Additional file 1: Figure S1. A bar plot of the taxa and their relative abundance of the extraction and sequencing mock controls compared to manufacturer profiles. Figure S2. A scatterplot showing the correlation between samples repeated within a run (WR, n = 74) and between runs (BR, n=28). Figure S3. A scatterplot showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) 16S copies vs final number of reads (A1 and A2), Shannon alpha diversity index (B1 and B2) and age of participant in years (C1 and C2). Figure S4. Ordination plots of showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) coloured by their 16S copies. Figure S5. Ordination plots showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) coloured by their number of reads. Figure S6. Ordination plots showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) coloured by the age of the participant. Figure S7. Rarefaction curves showing number of ASVs detected and 16S copies of samples. Figure S8. Rarefaction curves showing number of ASVs detected and number of reads of samples. Figure S9. Bar plot showing the profiles of biological samples with <100 16S copies (n=2) in comparison to Primestores profiles (n=43). Figure S10. Bar plot showing the profiles of biological samples with >100 to <1000 16S copies (n=10) in comparison to Primestores profiles (n=43). Figure S11. Ordination plots showing the profiles of a subset of biological samples with low 16S copies and the negative controls. Figure S12. Ordination plots showing the profiles of a subset of biological samples with low reads and the negative controls. Figure S13. Ordination plots showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) coloured by the run in which the sample was processed. Figure S14. Ordination plots showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) coloured by the country of sampling. Figure S15. Ordination plots showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) coloured by visit. Figure S16. Ordination plots showing the spread of biological samples (n=960) and the negative controls (primestore, n=43) coloured by the age at sampling. Figure S17. Output from decontamination analysis using the DECONTAM R package. Figure S18. Boxplot of Shann...