Probiotics are commonly used to reduce the risk of antibiotic associated diarrhoea (AAD). This study, in both mice and humans, investigated the effects of an 11 strain probiotic supplement and autologous faecal microbiome transplantation (aFMT) after antibiotic treatment. (Autologous meaning the person’s own, pre-antibiotic stool was transplanted.) Gut mucosa samples along the digestive tract and stool samples were investigated for microbiome composition and activity (transcriptome). The investigators found that without antibiotics the probiotics did not colonise very well, suggesting that our native microbiome offers resistance. After antibiotics, which would kill off much of our gut bacteria,the probiotics colonise the gut mucosa much better. However, the probiotics appear to then prevent the microbiome to return to its native, pre-antibiotic state. Whilst in those with the aFMT and in those who did nothing (“watchful waiting”) the microbiome returned to pre-antibiotic state fairly quickly, in the probiotic group even after 5 months the microbiome had not returned to its native composition. In vitro experiments suggest that the delay in the probiotic group is due to substances secreted by the probiotic bacteria, in particular Lactobacilli. The authors conclude that the potential benefits in terms of reducing the risk of AAD with probiotics may be offset with a delay in reconstitution of the native microbiome, and call for more research into aFMT and a more personalised approach to probiotic therapy.