PCA analysis of T-RFLP generated fingerprints of the bacterial community GSK1838705A purchase 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 this website 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.

T-RFLP analysis of the impact of Salmonella on the intestinal microbiota The impact of an inoculation with S. Enteritidis on intestinal microbiota was also evaluated. After inoculation, no clinical signs of infection were detected in the layers. However, colonisation of the intestinal microbiota was established, and S. Enteritidis Cyclosporin A clinical trial could be detected in samples from internal organs as well as in cloacal swabs [18, 19]. At the end of both studies, Salmonella was found in a few layers by culture and PCR. In the ileal samples, Salmonella was detected in 2/8 from AV by PCR, while other samples were negative. In the caecum, S. Enteritidis could be cultured in 2/8 samples from AV, 3/8 from both FC and CC. The concentration of S. Enteritidis in the positive samples was generally low, as culture

positive samples not always were positive by real-time PCR. T-RFLP profiles of intestinal microbiota positive for S. Enteritidis were compared with profiles where it had been eliminated. On the basis of the mean SD values calculated between Salmonella negative and positive samples from the same cage, no differences could be detected between Farnesyltransferase positive and negative samples within same cage (data not shown). When profiles were analysed by PCA, no discrimination was found between positive or negative samples within the same cages (Figure 1). 454 sequencing of the caecal microbiota The microbiota in the caecal samples from the first experiment were further characterized by 454 pyrosequencing of 16S rDNA gene libraries. Due to the high sample similarity observed in the T-RFLP analysis, we pooled the DNA from 10 cage mates and used this as template for 454 pyrosequencing. In total six samples were generated, one for each cage type before and after inoculation with Salmonella. From each sample, between 20,000 and 50,000 sequence reads could be used for analysis (Table 2). On the basis of 99% similarity these reads were sorted into OTUs.