The healthy human gut is colonized by roughly 1014 resident microbes. Among them, bacteria are most common. These microbes have a symbiotic relationship with the human intestinal tract. These microbes maintain the ecosystem of incomparable diversity, termed as microbiota and provides beneficial effects to their host 1. Major bacterial groups in the microbiota are gram-positive Firmicutes and gram-negative Bacteroidetes 2, 3. A vast number of microbes live within the distal parts of the gut, around 1011 cells per gram content 4. Colonic bacteria synthesize metabolic by-products that can influence both the differentiation and function of immune cells. Germ-free (GF) mice models are used to investigate the effect of gut microbiota on immune system development and function. Immune and metabolic defects were observed in germ-free (GF) mice due to lack of microbiota. GF mice produce extremely decreased amounts of SCFAs and increased amounts of indigestible oligosaccharide 5. GF and newborn mice exhibit biased Th2 immune response. When microbes are exposed to intestine at an early age, they modulate biased Th2 immune response which in turn stimulate differentiation of T helper cells e.g. Th1, Th17, regulatory T (Treg) cells. Treg cells are a crucial part of the adaptive immune system which controls inflammatory responses to maintain cellular homeostasis 6. It was reported that drinking water supplemented with acetate, propionate, and butyrate increases the number of colonic Tregs as well as accumulation of G-protein coupled receptor: GPR43 dependent colonic Tregs in germ-free mice 7. Moreover, for proper development and function of the immune system gut microbiota-derived Tryptophan (Trp) metabolites are very important. Indole is a by-product of Tryptophan (Trp) catabolism, which decreases bacterial intestinal epithelial cell (IEC) adhesion, motility, biofilm formation, and pathogen chemotaxis for enterohemorrhagic E. coli. Indole also induces host IEC barrier integrity, expression of anti-inflammatory IL-10 and inhibits inflammatory TNF-?- mediated IL-8 and NF-?B signalling. In a germ-free mice study it was reported that during dextran sodium sulfate colitis, oral indole therapy alleviated GI pathology, mortality and weight loss which confirmed functions of indole 8. Different immune cells for instance T-cells, macrophages, dendritic cells express cytokines like Interleukin-10 (IL-10) which is an anti-inflammatory cytokine. IL-10 plays an important role in intestinal mucosal immunity regulation as IL-10 deficient mice showed a spontaneous development of intestinal inflammation unless reared in a germ-free condition 9. It was observed that commensal microbiota stimulate intestinal macrophages via up-regulating pro-IL 1? activity which recruits neutrophil for pathogen eradication in a GF and conventionally raised mouse model. Another study showed that neutrophil count and macrophage function e.g. phagocytosis, microbicidal activities including phagocytic superoxide anion production is lower in GF mice 10.
Several studies conducted using germ-free mice which suggest that the commensal microbiota act on antigen presenting cells, differentiated T cells, lymphoid follicles and toll-like receptor (TLR) expression and promote local intestinal immunity 11,12,13. Gut microbiota can induce systemic immunity by increasing systemic antibody and splenic CD4+ T cells expression 14. Healthy gut microbiota can prevent colonization of enteric pathogens, called colonization-resistance (CR). Alteration in gut microbial composition unsettles CR. As a result, pathogens start to colonize in the gut and increase susceptibility to infections. This alteration can be caused by application of probiotics and drugs, exposure to antibiotics, changes in diet and a variety of diseases. Changes in the microbial composition are linked with a number of diseases, e.g. autoimmune and immune-mediated phenomena -inflammatory bowel diseases (IBD), obesity, allergies, type 2 diabetes and colorectal cancer (15). Changes in food habit -for example, a complete shift to animal-based to plant-based or vice versa alters microbial composition within just 24 h which could be reversed within 48 h of diet discontinuation 16. Additionally, circadian rhythm disruption could be linked with gut microbiota of animals fed a high-fat or high-sugar diet 17. Major changes in the intestinal microbiota can also be attributed to sustained systemic stress and inflammation 18. Autoimmune disease, a major medical concern in the world since the disease mechanisms responsible for its induction and development are poorly understood. In normal physiological conditions, the immune system shows tolerance to molecules recognized as ”self,”. For example, bio-molecules that are produced in endogenous tissues i.e. carbohydrate, protein and nucleic acid does not react with the immune system. When self-tolerance is lost, the immune system is deployed against one or more of the body’s own molecules which is the hallmark of the autoimmune diseases (AIDx). The primary cause of any AIDx is a reduced capacity for self-tolerance due to a failure in ”central” processes (i.e., in primary lymphoid organs) and/or ”peripheral” means (i.e., secondary lymphoid organs and/or inflamed tissues) for removing or repressing auto-reactive immune cell lineages 19. Autoimmune diseases like rheumatoid arthritis, IBD have been found associated with alteration in commensal microbiota. In IBD patients, a low number of Firmicutes and Bacteroidetes and high number of Proteobacteria have been observed. A research group observed that colonization of GF mice with Bacteroides fragilis stimulates immune system via a bacterial polysaccharide (PSA) mediated pathway as well as restores Th1 and Th2 balance 20.SCFA, acetate, butyrate and propionate, are among the most documented by-products, produced through fermentation of complex carbohydrates by gut bacteria. SCFA play a crucial role to strengthen the mucosal barrier 21 and to promote the development of regulatory T cells. SCFAs might affect immune cell development and function through specific binding of G protein-coupled receptors on immune or epithelial cells or through epigenetic changes. Their critical roles on health have been highlighted notably by my (future) supervisor and colleagues who have shown that diets low in complex carbohydrates, also commonly called dietary fibre, aggravates the development of food allergy, asthma and colitis in mice.
However, which types of complex carbohydrates are most efficiently fermented into SCFAs and in what dietary context is fully unknown. The first aim of this project is to identify which type of dietary fibre gives rise to highest levels of SCFA and thus to optimal mucosal immunity. Diet is subdivided into the macronutrients lipids, carbohydrates and proteins. Studies from Prof Simpson and Raubenheimer, close collaborators of my supervisor have shown complex interactions between macronutrients on health outcome. The second aim of my project is to determine how macronutrient composition might interfere with the effect of dietary fibre on the gut microbiota and immune function.
Finally, gut health seems central in many diseases with most non-communicable diseases associated with dysbiosis and increased gut permeability. Arthritis is one of the most debilitating non-communicable diseases on the rise. This autoimmune disease is characterized by joint swelling and pain currently alleviated with anti-inflammatory drugs but uncured. Ongoing studies from my supervisor suggest a key changes in the gut microbiota and mucosal immunity in autoimmune diseases. The third aim of this project is to determine whether beneficial manipulation of gut microbiota through dietary intervention can prevent or improve the disease.