Fig. 3.

Impact of four sequence processing approaches on observed associations of milk microbiota richness (observed OTUs/ASVs), diversity (inverse Simpson index), and overall composition with maternal, infant, early life, breastfeeding, and milk factors. We re-processed our published 16S rRNA gene sequencing milk microbiota dataset [19] using Qiime1 and Qiime2 with or without contaminant removal resulting in four datasets (see also Fig. 1a). Beta coefficients from univariate linear regression (richness and diversity) or R² from redundancy analysis (overall composition) are presented and colour coded within each microbiota feature. Results of Qiime2 with contaminant removal are originally reported in Moossavi et al. [19]. BF, breastfeeding; BMI, body mass index; C/S, Cesarean section; HMO, human milk oligosaccharide; NVD, normal vaginal delivery; PC1, Principal Component 1 * p < 0.05, ** p < 0.01, *** p < 0.001