Fig 1.
Map of sampling scheme and directionality of food waste movement on the farm.
Table 1.
Raw reads, unfiltered reads, and filtered hits for each sample.
Fig 2.
Bar chart of the total number of antibiotic resistance genes (ARGs) found by drug class and sample.
In this instance, results for each duplicate were combined into a single bar.
Table 2.
Selected ARGs, known functions and associated samples.
Fig 3.
Heatmap displaying the differences in abundance ratio of ARGs between samples.
Heatmap was scaled by row (individual ARGs) and created using the pheatmap package.
Fig 4.
Heatmap displaying the differences in abundance ratio of virulence factors between samples.
Heatmap was scaled by row (individual virulence genes) and created using the pheatmap package.
Table 3.
Selected virulence genes, function, associated organism and sample.
Fig 5.
Nonmetric Multidimensional Scaling (NMDS) plot using Bray-Curtis distance of the microbiome of each a) sample and b) group. Food wastes refer to all samples collected off-farm.
Fig 6.
Heatmap of the top A) 20 bacterial species in all samples, B) members of the Actinobacteria Phylum, and C) EKSCAPE pathogens. The Phylum of each species precedes each species name. Heatmap is scaled as the log10 percent read abundance within each sample, with abundances <0.1% all being represented as the same color.
Table 4.
Summary of diversity metrics for each sample.
Table 5.
Results of Pearson correlation testing.