Several species of Prevotella, including Prevotella melaninogenica, are also potential pathogens that mostly occur in the upper digestive tract. Bacteroides spp. are in general mutualistic, and have been described to benefit their host by excluding potential pathogens from colonizing the gut. However, other studies have also shown possible negative effects of increased Bacteroides spp. in the gut. So all these bacteria described above have both beneficial and pathogenic characteristics. It should be noted, however, that in general, relative abundance of the phylum Bacteroidetes, encompassing both genera Prevotella and Bacteroides, was decreased in T2 animals at day 55, whereas it was increased at day 176. Fusobacteria have a potent lipopolysaccharide, and are classified as pathogenic. In conclusion the data presented here may indicate that the specific microbial composition in the T2 animals kept under the experimental conditions, i.e. antibiotics and environment, is unfavourable for these microbial species. ACBC Despite the differences in gene expression at day 55 in both ileum and jejunum between the treatment groups, only the ileum displayed differences in immune related processes after DAVID analysis. This contrasts our previous data obtained for day 8 after birth that showed a major down-regulation of immune related processes in both jejunal and ileal tissue in the animals treated with antibiotic. These observations are in agreement with the fact that differentiation of ileal and jejunal tissue occurs, and that in differentiated and matured ileum immunological structures like Peyer��s patches are much more abundant as compared to jejunum. To have a more complete picture of the different processes being affected by the treatments, we in addition performed functional Gene Set Enrichment Analysis, and superimposed gene expression values over known pathways for ��adult�� life time-points. The GSEA results for day 55 were in concordance with the DAVID functional analyses. However, by taking into account the entire transcriptome, we observed that GSEA analyses showed additional enriched immunological processes compared to DAVID for T3 pigs. To investigate whether the immune processes observed locally in ileal tissue at day 55 were also present systemically, we performed transcriptomic analyses on blood samples. These blood transcriptomics data showed no dominance of immune processes in the different comparisons between treatments. For 176 day old pigs, similar functional analyses were performed using DAVID and GSEA. However, the DAVID analyses did not result in any significantly enriched functional annotation clusters, which is likely due to the fact that almost no genes were significantly differently expressed between the treatments. In contrast, the GSEA for pigs of day 176 A 61603 hydrobromide resulted in multiple significantly enriched gene sets, indicating that despite the more pronounced differences in microbial composition in adult life, host gene expression is not always changing accordingly.