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.

The microorganisms that colonize the gastrointestinal tract have been recognized over the last several decades to have a significant bearing on the health trajectories of the hosts that harbor them. The collection of these gut microbes display links with acute and chronic disease, garnering substantial interest in leveraging the microbiome for improved health states. How these microbes assemble as a complex community and interact with each other, and the host depends on a multitude of factors. In adulthood, diet is one of the main moderators, having a significant influence on community composition and the functional output captured in the metabolites produced and/or modified by the gut microbiome. Thus, the assembly of microbes in the gut are tightly intertwined with health. In this dissertation, I examine the impact of diet and feeding behaviors on the gut microbiome and what features may be grounding or responsive under such pressures. Specifically, I first explore the avian gut microbiome as a barometer of nutritional and environmental influence on host health. Birds have continually displayed robust physiology under dietary pressures, placing them in an important, though underutilized, position within the translational science framework. Second, I describe the association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample. Food insecurity provides its own set of unique pressures, such as unintentional calorie restriction, and inconsistent dietary intake and access to healthy food options. Third, I examine the effect of a one vs. two-consecutive days of intermittent fasting on the gut microbiome, the plasma metabolome, and associated clinical outcomes in overweight and obese adults. Growing in scientific and lay popularity, dietary fasting has been noted to induce changes in the diversity of gut microflora and gut motility, though different fasting lengths have not been assessed in the context of the human microbiome. Overall, this collection of work underscores that the community of microbes in the gut are individualized, resilient, and baseline composition and functioning are germane to how an individual may react to a particular dietary intervention.