The impact of dietary components on gut microbiome modulation and health
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Full Text E-thesis
Date
2025
Authors
Koc, Fatma
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Publisher
University College Cork
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Abstract
The human gut microbiome plays a critical role in maintaining overall health, influencing key physiological processes such as digestion, immune function, and behaviour. A deeper understanding of the complex interactions between the gut microbiome, diet, and disease is essential for advancing strategies to promote health and manage chronic conditions. This thesis explores the relationships between dietary components, the gut microbiome, and their implications for health, focusing on various dietary fibres, fermented foods, and microbiome interventions. Chapter 1.1 reviews and discusses an overview of the gut microbiome, its role in human health, and the current models used to study it, including in vitro fermentation systems, organoid and animal models. These models allow for the examination of microbial dynamics, host-microbiome interactions, and the influence of diet and disease. In vitro models such as batch and continuous culture systems offer controlled environments for studying microbial interactions, while animal models especially pigs provide more physiologically relevant insights into human microbiome dynamics. This chapter highlights the importance of selecting the appropriate model for microbiome research to bridge the gap between bench and bedside. Chapter 1.2 delves into the role of dietary fibre in shaping the gut microbiome. Despite recommendations to consume 25-38g/day of fibre, many individuals fall short, leading to imbalances in the gut microbiota and increased inflammation, which are linked to several non-communicable diseases. This chapter discusses the impact of different fibre types on gut health and underscores the importance of personalized dietary fibre strategies to optimize gut microbiome health based on individual microbiota profiles. Chapter 2 investigates the prebiotic potential of superheated steam (SHS)-treated wheat and oat bran fibres. The results from in vitro digestion and fermentation study demonstrate that SHS treatment enhanced the fibres’ ability to modulate the gut microbiota, with significant shifts in microbial composition, such as increased Ruminococcus and decreased Escherichia-Shigella in faecal samples fermented with SHS treated oat fibres. These findings suggest that SHS treatment may improve the prebiotic properties of dietary fibres and their potential to influence gut health. Chapter 3 explores the impact of low and high FODMAP biscuit models on gut microbiota, focusing on formulations such as Biscuit Flour Control (BiFC), Low-FODMAP Control (LFC), Low-FODMAP High-Fibre Prototype (LFP), and Wholemeal Flour Control (WMC). In vitro colonic fermentation revealed that LFP fermented faecal samples exhibited increased microbial diversity and a reduced relative abundance of Escherichia-Shigella compared to other formulations. The study suggests that manipulating the formulation of biscuits may offer a practical approach to modulating the gut microbiota and managing symptoms of irritable bowel syndrome (IBS). Chapter 4 examines the development of whole-grain sourdough bread with reduced FODMAP content, using different lactic acid bacteria (LAB) strains, to influence gut microbiota. In vitro fermentation studies showed that sourdough fermentation with Lactiplantibacillus plantarum FST1.7 enhanced acetate production and positively correlated with beneficial bacteria such as Bifidobacterium following in vitro colonic fermentation of pre-digested bread. This chapter highlights the potential of sourdough fermentation as a tool for creating functional foods that support gut health, particularly for individuals with IBS. Chapter 5 investigates tarhana, a traditional fermented food, and its impact on the gut microbiome, specifically focusing on the effects of different flour types and fermentation methods. Using in vitro colonic fermentation, the study demonstrates that sourdough-fermented tarhana with purple potato and chickpea flour demonstrated significant reductions in Veillonella and Escherichia-Shigella while increasing acetate and propionate levels. These findings underscore the potential of tarhana as a personalized functional food to support gut health and potentially alleviate symptoms in individuals with IBS or other gut-related disorders. Chapter 6 explores the potential of combining probiotics (Lactobacillus mucosae DPC6426) and dietary fibre as a synbiotic approach to modulate metabolic syndrome (MetS) in a porcine model. This study found that the synbiotic combination improved metabolic profiles, including lipid and amino acid metabolism, and enhanced insulin sensitivity. Faecal metabolomic analysis revealed increased levels of spermidine and 3-deoxyglucosone, while serum metabolomics showed elevated lysophospholipids, underscoring the potential of probiotics and fibre in addressing MetS and related cardiovascular risks. Chapter 7 addresses the gut microbiome changes in infants with congenital heart disease (CHD) undergoing cardiopulmonary bypass surgery (CPB). Post-operative samples showed microbial shifts including elevated Enterococcus, Akkermansia, and Staphylococcus. One infant who developed post-operative necrotizing enterocolitis (NEC) exhibited a pre-operative dominance of Enterococcus (93%), identifying potential microbial biomarkers for NEC risk. The study reveals significant alterations in the gut microbiota pre- and post-surgery, highlighting the importance of understanding the microbiome's role in the health of vulnerable populations such as infants with CHD. In conclusion, this thesis demonstrates how dietary components, fermented foods, and targeted probiotic interventions can modulate the gut microbiota to support health and manage disease. Each chapter builds on a foundation of understanding the gut microbiome's complexities and its interactions with dietary components. Early chapters establish the role of dietary fibres and fermentation in shaping microbial communities, revealing significant potential for innovations like SHS-treated fibres, low-FODMAP biscuits, sourdough breads and tarhana with different production materials in modulating gut health, while the synbiotic approach in Chapter 6 illustrates a promising intervention for metabolic syndrome (MetS). The final chapter, GuMiBear, brings these insights into a translational context, focusing on vulnerable populations, such as infants with CHD. The observed microbial shifts, including biomarkers for NEC. underscore the critical need for microbiome-focused strategies in clinical care. These findings not only validate the preceding work on the importance of personalized dietary strategies but also extend its relevance to managing gut microbiome-related challenges in at-risk populations.
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Keywords
Dietary fibre , Gut microbiome , Fermentation , In vitro digestion , Short chain fatty acids , Congenital heart disease , Metabolic syndrome , Metabolomics
Citation
Koc, F. 2025. The impact of dietary components on gut microbiome modulation and health. PhD Thesis, University College Cork.