Fig. 2

Quality control and decontamination of microbiota samples. a Scatter plots showing the prevalence of bacterial and fungal taxa in samples versus negative controls (extraction and PCR water controls), with taxa in red representing those that were identified as contaminants and those in green representing taxa retained for downstream analyses. b Violin plots with log-transformed bacterial and fungal read counts for extraction, PCR water and swab controls, a summary of read counts for excluded samples in red, and samples in green. c Relative abundance data for bacterial taxa in each sample both in the raw data and following the 2-step quality control measures (removal of contaminants and filtering by read counts, abundance and prevalence). Nasal and oral samples are shown on the left, and controls are shown on the right. d Corresponding relative abundance data for fungal taxa