Foods to optimise the infant colonic microbiome for our lifelong health and well-being : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Nutritional Science at Massey University, Manawatū, New Zealand

Abstract

Diet is a key factor in shaping the composition and function of the colonic microbiota, which in turn has a strong influence on human health. The transition from breastmilk to solid foods (weaning) is critical for the maturation of colonic microbes. However, this period is often overlooked in diet-microbiota research, and the effects of many complementary foods on the infant colonic microbiota remain uncharacterised. This thesis aimed to identify foods that support the development of the colonic microbiota in weaning infants using a combined in silico and in vitro approach. Computational modelling tools are emerging tools to rapidly and inexpensively study interactions between dietary compounds and gut microbial communities, generating preliminary insights that can be further evaluated experimentally. A metagenome-scale community metabolic model was employed to predict the effects of 89 foods commonly introduced to New Zealand weaning infants on infant colonic microbiota composition and function, using faecal sample data as a proxy. Foods with the greatest impact on short-chain fatty acid production when combined with breastmilk were identified, notably foods rich in fibre and polyphenols. The effects of these identified foods on the colonic microbes of New Zealand weaning infants were further evaluated in vitro through food digestion and faecal fermentation. Foods were tested individually or combined with infant formula, other foods, or both, resulting in 53 samples. Blackcurrants, raspberries, and strawberries resulted in the greatest microbial production of acetate and propionate, also increasing the relative abundance of saccharolytic bacterial genera. Similarly, black beans, when combined with infant formula, resulted in the greatest butyrate production and increased the relative abundance of bacteria specialising in degrading complex plant polysaccharides. These foods are promising candidates for future intervention trials involving weaning infants. The knowledge generated by this thesis can guide the design of future diet-colonic microbiota studies, ultimately contributing to improved nutritional recommendations and food formulations for weaning infants. Additionally, by assessing the predictive accuracy of the metagenome-scale community metabolic model, this thesis highlighted the limitations of current modelling approaches but also their potential in accelerating diet-colonic microbiota investigations when combined with traditional methodologies.