Extended Data Fig. 5: Species associated with batch effects visualized by PCA also do not show signal reproducibility.
From: Human placenta has no microbiome but can contain potential pathogens
a, PCAs of selections of samples from cohort 2 (16S), or of all cohort 2 samples as shown here, allows for the identification of batch effects and allows for the identification of contaminating species associated with the use of specific DNA isolation methods, kits and/or other reagents. An analysis of all samples shows that principal components 3 (x axis) and 4 (y axis) are strongly correlated with the use of Qiagen or specific Mpbio DNA isolation kits. b, Examples of bacteria detected in high abundance and frequency when processed with the Qiagen (x axis) and/or Mpbio (y axis) DNA isolation kits. Patterns that lack positive correlation (compare with Fig. 2a) demonstrate that signals are not sample- but batch-associated.
