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The digestive tract works through a complex network of integrative functions. At the level of the gut, this integration occurs between the immune, neuromotor and enteroendocrine systems, coordinating the physical and chemical elements of the intestinal barrier in order to facilitate digestion whilst protecting the gut from unwanted components of the luminal contents. Gastrointestinal function is controlled and coordinated by the central nervous system to ensure effective motility, secretion, absorption and mucosal immunity. It follows that perturbations in this complex network could lead to gut dysfunction and symptom generation. Recently, attention has been focused on the emerging hypothesis that gut luminal content contributes to determine normal GI function and on the therapeutic possibilities arising from modulating its impact on gut physiology and immunity using probiotic bacteria. In this issue of Neurogastroenterology and Motility, two papers explore the effect of specific probiotic bacteria on spinal neuronal activation and in vitro muscle contractility. These papers support the notion that the composition of the intestinal microbiota can influence gut neuro-motor function and enhance our understanding on the mechanisms of action underlying the effects of specific probiotics on gut functional disorders.