PCA comparison of T-RFLP profiles of the caecal flora in laying hens housed in different cage systems. PCA analysis of T-RFLP generated fingerprints of the bacterial community in caecal samples from 2 experimental studies. The first plot shows all samples from both experiments coloured according to sampling time and salmonella status. Samples collected before inoculation with S. Enteritidis (blue) were clearly separated from samples collected 4 weeks PI (red and yellow). The second experiment (green, light blue) was also clearly separated from the first experiment (X = 20.7%, Y = 10.1%, Z = 9.0%). Yellow and light blue represents samples positive for Salmonella. In the second plot, the same samples are marked according to cage system. Each cage type are separated in clusters with the major variance being 20.7% between experiments and Y = 10.7% between cages. Red dots: Aviary, Green dots: Conventional cage, Blue: Furnished cage.