Evaluation of full-length versus V4-region 16S rRNA sequencing for phylogenetic analysis of mouse intestinal microbiota after a dietary intervention

The composition of microbial communities is commonly determined by sequence analyses of one of the variable (V) regions in the bacterial 16S rRNA gene. We aimed to assess whether sequencing the full-length versus the V4 region of the 16S rRNA gene affected the results and interpretation of an experiment. To test this, mice were fed a diet without and with the prebiotic inulin and from cecum samples, two primary data sets were generated: 1) a 16S rRNA full-length data set generated by the PacBio platform; 2) a 16S rRNA V4 region data set generated by the Illumina MiSeq platform. A third derived dataset was generated by in silico extracting the 16S rRNA V4 region data from the 16S rRNA full-length PacBio data set.