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).