, Proteobacteria and Bacteroidetes in the oropharynx was most similar to saliva, with more Proteobacteria than the distal esophagus or mouth.  While Firmicutes were prevalent at both sites, distinct families within this phylum dominated numerically in each.  In both sites there was an inverse correlation between the prevalence of Firmicutes and another phylum: in the oropharynx between Firmicutes and Proteobacteria and in the nostril between Firmicutes and Actinobacteria.  In the nostril, this inverse correlation existed between the prevalence of the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups of organisms.