Characterizing the Influence of Dietary Fibre Consumption on the Composition and Function of Fibre Fermenting Bacteria in the Infant Gut Microbiome
By COLIN Y. BRUCE, B.Sc.
A Thesis Submitted to the School of Graduate Studies in partial fulfilment of requirements for the degree Doctor of Philosophy
McMaster University, Hamilton, Ontario, Canada
Abstract:
The gut microbiome undergoes significant change over the course of infancy, transitioning from a sparse immature community to a more diverse mature community over the first 3 years of life. This maturation is thought to be mediated by the transition from an immature milk diet to an adult-like solid food diet, particularly through the consumption of complex oligosaccharides such as dietary fibres. However, to date there has been little examination of the effects of dietary fibre consumption on the infant gut microbiome. In this work, I investigated the influence of dietary fibre consumption during infancy on the composition and function of the fibre fermenting bacterial population of the infant gut microbiome across two study populations of infants. I applied a combination of 16s rRNA gene sequencing and shotgun metagenomic sequencing to determine whether the composition of the infant gut microbiome was influenced by fibre consumption. To assess the fibre content of the infant diet I used multiple descriptors of dietary fibre intake including: adherence to a plant foods based diet, calculated daily fibre consumption, and the introduction of solid foods. I showed that across these three descriptors of fibre consumption in the infant diet there were not large scale gut microbial community changes. Instead, the effects were limited to individual microbial taxa, largely those containing genes for the metabolism of dietary fibres. These fibre fermenting bacterial populations, and the genes that allow the metabolism of dietary fibres, were consistently at higher abundance in populations consuming higher fibre diets than those consuming lower fibre diets, suggesting an increased ability to metabolize dietary fibres. However, the effects were also highly individual and varied between participants, likely due to the specifics of their diet. Together, this work shows that while the effects of dietary fibre consumption during infancy varies between individual, there is an increase in fibre metabolism following the increase in fibre consumption.
Colin successfully defended his PhD today: September 29, 2025. Congratulations Colin! See Dr. Bruce’s publications during his PhD studies here.
