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Nutrition-related factors together with components of the gut-associated microbial ecosystem (gut microbiota) emerge as prime environmental triggers for the development and modification of lifestyle-related chronic diseases including chronic inflammatory disorders of the gastro-intestinal tract such as Crohn's disease and ulcerative colitis. Although a variety of susceptibility genes were identified in genome-wide association studies, the impact of environmental factors in initiating or promoting the development of these complex diseases are unknown. Nutrigenomics is a transdisciplinary approach to understand the subtle but contentious impact of nutrition and/or microbes as prime environmental triggers in shaping the dynamic range between health and diseases. Profiling technologies such as transcriptomics, proteomics, and metabonomics at the interface of the host's genetic make-up and its metabolic phenotype are implemented to identify cellular and molecular targets to develop novel hypothesise with respect to the functional role of diet and gut bacteria in modulating chronic degenerative diseases including inflammatory bowel disease.