Fig. 3

Comparison of the expected bacterial composition and the observed OTU composition obtained with Illumina-amplicon rpoB sequencing in the mock1 community (FROGS process). Phylogenetic trees based on the rpoB 430 bp-region Muscle alignment were inferred with MEGA7, with a PhyML-based maximum likelihood algorithm and the GTR model for: (a) individual Sanger sequencing of rpoB gene fragment for the 19 taxa making up the experimental mock communities (Expected_rpoB); (b) the observed OTUs obtained after Illumina-amplicon rpoB sequencing of the mock1 community (OTUs of the three replicates are summed), but only OTUs with an abundance > 0.1% of total reads in individual replicates were included in the analysis (threshold = 0.1%); (c) As in B, but only OTUs with an abundance > 1% of total reads in individual replicates were included in the analysis (threshold = 1%). The OTUs corresponding to the same taxa from the 19 bacterial components of the mock community are highlighted in the same color. The sum of read numbers is indicated after the OTU name. Bootstrap values (percentages of 1000 replicates) of more than 80% are shown at the nodes