Additional file 10 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens
2020-05-13T03:40:22Z (GMT) by
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.