Breastfeeding has modest impact on the gut microbiome in neonates born by caesarean section within the first 3 weeks of life
To evaluate the impact of breastfeeding on the neonatal gut microbiome, we analyzed stool samples from exclusively breastfed and exclusively formula-fed neonates collected at 3 weeks of age. Meconium samples had also been collected at birth but the amount of DNA extracted from these samples was consistently < 0.15 ng/μL. PCR amplification using 16S primers on these DNA samples yielded undetectable product for further analysis, reflecting minimal or no microbial colonization immediately after birth.
In the stool samples at 3 weeks of age, following microbial 16S rRNA gene amplification, a median frequency of 18,354 amplicon sequence variants (ASV) per sample were retained after trimming and filtering. The composition of gut microbiota from exclusively breastfed and exclusively formula-fed neonates was broadly similar and no differences in any alpha or beta diversity metrics were seen (Figure 6a). Principal component analysis (PCA) of gut microbiota composition of exclusively breastfed and exclusively formula-fed neonates demonstrated that individuals in these groups cluster closely together, and breastfeeding is associated with the presence of Gemella (Figure 6b). Linear discriminant analysis (LDA) effect size (LEfSe) revealed enrichment of the Veillonella and Gemella taxa in exclusively breastfed neonates (Figure 6c). Random Forest (RF) analysis identified the presence of Staphylococcus , followed by that of Gemella to be the most significant parameters distinguishing the two groups of exclusively breastfed and exclusively formula-fed neonates (Figure 6d).