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Fig. 4 | BMC Microbiology

Fig. 4

From: rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

Fig. 4

Comparison of expected bacterial composition and the observed OTU composition generated by Illumina-amplicon 16S sequencing for the mock1 community (FROGS process). Phylogenetic trees based on the 16S rRNA-V3 V4 region Muscle alignment were inferred with MEGA7, a PhyML-based maximum likelihood algorithm and the GTR model for: (a) individual Sanger sequences of the V3 V4 region of the 16S rRNA gene of the 19 taxa making up the experimental mock communities (Expected_16S); (b) the observed OTUs obtained after Illumina-amplicon 16S 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

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