Figure 1.
Body weight of sow-reared and isolator-reared animals.
Body weight (BW) of all experimental animals at day 28 and 56 is shown. At day 28, a significant reduction in BW was observed for animals housed in isolators compared to sow-reared animals. InIs and OIs animals were significantly heavier than IN animals at day 56.
Figure 2.
Gut morphology of sow-reared and isolator-reared animals.
Representative microscopy images of haematoxylin and eosin–stained cross-sections of tissue taken at 75% of the length of the small intestine from pigs at: (A) day 5 (original magnification 10×), (B) villus tips at day 5 (original magnification 20×), (C) day 28 (original magnification 10×), and (D) day 56 (original magnification 10×).
Figure 3.
Bacterial diversity of the mucosa-adherent microbiota.
DGGE microbial profile at days 5, 28 and 56 in indoor pigs reared in isolators (A) and outdoor pigs reared in isolators (B) at days 5, 28 and 56. The overall DGGE profile showed a highly diverse microbiota at all three sampling time-points, increasing from day 5 towards day 56. Comparisons of DGGE pattern profiles in InIs animals (C) and OIs animals (D) were performed using Dice's similarity coefficient and visualized by dendrograms using the UPGMA algorithm.
Figure 4.
Ileum transcriptome differences between indoor isolator-reared and outdoor isolator-reared animals.
Venn diagram of differentially expressed genes at each time-point is shown for the two treatment groups (P<0.01, −2≤ fold change ≥2).
Table 1.
Verification of microarray results by real-time PCR.
Figure 5.
Pathway analysis of genes differentially expressed in indoor isolator-reared and outdoor isolator-reared animals.
Differentially expressed genes (P<0.05) were imported into GeneGo MetaCore analytical software to determine significantly enriched canonical pathways in each group. Data represent the distribution in cell process categories of statistically significantly enriched pathways (P<0.05) between the two treatment groups.
Table 2.
Immune response pathways in animals housed in different environments at day 5, 28 and 56.
Figure 6.
Heatmap of IFN-induced gene subset.
A heatmap of IFN-related genes was generated from a subset extracted from the list of significantly expressed genes. Columns represent individual arrays, while rows represent specific genes of interest. The Z-score depicts a measure of distance, in standard deviations, away from the mean. The relative value for each gene is depicted by color intensity, with green indicating upregulated and red indicating downregulated genes.