The indigenous microbiota is the population of microorganisms normally present on the surface and mucosa of an individual, where it performs essential health functions, including the colonisation resistance (CR) against pathogens. To identify the bacteria responsible and the mechanisms involved in the CR, the germ-free (GF) animal model has been used, because in vitro studies cannot always be extrapolated to what occurs in vivo. In this study, ex vivo antagonism assays against seven enteropathogenic bacteria using stools from 15 healthy human donors confirmed that the CR showed individual variation. Using in vitro antagonism assays, 14 strains isolated from dominant faecal microbiota of donors with elevated CR were selected for mono-association in GF mice to test the in vivo antagonism against Salmonella enterica ser. Typhimurium. Mice mono-associated with Enterococcus hirae strain 8.2, Bacteroides thetaiotaomicron strain 16.2 and Lactobacillus ruminis strain 18.1 had significant reductions in faecal counts of the pathogen during the challenge. After five days of infection, the group associated with E. hirae 8.2 showed a reduction in the translocation of S. Typhimurium to the spleen, while the group associated with L. ruminis 18.1 presented an increased translocation to the liver. The histological data confirmed these results and revealed that the mice associated with E. hirae 8.2 showed fewer lesions on ileum and liver, compared to the damage caused by S. Typhimurium alone, while in mice associated with L. ruminis 18.1 there was significantly worse lesions. Concluding, from the dominant faecal microbiota from healthy human with high CR, through ex vivo, in vitro and in vivo assays, a bacterium was characterised for its high CR potential, being a candidate for probiotic use.