Figure 3.

Figure includes animals that became Salmonella-positive after transport. We compared fecal samples collected from the same pig on the farm and at the slaughterhouse (N=11) (Test 2). (A) Dissimilarities in fecal microbiota composition represented by the non-metric multidimensional scaling (NMDS) ordination plot, with the Bray-Curtis dissimilarity index calculated on unscaled OTU abundances The centroids of each group are featured as the group name on the graph (“envfit”; Vegan R package). Samples are colored by the status of Salmonella: H-NEG (negative animals sampled on the farm, pink) and S-POS (positive animals sampled at the slaughterhouse; blue). Larger filled circles indicate group centroids. (B) Box plot graph representation of the alpha diversity (Shannon index), beta diversity (Whittaker’s index), and richness (total number of OTUs present in each sample) using the rarefied OTU table; samples are colored by the status of Salmonella: H-NEG (negative animals sampled on the farm, pink) and S-POS (positive animals sampled at the slaughterhouse; blue).