Figure 1.
16S rRNA gene library rarefaction curves from isolator-reared animals at multiple OTU cutoff levels.
Rarefaction curves were generated by plotting the number of phylotypes (OTUs) against the number of clones sequenced. At 99% cut-off, rarefaction analysis of clone libraries suggested that both the InIs (A) and OIs (B) group possessed a highly diverse mucosa-associated bacterial community. Clearly, even after sampling >1000 clones for each treatment group, the number of OTUs continued to increase even as OTU definitions relaxed towards 95% (genus level).
Figure 2.
16S rRNA gene library collector's curves from indoor isolator-reared and outdoor isolator-reared animals.
Collector's curves of the observed (black) and estimated (Chao1 (blue) and ACE (pink)) phylotype richness calculated at 99% OTU cut-off level from indoor isolator-reared (A) and outdoor isolator-reared animals (B). The relatively constant estimates of the number of unobserved phylotypes in each treatment group as observed richness increases indicate that estimated richness is likely to increase further with additional sampling.
Table 1.
Indices of diversity, richness and library coverage for 16S rRNA gene libraries (N = 5).
Table 2.
Taxonomic composition of the mucosa-associated microbiota of indoor and outdoor isolator-reared animals and their sow-reared counterparts.
Figure 3.
Phylogenetic distribution and abundance of the Firmicutes phylum in the mucosa-associated microbiota from isolator-reared animals (N = 5).
Figure 4.
Abundance of Lactobacillaceae in the mucosa-adherent microbiota of isolator-reared animals (N = 5).
Figure 5.
Phylogenetic distribution and abundance of Bacteroidetes in the mucosa-associated microbiota of isolator-reared animals (N = 5).
Figure 6.
Phylogenetic distribution and abundance of Proteobacteria in the mucosa-associated microbiota of isolator-reared animals (N = 5).