Complementary feeding to nourish the infant gut microbiome : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Nutritional Science at Massey University, Palmerston North, New Zealand

Abstract

The transition from milk-feeding to consuming a range of solid foods during the first 1000 days of life constitutes the most dramatic dietary shift in the human lifespan. This period coincides with the development of host-microbial processes. This PhD dissertation aimed to identify relationships between complementary feeding and characteristics of the developing microbiome of the infant using faecal samples as a proxy of the large intestine. The composition and gene abundances of the microbiome and the metabolites of dietary, host, and/or microbial origins were detected and analysed. The Nourish to Flourish pilot clinical study was conducted to inform subsequent study designs and develop sampling and processing protocols for research in weaning infants. The faecal samples were analysed to characterise the microbiome and metabolome at 4, 9, and 12 months of age. These data revealed greater shifts during the introduction of solid foods between 4 and 9 months of age than during the continued diversification of solid foods in the diet between 9 and 12 months of age. The changes occurring in the microbiome and metabolome in faecal samples were then interpreted in the context of milk-feeding behaviours and associated dietary diversification. The associations between the faecal microbiome and metabolome and dietary nutrient composition estimates were identified and evaluated. The patterns of association that emerged were varied and showed low prediction values but supported published evidence about relationships between specific nutrients, microbial taxa, and predicted functional pathways based on microbial gene abundance. Correlation networks between dietary food groups and relative abundance of microbes, KEGG pathway abundance, and metabolites revealed patterns that implicate the food matrix by protein-rich foods compared to the relatively weak effect of starchy foods on the luminal environment. This research demonstrates the window of opportunity for the greatest influence of solid foods on the infant gastrointestinal environment is prior to 9 months of age. However, the impact of continued milk feeding behaviours is likely to be relatively greater than solid foods later in the complementary feeding window. This research provides a basis for selecting food products that can benefit the infant's development by modulating the microbiome and metabolome in the gastrointestinal tract.