If you read the full paper in the conclusions the authors say they don't know if the observed volumetric changes in the grey matter are related to primary alterations in brain, or if they are a consequence of altered visceral signaling to the brain. In other words, they still don't know if IBS is a result of problems in the gut, the brain or both or even if there are a variety of subtypes each with its own specific cause. What the study does show is the IBS is an organic problem and it is not caused psychological disorders.
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