Fig. 3

A Differentially abundant organisms between malignant and benign tissue samples identified in the discovery cohort were tested for their differential abundance in an independent validation cohort. Of the five organisms tested, three showed a significant difference in their abundance (adjusted p value < 0.05; marked by asterisk). Malignant tissue sample was associated with significant over-abundance of Shewanella, and significant under-representation of Staphylococcus saprophyticus, and Vibrio parahaemolyticus, as compared to the benign tissue samples. Bacteroides fragilis and Saimiriine betaherpesvirus showed a trend similar to that seen in the discovery cohort, although the differences did not reach statistical significance in the validation cohort. Error bars correspond to the standard error of the log₂ fold change. Dotted line corresponds to a log₂ fold change cut-off value of |0.58|. B–H Normalized microbial read counts (x-axis) for each patient sample (y-axis) of B. fragilis (B), S. betaherpesvirus (C), Shewanella (D), S. saprophyticus (E), and V. parahaemolyticus (F). Values are given on a log₁₀ scale. Vertical lines denote mean values