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Fig. 4 | BMC Microbiology

Fig. 4

From: Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

Fig. 4

Effect of in silico decontamination on taxonomic profiles of culture dilutions and negative extraction controls. Means for three samples obtained in separate DNA extraction experiments are given. The R-OTU (the ratio between mean ‘absolute’ abundance of OTUs in negative extraction controls and culture samples) cut-offs of 1 to 0.001 were applied for decontamination. This ratio was calculated from the relative OTU abundance and qPCR data obtained using the S. aureus standard curve. Dilutions of the master stock are indicated from 1E0 (no dilution) to 1E-8 (10−8). EC, E. coli; SA, S. aureus. NEC_W, negative extraction controls obtained by substituting culture for water; NEC_B, negative extraction controls obtained by substituting culture for lysis buffer; ND, no decontamination was performed

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