Phylogenetic distribution of clones obtained from mucosa-adherent ileal and fecal samples in different housing environments. The majority of clones were assigned to the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The Firmicutes phylum was significantly increased in the OUT group compared to the IR group (P < 0.05). The Bacteroides phylum was significantly increased in both the INS and OUTS fecal libraries compared to the mucosa-adherent ileal libraries. Values are expressed as means ± SEM (N = 4).