Positive modulation of gutmicrobiota in laying chickensmay offer a strategy for reduction of Salmonella Typhimurium shedding and production of safer poultry products. In the current study, the caecal 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, synbiotics and/or Salmonella Typhimurium challenge. The load of Salmonella Typhimurium in various organs was quantified. Irrespective of the probiotics and synbiotics supplementation and Salmonella Typhimurium 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 and synbiotics supplementation increased (false discovery rate; FDR < 0.05) the abundance of Ruminococcus, Trabulsiella, Bifidobacterium, Holdemania and Oscillospira, indicating their role in maintaining gut health through lowering luminal pH and digestion of complex polysaccharides. Salmonella Typhimurium challenge decreased the abundance of Trabulsiella, Oscillospira, Holdemania, Coprococcus, Bifidobacterium and Lactobacillus and increased Klebsiella and Escherichia, indicating its role in caecal dysbiosis. Although probiotics and synbiotics supplementation positively modulated the caecal microbiota, they were not effective in significantly (P > 0.05) reducing Salmonella Typhimurium load in caecal tissue and invasion into vital organs such as liver and spleen. The early colonisation of laying chick caeca by probiotics and synbiotics had the potential to positively influence luminal microbiota; however, the microbial abundance and diversity were not sufficient to significantly reduce the shedding of Salmonella Typhimurium in faeces or invasion into internal organs during this study.