A Phylum Class Order Taxonomy Other Taxonomy Unclassified Bacteria Actinobacteria Actinobacteria Coriobacteriales Coriobacteriaceae Proteobacteria γ-proteobacteria Enterobacteriales Enterobacteriaceae Unclassified Bacteroidetes Bacteroidetes Bacteroidia Bacteroidales Unclassified Bacteroidales Unclassified Firmicutes Unclassified Clostridiales Clostridiales Incertea Sedis XIV Clostridia Clostridiales Clostridiaceae Lachnospiraceae Peptostreptococcaceae Firmicutes Ruminococcaceae Planococcaceae Bacillales Staphylococcaceae Bacillaceae Bacilli Enterococcaceae Lactobacillales Streptococcaceae Lactobacillaceae Erysipelotrichi Erysipelotrichales Erysipelotrichaceae B Untreated MNV MNV Recovery 100% 80% Ileum 60% Contents 40% 20% 0% 100% 80% Ileum Wall 60% 40% 20% 0% 100% 80% 60% Cecum 40% 20% 0% 100% 80% 60% Feces 40% 20% 0% Supplemental Figure 1. MNV treatment alters the composition of the microbiota. (A) Color code for the most predominant bacterial populations found in the murine intestine. (B) Phylogenetic classification of 16S rDNA frequencies in the ileum, cecum or feces collected from untreated mice, mice treated with metronidazole+neomycin+vancomycin (MNV), or mice allowed to recover for two weeks from the MNV treatment. Each bar represents the microbiota composition of an individual mouse. A Phylum Class Order Taxonomy Other Taxonomy Unclassified Bacteria Actinobacteria Actinobacteria Coriobacteriales Coriobacteriaceae Proteobacteria γ-proteobacteria Enterobacteriales Enterobacteriaceae Unclassified Bacteroidetes Bacteroidetes Bacteroidia Bacteroidales Unclassified Bacteroidales Unclassified Firmicutes Unclassified Clostridiales Clostridiales Incertea Sedis XIV Clostridia Clostridiales Clostridiaceae Lachnospiraceae Peptostreptococcaceae Firmicutes Ruminococcaceae Planococcaceae Bacillales Staphylococcaceae Bacillaceae Bacilli Enterococcaceae Lactobacillales Streptococcaceae Lactobacillaceae Erysipelotrichi Erysipelotrichales Erysipelotrichaceae B Untreated Ampicillin Vancomycin Ampicillin Recovery Vancomycin Recovery 100% 80% 60% Feces 40% 20% 0% 100% 80% Ileum 60% Wall 40% 20% 0% Supplemental Figure 2. Antibiotic treatment alters the composition of the fecal and ileum wall microbiota. (A) Color code for the most predominant bacterial populations found in the murine intestine. (B) Phylogenetic classification of 16S rDNA frequencies in the ileum wall or feces collected from untreated mice, mice treated with ampicillin or vancomycin, or mice allowed to recover for two weeks from antibiotic treatment. Each bar represents the microbiota composition of an individual mouse. Patient A Patient B Patient C Patient D Patient E Supplemental Figure 3. Antibiotic treatment in patients undergoing allo-HSCT. Antibiotic treatment that each patient received during the transplant course is indicated in blue. The dates of the transplant course are indicated as 0 (day of the transplant), negative value (days before the transplant), positive value (days after the transplant). All antibiotics were administered intravenously except for TMP-SMX and atovaquone, which were administered orally, and pentamidine, which was inhaled. TMP-SMX: Trimethoprim + sulfamethox- azole. The days when the stool samples were collected are indicated in green. The VRE bacteremia period for patients A and B is indicated in red. Patient A Patient B 100 100 s s l l e 10 e 10 v v e e l l e e n ND n 1 e e 1 g g A A n n a 0.1 a 0.1 v v 0.01 0.01 VRE - 5 +8 +18 +21 +29 +57 VRE - 6 +1 +8 +14 blood blood culture Fecal Samples culture Fecal Samples Supplemental Figure 4. VRE intestinal expansion in allo-HSCT patients that developed VRE bacteremia. van A gene levels as assessed by qPCR of fecal samples from the two patients that developed VRE bacteremia (see methods). Samples were collected during the transplant course. The timing of the transplant course is indicated as 0 (day of the transplant), negative value (days before the transplant), positive value (days after the transplant). The number of van A gene copies was normalized to the number of 16s rDNA copies in each sample, as assessed by qPCR. Results are expressed relative to the van A gene levels from a pure culture of the VRE strain obtained from the blood culture (assigned as 100%). ND: Non-detectable. Supplemental Table 1. Patients clinical information. Time of VRE VRE Duration Underlying Transplant engraftmen Post-HSCT screening screening Onset of VRE Patient Age/sex t rectal swab rectal swab of VRE cancer type complications bacteremia (ANC>100 culture. culture. bacteremia 0) Before HSCT After HSCT Negative Positive (day Poor graft function, T-cell +52) umbilical CMV viremia, A 41/male lymphoblastic Day +30 Day +75 7 days cord blood suspected GVHD of lymphoma gut T-cell acute Positive Positive lymphoblastic umbilical Not Respiratory failure, B 57/female cord blood engrafted encephalopathy Day +4 18 days leukemia diffuse large B- umbilical Clostridium difficile Negative Positive (day C 53/male cell lymphoma cord blood Day +11 diarrhea +12) n/a n/a Negative Negative Delayed engraftment, relapsed umbilical hematuria from BK D 46/female follicular Day +40 virus, left lower lobe n/a n/a lymphoma cord blood ground glass opacity non- Negative Negative diffuse large B- biopsy-proven GVHD E 61/female myeloablat Day +11 n/a n/a cell lymphoma ive of the gut ANC: Absolute Neutrophil Count. n/a: non applicable. GVHD: Graft vs Host Disease .