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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 gut causing 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 internal 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.

Salmonella Typhimurium infection disrupts but continuous feeding of Bacillus based probiotic restores gut microbiota in infected hens