Crohn’s disease is a chronic inflammatory disorder of the gastro-intestinal tract. It is thought to result from an abnormal, ongoing immune response to environmental factors, likely luminal bacteria, in genetically susceptible individuals. The association of microbes with Crohn's disease is complex: no single causative organism has been identified; bacterial community imbalance (dysbiosis) and reduced alpha diversity is often reported, and accordingly alterations in metabolic functions of the gut microbiota, such as shifts in oxidative stress pathways and a decrease in butanoate and propanoate metabolism gene expression; an increase in pathobionts such as Enterobacteriaceae, specifically E. coli, and subsequent decrease in Firmicutes, including the butyrate-producing Faecalibacterium prausnitzii, is observed. Our emerging understanding of what drives changes in the mucosal gut microbiota in the context of Crohn's disease will be discussed.