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There are 10-100 trillion microorganisms in the human gastrointestinal tract. These microorganisms mostly consist of bacteria. Fascinatingly, between the small and large intestine alone there are 10 times more bacterial cells than there are cells in the entire human body. This means there are 100 times more bacterial genes than human genes in your body. Together all of these bacterial genes are referred to as the “microbiome”. The variety of bacterial species that live in your intestines are different from one person to the next. Factors such as the mode of birth delivery can influence this but diet is one of the major factors in shaping who lives there. The microbiome is the most complex and diverse ecosystem on our planet and it resides inside each and every one of us.

In recent years, scientists have shown that the large numbers of bacteria that are always carried in the human gut are important for our health. They are involved in extracting energy from our food, producing certain vitamins, keeping dangerous bacteria at bay, and even fine-tuning our own defence mechanisms or immune system. Differences were found between bacterial species in healthy humans and in those with certain diseases such as obesity, diabetes and inflammatory bowel disease. Thus, changes to the microbes which live inside your gut can contribute to the development and progression of these chronic diseases. Diet is one of the main factors which can cause these changes to occur. What we eat determines what species of bacteria live within us. Just as we eat to provide our body with nutrients and energy, we also eat to feed our microbes. Without being provided with the specific food sources bacteria require their populations will not survive within our gut.

Fibre is an essential food source of certain bacterial species which have health-promoting benefits in the setting of IBD and obesity among other gut and metabolic diseases. Once these microbes break down fibre, the resulting molecules can enter into our own human cells and aid in the prevention of several diseases. In addition, this method may also be valuable in treating various diseases.
We at FIBREMET are investigating the relationship between different types of fibre and the gut bacteria in inflammatory bowel disease and those metabolically challenged. The findings of this project will allow us to make recommendations for diet and food ingredients for people subject to these ailments. In addition, these findings will benefit the Irish consumer and Irish food industry.

  • To assess the composition of microbiota in individuals with inflammatory bowel disease and metabolic dysfunction and to track changes induced to gut microbiota composition by specific fibre types.
  • To identify correlations between diversity and composition of the gut microbiota induced by specific fibre types and its subsequent effect on host metabolism.
  • To assess what specific fibre types may be beneficial for patients of inflammatory bowel disease and metabolic syndrome to improve health.
  • The identification of fibre type which may be incorporated into dietary ingredients and/or foodstuffs which are of benefit to the health of the general public to aid in the prevention of these ailments.

There are thousands of different phylum of gut bacteria which reside in the human gastrointestinal tract (1). Disruptions to the normal balance between the gut microbes and our own body have been associated with obesity (2), inflammatory bowel disease (3) and irritable bowel syndrome (4). Diet has a major impact on the composition of the gut microbiome and its diversity and richness. Different components of the diet will shape these bacterial communities (5) which in turn will affect host metabolism and homeostasis. Over the last few decades, the common dietary practice has changed in more developed countries. These newly industrialised countries, including Ireland, now consume what is referred to as the “Western diet”, an unhealthy diet which is rich in saturated fat and low in fibre. There is a direct correlation between increased Western diet consumption and increased incidence of IBD and metabolic diseases such as obesity and type II diabetes which are becoming more prevalent in Ireland and are expected to increase steadily over the next decade in all industrialised countries (6,7). In 2017 62% of Irish people were considered overweight or obese (9). Furthermore, ill-health in IBD populations represents a real burden on our health services with the annual cost to the exchequer estimated at approximately €15,521/patient/annum (8). Nationally, the burden of metabolic ill-health. Thus, this project aims to identify specific fibre types which may be used to improve the health of IBD patients and those metabolically challenged. Furthermore, this study will provide recommendations to the general public with regards to fibre types which may be incorporated into functional foodstuffs to aide in the prevention of metabolic illness.

(1) Rajilić‐Stojanović, M., Smidt, H. and De Vos, W.M., 2007. Diversity of the human gastrointestinal tract microbiota revisited. Environmental Microbiology, 9(9), pp.2125-2136.

(2) Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023 (2006).

(3) Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA 104, 13780–13785 (2007).

(4) Kassinen, A., et al., The faecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology, 2007. 133(1): p. 24-33

(5) Makki, K., Deehan, E.C., Walter, J. and Bäckhed, F., 2018. The impact of dietary fibre on gut microbiota in host health and disease. Cell host & microbe, 23(6), pp.705-715.

(6) Hope, B., Shahdadpuri, R., Dunne, C., Broderick, A.M., Grant, T., Hamzawi, M., O'Driscoll, K., Quinn, S., Hussey, S. and Bourke, B., 2012. The rapid rise in the incidence of Irish paediatric inflammatory bowel disease. Archives of disease in childhood, 97(7), pp.590-594.

(7) Kaplan, G.G., 2015. The global burden of IBD: from 2015 to 2025. Nature Reviews Gastroenterology & Hepatology, 12(12), p.720.

(8) Gut Decisions Leading change to improve the lives of people with Crohn’s and colitis. available from:

(9) Health - CSO - Central Statistics Office Available from: n2017/hlt/

  • The microbiome of each individual recruited to FIBREMET will be determined using the next generation sequencing techniques, shotgun metagenomic sequencing and 16S rRNA amplicon sequencing.
  • We will measure a range of metabolites which are involved in the pathology of inflammatory bowel disease and obesity such as bile acids and fatty acids.
  • Correlations will be explored between the microbiota composition and a range of health indices such as body mass index (BMI), blood biochemistry and novel biomarkers of metabolic health.