Batch effects account for the main findings of an in utero human intestinal bacterial colonization study

摘要

Batch effect analysis of V4 16S rRNA gene amplification data with a focus on Micrococcus (OTU10). Source data: Supplemental Table 2 of Rackaityte et al. [2]. a, b Principal components 1 and 2 (PC1 and PC2), respectively, show a distinct microbial profile shift after sample 80 (ID 1616 L), as indicated with a dashed vertical line and designated as batch 1 and batch 2 as indicated in a. A sub-analysis of PC1 and of PC2 with the meconium samples only is shown to the right of both figures. c The Micrococcus signal (OTU10) is part of this profile shift. dMicrococcus (OTU10) signals from batch 1 (samples 1–80 all meconium) vs meconium only samples from batch 2 or vs all negative controls from batch 2 show that the OTU10 signal is batch associated. e The phenotypic characterization of the lamina propria (LP) T cells shows that samples corresponding to batch 1 had significantly higher proportions of PLZF+CD161+T cells compared to samples corresponding to batch 2. Interquartile ranges are shown, and comparisons indicated by brackets have P values shown above them (Mann-Whitney U test)