Background:The gut microbiota plays an important role in the colonisation resistance and invasion of pathogens. Salmonella Typhimurium has the potential to establish a niche by displacing the microbiota in the chicken gutcausing continuous faecal shedding that can result in contaminated eggs or egg products. In the current study, we investigated the dynamics of gut microbiota in laying chickens during Salmonella Typhimurium infection. The optimisation of the use of an infeed probiotic supplement for restoration of gut microbial balance and reduction of Salmonella Typhimurium load was also investigated. Results:Salmonella infection caused dysbiosis by decreasing (FDR<0.05) the abundance of microbial genera, such as Blautia, Enorma, Faecalibacterium, Shuttleworthia, Sellimonas, Intestinimonas and Subdoligranulum and increasing the abundance of genera such as Butyricicoccus, Erysipelatoclostridium, Oscillibacter and Flavonifractor. The higher Salmonella Typhimurium load resulted in lower (P<0.05) abundance of genera such as Lactobacillus, Alistipes, Bifidobacterium, Butyricimonas, Faecalibacterium and Romboutsia suggesting Salmonella driven gut microbiota dysbiosis. Higher Salmonella load led to increased abundance of genera such as Caproiciproducens, Acetanaerobacterium, Akkermansia, Erysipelatoclostridium, Eisenbergiella, EscherichiaShigella and Flavonifractor suggesting a positive interaction of these genera with Salmonella in the displaced gut microbiota. Probiotic supplementation improved the gut microbiota by balancing the abundance of most of the genera displaced by the Salmonella challenge with clearer effects observed with continuous supplementation of the probiotic. The levels of acetate and butyrate in the faeces were not affected (P>0.05) by Salmonella challenge and the butyrate level was increased by the continuous feeding of the probiotic. Probiotic supplementation in Salmonella challenged chickens resulted in higher level of propionate. Continuous probiotic supplementation decreased (P<0.05) the overall mean load of Salmonella in faeces and had a significant effect on Salmonella load reduction in intal organs. Conclusions:Salmonella challenge negatively impacts the diversity and abundance of many gut microbial genera involved in important functions such as organic acid and vitamin production. Strategic feeding of a Bacillus based probiotic helps in restoring many of the microbial genera displaced by Salmonella Typhimurium challenge.