FIG 3 .

C. difficile colonization alters gene transcription of taxonomic groups differentially between antibiotic pretreatments. Each point represents a unique gene from the respective metagenomic assembly. Coordinates were determined by the log₂-transformed difference in transcription level between C. difficile-infected and mock-infected conditions for each gene. Outliers were defined using linear correlation and a squared residual cutoff of 2. Euclidean distance of outliers to the x = y line was also calculated. The coloring of each point indicates the genus from which the transcript originated, and the gray points denote those genes with consistent transcription levels between conditions as defined by outlier analysis. Antibiotic pretreatments: streptomycin (A), cefoperazone (B), and clindamycin (C).