Community diversity in anterior nares and oropharynx according to swab type. The species richness, Shannon diversity index (H′), Simpsons diversity index (1-D), and Pielou’s evenness index of communities collected by three different swabs (swab 1, flocked nylon swab; swab 2, rayon swab; swab 3, polyurethane tipped swab) are shown. The whiskers of the plots indicate 10–90 percentiles. The number of swabs analyzed were 54 (swab 1), 52 (swab 2) and 44 (swab 3) nasal swabs and 39 (swab 1), 34 (swab 2) and 37 (swab 3) oropharyngeal swabs. There was no statistically significant difference in the diversity observed in communities obtained with the different swabs, whereas communities taken from the nares or the oropharynx were significantly different (p < 0.0001).