THE IMPACT OF SOLID FOOD INTRODUCTION ON MICROBIAL SUCCESSION IN THE INFANT GUT

Abstract

Succession of the gut microbial community in infancy is marked by natural disturbances such as the introduction of solid food, the details and timing of which may be important factors in shaping the microbiome and, ultimately, human health. Previous gut microbiome studies focused on molecular profiles of bacterial communities generated through amplicon-based sequencing or metagenomics. Although providing a genus level profile of the microbiome, this approach does not functionally address microbial metabolism or interactions. This thesis explores the impact of solid food introduction on the developing gut microbiome of a breastfed, vaginally-born infant from the Baby & Mi prospective birth cohort. To investigate this, we designed a targeted culture strategy to complement molecular profiling and applied it to a longitudinal sample over a period of 25 days during the transition to solid foods. Upon observing community and specieslevel changes throughout the course of the study, we were prompted to explore strainlevel and functional changes over that period. This was executed using bacterial functional phenotype screens, to measure bacterial strain metabolism of fiber substrates for genera of interest. Data show that our targeted culture strategy is more sensitive than 16S rRNA gene sequencing of stool alone at capturing bacteria of interest in the infant gut. Using this culture strategy, we show that alpha diversity is primarily driven by species evenness rather than richness following solid food introduction. Additionally, some phylotypes within the same genus show different patterns of change in relative abundance following solid food introduction. To explore this further, we use cultured isolates from the longitudinal study and show that different isolates of the same species may utilize substrates differently (e.g. Enterococcus faecalis, Bacteroides ovatus) and others may utilize substrates in the same way (e.g. Bifidobacterium breve, Paeniclostridium sordelli). We also show that isolates of the same species acquired before solid food introduction may differ from ones acquired after (e.g. Enterococcus faecalis), or may remain the same (e.g. Bifidobacterium breve). Combining targeted-culturing with molecular profiling methods such as 16S rRNA gene sequencing and metagenomic approaches can provide us with more comprehensive and detailed functional data regarding how the gut microbiome responds to a disturbance, such as solid food introduction, during infancy.