Fig. 2

Antibacterial antibiotic exposures and microbiota heatmap. a Probability of exposure to each class of antibacterial antibiotics over time, with time measured in days and relative to the first day of chemotherapy. Linezolid and daptomycin were grouped together with intravenous vancomycin. Exposure for a typical patient starts with fluoroquinolone prophylaxis, followed by neutropenic fever, when fluoroquinolone is changed to broader-spectrum antibiotics (especially cefepime, piperacillin-tazobactam, and vancomycin); hence, there is an initial decline in the fluoroquinolone curve, but rises in other antibiotic curves. Antibiotic pressure peaks in weeks 2 and 3. Concurrent with clinical and hematopoietic recovery in week 4, broad-spectrum antibiotics are discontinued or de-escalated to prophylactic fluoroquinolones, the latter explaining the late rise in the fluoroquinolone curve. b Heatmap of the 20 most abundant genera. Each column indicates a sample, and each row represents genus-level mapping of an OTU. f (family) and o (order) indicate OTUs that were unclassifiable to deeper levels. OTU relative abundances were Z-transformed (indicated by the color gradient). Rows were ordered by their mean values and columns by sample collection day (color bar at top) relative to the first day of chemotherapy, with lighter colors indicating earlier days