The normal gut microbiota plays an important role in host nutrients metabolism, immunomodulation and maintenance of structural integrity of the gut mucosal barrier. Probiotics and prebiotics are used for modulation of gut microbiota in various disease conditions. Salmonella Typhimurium (ST) causes gastroenteritis in humans that often trace back to consumption of contaminated egg or egg products. Positive modulation of gut microbiota laying chickens may offer a strategy for reduction of ST shedding and production of safer poultry products. In the current study, the cecal luminal microbiota of laying chicks was studied using 16S rRNA amplicon sequencing on DNA obtained from the chicks that were offered supplementation with commercial probiotics and/or ST challenge. The load of ST in various organs was quantified. Irrespective of the probiotics supplementation and ST challenge, caecal microbiota was dominated by 22 distinct bacterial genera and 14 families that clustered into Actinobacteria, Proteobacteria and Firmicutes at phylum level. Taken together, probiotics supplementation increased (FDR<0.05) the abundance of Ruminococcus, Trabulsiella, Bifidobacterium, Holdemania and Oscillospira, indicating their role in maintaining gut health through lowering liminal pH and digestion of complex polysaccharides. ST challenge decreased the abundance of Trabulsiella, Oscillospira, Holdemania, Coprococcus, Bifidobacterium and Lactobacillus and increased Klebsiella and Escherichia, indicating its role in cecal dysbiosis. Measured by linear discriminant analysis effect size method (LEfSe), group specific biomarkers were affected by probiotics supplementation and ST challenge. Although probiotics supplementation positively modulated the cecal microbiota, they were not effective in significantly (P>0.05) reducing ST load in cecal tissue and invasion into vital organs such as, liver and spleen. Probiotics supplementation positively modulated the gut microbiota, while the ST challenge disrupted the abundance of vital microbial communities. The early colonisation of laying chick ceca by probiotics had the potential to positively influence luminal microbiota; however, the microbial abundance and diversity were not sufficient to significantly reduce the shedding of ST in feces or invasion into internal organs during this study.