A comparison of bacterial communities in feces of breastfed infants determined by 454 pyrosequencing and Illumina MiSeq (1017.5)

Abstract

Because various molecular techniques are used to evaluate microbial community structure in biological samples, understanding if results are comparable among methods is critical. We hypothesized two of the most commonly‐used techniques, 454 pyrosequencing and Illumina MiSeq, similarly describe bacterial communities in breastfed infants’ feces. To test this, DNA from 25 samples was processed using both techniques; universal primers designed to amplify the V1‐V3 region of the 16S rRNA bacterial gene were used. Bacterial community profiles were clustered using Bray‐Curtis dissimilarity and the average linkage algorithm. Of the 15 most abundant genera detected in the samples, only 8 were common between the 2 methods. Diversity was similar (Shannon, P=0.08), but evenness was different between methods (Simpson, P=0.001). Our data somewhat support the hypothesis that these methods produce similar results in terms of diversity; however, the methods differ in terms of overall community composition and evenness. In conclusion, these potential differences need to be considered when comparing bacterial community data across sequencing methods ‐ at least for feces of breastfed infants.