Fig. 1

Patient condition, drug exposure, and intestinal microbiome composition during treatment. The study subject was admitted to Stanford Hospital with myelodysplastic syndrome and myelofibrosis and subsequently underwent hematopoietic cell transplantation (HCT, denoted by a red line). Stool samples were collected prior to HCT and over the following 5 weeks as the patient underwent chemotherapy, antibiotic treatment, and immunosuppression. Taxonomic classification of shotgun metagenomics sequencing reads (Illumina TruSeq Nano DNA) reveals pronounced dysbiosis emerging following HCT with gut domination by Bacteroides caccae, a commensal bacterium. Relative abundances of each species are determined using reads that are classified at the species level. The relative abundance of the species in the samples was determined after removing human and viral reads from the data. For this figure, the top 9 most abundant species in the shotgun metagenomics data are shown. Relative abundance data for all the species-level classification is shown in Additional file 2: Table S1. For a more detailed view of the species-level and genus-level classifications of all the samples, refer to Additional file 1: Fig. S1