Fig. 2

OTU richness across the samples before and after in silico decontamination. R-OTU (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; NTC_W, no-template PCR controls; ND, no decontamination was performed