Fig. 1

Alpha diversity metrics for samples pooled by EHEC testing status for the all hide OTUs (AHO) dataset. Jackknifed alpha diversity metrics (Faith's phylogenetic diversity, Chao1 estimator, and observed OTUs) were calculated with Qiime’s “alpha_rarefaction.py” script. Faith's phylogenetic diversity, the chao1 index, and observed OTUs were calculated for ten jackknifes at a depth of 95 % of the reads contained in the smallest metadata group. Error bars represent the standard error of the jackknife estimate. The width of the bar shows the number of sequences contained in each metadata category, while the small numbers inside the bars indicate the number of samples in each category. Within each chart, bars with different letters were significantly different at an alpha level of 0.05 with the Bonferroni correction as determined by the Mann-Whitney test. a Samples pooled by EHEC testing status into four groups: EHEC negative, E. coli O157 positive, non-O157 positive and positive for both E. coli O157, and any of the tested non-O157 serogroups. b Samples pooled by number or EHEC serogroups present in each sample