Alteration of Gut Microbiota Composition and Diversity in Acute and/or Chronic Graft-versus-Host Disease Following Hematopoietic Stem Cell Transplantation: A Prospective Cohort Study

Abstract

Changes in gut microbiome composition have been implicated in the pathogenesis of graft-versus-host disease (GvHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Our objective was to explore the microbial abundance in patients with GvHD after allo-HSCT. We conducted a single-center, prospective study in patients who underwent allo-HSCT and developed grade II or higher acute GvHD and/or moderate or severe chronic GvHD, to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected fecal specimens at -2 to +2 (T1), +11 to +17 (T2), +25 to +30 (T3), +90 (T4), and +180 (T5) days to assess changes in gut microbiota, with day 0 being the day of allo-HSCT. We included 20 allo-HSCT recipients in the study. Compared with timepoint T1, at timepoint T4 we found a significant decrease in the abundance of Proteobacteria phylum (14.22% at T1 vs. 4.07% at T4, p = 0.01) and Enterobacteriaceae family (13.3% at T1 vs. <0.05% at T4, p < 0.05), as well as a significant increase in Enterococcus species (0.1% at T1 vs. 12.8% at T4, p < 0.05) in patients who developed acute GvHD. Regarding patients who developed chronic GvHD after allo-HSCT, there was a significant reduction in the abundance of Eurobactereaceae family (1.32% at T1 vs. 0.53% at T4, p < 0.05) and Roseruria genus (3.97% at T1 vs. 0.09% at T4, p < 0.05) at T4 compared with T1. Alpha and beta diversity analyses did not reveal a difference in the abundance of bacteria at the genus level in GvHD patients at T4 compared with T1. Our study reinforces results from previous studies regarding changes in gut microbiota in patients with acute GvHD and provides new data regarding the gut microbiome changes in chronic GvHD. Future studies will need to incorporate clinical parameters in their analyses to establish their association with specific changes in gut microbiota in patients with GvHD after allo-HSCT.

Keywords: graft-versus-host disease; gut microbiota; microbial abundance; microbial diversity; stem cell transplantation.

Figure 1

(A). Alpha diversity analysis using the Shannon index at the genus level across the pre-defined study timepoints in patients with aGVHD and cGVHD. Abbreviations list: aGVHD: acute graft-versus-host disease; cGVHD: chronic graft-versus-host disease; (B). Alpha diversity analysis using the inverse Simpson index at the genus level across the pre-defined study timepoints in patients with aGVHD and cGVHD. Timepoints T1, T2, T3, T4, and T5 correspond to −2 to +2, +11 to +17, +25 to +30, +90, and +180 days following stem cell transplantation. Median values are presented in the figures. Abbreviations list: aGVHD: acute graft-versus-host disease; cGVHD: chronic graft-versus-host disease.

Figure 2

(A). LDA coupled with effect size measurements identifies Firmicutes, Bacilli, Lactobacillales, Enterococcus, and Enterococcaceae as significantly enriched taxa at timepoint 4, while the abundance of Proteobacteria, Enterobacteriaceae, Enterobacteriales, and Gammaproteobacteria is significantly reduced at timepoint 1 in patients with aGVHD. (B). Cladogram generated by LEfSe indicating differences in the abundance of taxa between timepoint 1 and timepoint 4 in patients with aGVHD. Each successive circle represents a phylogenetic level (phylum, family, genus, species). Regions in green indicate taxa enriched during timepoint 4, while regions in red indicate a reduction in the abundance of taxa during timepoint 1. Bacilli, Lactobacillales, Enterococcus, and Enterococcaceae, were significantly enriched at timepoint 4, while the abundance of Gammaproteobacteria, Enterobacteriales, and Enterobacteriaceae was significantly reduced at timepoint 1 Abbreviations list: aGVHD: acute graft-versus-host disease; LEfSe: Linear discriminant analysis Effect Size.

Figure 3

(A). LDA coupled with effect size measurements indicates that the abundance of Alistipes, Rikinellaceae, Eubacteriaceae, Coiobacteriales and Coriobacteriaceae at timepoint 1 is significantly reduced in patients with cGVHD. (B). Cladogram generated by LEfSe indicating differences in the abundance of taxa at timepoint 1 in patients with cGVHD. Each successive circle represents a phylogenetic level (phylum, family, genus, species). Regions in red indicate reduction in the abundance of taxa at timepoint 1. The abundance of Coriobacteriaceae, Alistipes, Rikenellaceae, and Eubacteriaceae was significantly reduced at timepoint 1. Abbreviations list: cGVHD: chronic graft-versus-host disease; LEfSe: Linear discriminant analysis Effect Size.