Determining gastrointestinal responses to aspects of dairy and protein intakes through faecal metagenomics and proteomics

Introduction: Gastrointestinal (GI) homeostasis supports optimal food digestion and contributes to immune, metabolic and mental health. Disruption of this balance, underpinned by gut microbial dysbiosis and inflammation, leads to GI dysfunction. Food intake is an important determinant of GI homeostasis, where bioactive dairy proteins, fermented dairy and habitual protein intakes can potentially influence GI parameters. This thesis aims to determine gastrointestinal responses to aspects of dairy and protein intakes through faecal metagenomic and proteomic approaches. Methods: A systematic review following PRISMA guidelines determined the effects of dairy consumption on the gut microbiome and symptoms in GI disease cohorts. Study 1 was a 6-week parallel intervention investigating the effects of casein hydrolysate supplementation (4g/day) on the faecal microbiome (whole-genome sequencing) and GI parameters (clinical, self-reported) in an ulcerative colitis (UC) cohort (n=26), relative to a maltodextrin control. Study 2 involved secondary analysis of the faecal microbiome (16S rRNA) using samples from a 6-week parallel intervention comparing unmelted Cheddar cheese, melted Cheddar cheese, and a butter control in a healthy cohort (n=69). Major global dietary protein sources, species and protein sequences were assembled into a novel proteomics sequence database (MajorFoodProt). Faecal samples from Study 1 were analysed by mass spectrometry and bioinformatics utilising MajorFoodProt to explore faecal dietary protein persistence and aspects of dietary intake and disease. Results: Data from 26 interventions showed several fermented dairy products alter gut microbial characteristics favouring the host and improve symptoms in GI disease cohorts. Casein hydrolysate supplementation did not alter gut microbial structure or GI parameters, relative to control, in a UC cohort. Unmelted Cheddar cheese consumption significantly increased gut microbial alpha diversity and abundances of three fermenting microbes. MajorFoodProt collated 5578 dietary protein sequences from 101 foods into a database. Dietary proteins (36 plant, 17 animal) were identified in the faecal UC proteome, and digestive protease abundance negatively correlated with GI inflammation. Conclusions: Certain fermented dairy foods and their matrices can influence the gut microbiome; future work should explore this further. Applying faecal proteomics to identify dietary proteins is feasible, and deeper insights into dietary protein digestion in UC are needed.