HCT is characterized by an early dysbiosis that is slow to recover. (A) α-diversity (as measured by the Simpson reciprocal, a parameter that considers the relative abundance of each unique bacterial taxa to summarize overall diversity) in 8073 stool samples from 1079 unique patients who underwent HCT at MSKCC between 2014 and 2018. Demographics are tabulated in supplemental Table 1. (B) α-diversity of 491 stool samples from 53 unique cGVHD patients (red) and 1702 stool samples from 171 unique controls (blue). One patient in the case group had 2 samples available (day 100 and day 7), but both had insufficient reads to include in this analysis. Samples collected from inpatients are shown as filled symbols, and outpatient collections are shown in open symbols. The solid blue line summarizes the cGVHD cases and the dotted line the controls. (C) Fecal microbial taxa pretransplant (day −30 to day −6; n = 43 cases, 168 controls), periengraftment (closest sample to day 14 [d14]; n = 42 cases, 144 controls), and peri-day 100 (closest sample to day 100 [d100], within the day 70 to day 130 window; n = 9 cases, 36 controls). Patient demographics are described in supplemental Table 1. The orange bar below each bar plot denotes cGVHD cases, and the blue denotes controls. Legend describing the color scheme for bacterial taxa of interest is shown below panel D, as we have previously described.¹⁵  These color schemes were developed to highlight common taxonomic patterns in microbiota community in allo-HCT patients. Each genus is assigned to a distinct color shade derived from a basal color that is assigned to a higher-rank taxonomic group in the data set, facilitating the visualization of both genus-level and higher-rank taxonomic information. Abbreviations are as follows: (f), family; (g), genus; (o), order; (p), phylum. (D) Shotgun metagenomic sequencing of available day 100 stool samples. Linear discriminant analysis of effect size analysis shown, using a value of P ≤ .05 (n = 8 cGVHD; n = 37 controls). Green squares denote pathways relevant to SCFA metabolism.