Longitudinal Characterization of Changes in the Infant Gut Microbiome Over the First Year of Life: Does the Trajectory Differ by Feeding Mode Pumped vs at Breast?

This study evaluates the effects of feeding modes on the infant gut microbiome, especially focusing on the unique microbial composition provided by human milk. It analyzed the gut microbiome of 51 mother-infant dyads and identified significant differences in microbial diversity related to feeding practices. Alpha diversity results, measured using the Shannon diversity index (H = 38.134, p = 1.05e^-7) and Faith's Phylogenetic Diversity (H = 45.999, p = 2.45e^-9), showed that breastfeeding, in any form, supports microbial alpha diversity comparable to exclusive breastfeeding that was lower in infants receiving breast milk compared to formula and cow’s milk. In contrast, formula or cow's milk led to a distinctly different microbiome. This study utilized both unweighted and weighted UniFrac metrics to assess the impact of feeding modes on microbial community structure or beta diversity. Using these metrics, and PERMANOVA testing, significant differences were observed between several feeding modes. Cow’s milk and formula did not differ for gut microbiome community structure but all modes of feeding that included breastmilk were significantly different from both cow’s milk and formula (q < 0.005). Additionally, breastmilk fed at breast resulted in a significantly different community structure than in infants fed breastmilk at breast and pumped for bottle feeding. Multivariate models of beta diversity metrics, including both subject ID and time, suggested that individual differences accounted for 48% of the variance, while feeding mode accounted for 2%. Despite the smaller explained variance of feeding mode, the association between feeding mode and unweighted UniFrac was statistically significant (p = 0.01). Interestingly, while feeding mode was a significant factor in microbial community diversity, it did not significantly associate with the abundance of Bifidobacterium (p = 0.31) or Lactobacillus (p = 0.21). Covariate inclusion in models revealed that subject ID (individual baby) was the only substantial contributor (p < 0.0001) to the variance in Bifidobacterium abundance. These findings emphasize breast milk's critical role in the development of a healthy gut microbiome and highlight the complex interplay between diet, genetics, and microbial colonization. These insights suggest that while individual genetics are a driving force, breast milk consumption contributes significantly to the gut microbiome diversity and community composition, particularly when compared to formula or cow’s milk consumption. Further research into the mechanisms driving the establishment and maintenance of the infant gut microbiome are warranted.