Differential expression of 39 selected genes in the chicken caeca following their colonisation with microbiota of different composition. Each column indicates fold induction (or suppression) in comparison to the expression of particular gene in germ-free chickens determined by qRT PCR. ENT, chickens colonised with E. faecium, EC, chickens colonised with E. coli; TETRA, chickens colonised with tetra flora; CONVENTIONAL, chickens colonised with conventional microbiota; KILLED, chickens treated with killed tetraflora (tested only for immunoglobulin transcription). Fold changes and statistical significances shown in this figure were calculated from average expressions in all germ free, E. coli, E. faecium, tetraflora or heat killed tetraflora inoculated chickens, as well as all conventional chicken irrespective of their age. *Significantly induced or suppressed genes in comparison to their expression in germ-free chickens (t test, p < 0.05).