10.6084/m9.figshare.12292031.v1
Shantelle Claassen-Weitz
Shantelle
Claassen-Weitz
Sugnet Gardner-Lubbe
Sugnet
Gardner-Lubbe
Kilaza S. Mwaikono
Kilaza S.
Mwaikono
Elloise du Toit
Elloise
du Toit
Heather J. Zar
Heather J.
Zar
Mark P. Nicol
Mark P.
Nicol
Additional file 10 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens
Springer Nature
2020
16S rRNA gene
Bacteriome
Contamination
High-throughput sequencing
Low biomass
Mock controls
Negative controls
Optimization
Reproducibility
Respiratory
2020-05-13 03:40:22
Figure
https://springernature.figshare.com/articles/figure/Additional_file_10_of_Optimizing_16S_rRNA_gene_profile_analysis_from_low_biomass_nasopharyngeal_and_induced_sputum_specimens/12292031
Additional file 10. Shifts in OTU-level proportions prior to and following the removal of “potential contaminants” using two in silico approaches for contaminant identification. Per specimen shifts (n = 148) in bacterial proportions are shown for eight OTUs classified as four genera A) Staphylococcus, B) Streptococcus, C) Acinetobacter and D) Stenotrophomonas. Open circles and smoothing splines (representing a factor of 2x the standard deviation) denote bacterial proportions (Y-axis) for each of the specimens (X-axis). Red: Proportions prior to decontamination; Blue: Proportions following the removal of “potential contaminants” identified using the “NTConly” approach; Yellow: Proportions following the removal of “potential contaminants” identified using the “NTC + decontam” approach.