Due to differences in the amount of sequence reads obtained from individual samples,

the relative distribution of sequences was calculated on the basis of the total number of reads from the sample. OTUs that accounted for > 1% of the total number of sequences were considered as dominant species. Table 2 The distribution of sequence reads, OTU’s in absolute numbers and the ratio between Firmicutes and Bacteroides in pooled caecal samples   Conventional Evofosfamide mw cage Furnished cage Aviary   Before inoculation 4 weeks PI Before inoculation 4 weeks PI Before inoculation 4 weeks PI Number of reads 51,863 21,714 42,885 42,520 51,715 40,410 Number of OTU/total number of OTU 185/197 178/197 196/197 193/197 195/197 193/197   93.9% 90.4% 99.5% 98.0% 99.0% 98.0% Firmicutes/Bacteroides ratioa 0.81 0.61 0.87 0.74 0.69 0.68 a The ratio was calculated by dividing all OTU that could be affiliated to Firmicutes (Clostridia and Bacilli)

by the number of OTU’s from Bacteroides. In total, 197 different OTUs were identified, and 196 and 195, respectively, out of these were found in non-inoculated samples from AV and FC, however, for CC a progressive decrease in numbers of OTUs was observed in both samples before and after inoculation with Salmonella. In these cages, 185 OTUs were identified before inoculation and 178 OTUs four weeks after inoculation, while in the other cages 193 OTUs were detected at the end of the experiment. Due to a different number of reads obtained Staurosporine clinical trial from each sample, normalized prevalence values

of each OTU were calculated. Using a cut-off value of 0.01%, the difference in diversity between cages was still observed where the BIBW2992 mouse dominating genera in CC constituted a larger proportion Phosphatidylinositol diacylglycerol-lyase of the microbiota at the expense of fewer OTU’s, compared to the two other cages (Figure 2). Figure 2 The distribution of OTU’s according to the prevalence in the microbiota. The number and prevalence of OTU based on the relative prevalence in each sample (cut off < 0.01%). The number of different OTU’s in the group of less abundant genera was highest in furnished and aviary cage, in contrast to conventional cage where we observed fewer but more dominating genera. The consensus sequence from each OTU was compared against the Ribosomal Database (RDP server) to find the most related species or genus. Though many of the bacterial species in the caecal microbiota still remain to be characterized, it was possible to classify 92% of all OTUs to phylum level, and out of these were 86% classified to class level and 55% to genus level. Although variation was observed in the relative presence that colonized the caecum, it was the same group of genera that were dominating in all cages before and after inoculation, accounting for more than 74% of the total amount of reads (Table 3).