Metagenomic analysis of the stool microbiome in patients receiving allogeneic stem cell transplantation: loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal graft-versus-host disease.
Next-generation sequencing of the hypervariable V3 region of the 16s rRNA gene isolated from serial stool specimens collected from 31 patients receiving allogeneic stem cell transplantation (SCT) was performed to elucidate variations in the composition of the intestinal microbiome in the course of allogeneic SCT. Metagenomic analysis was complemented by strain-specific enterococcal PCR and indirect assessment of bacterial load by liquid chromatography-tandem mass spectrometry of urinary indoxyl sulfate. At the time of admission, patients showed a predominance of commensal bacteria. After transplantation, a relative shift toward enterococci was observed, which was more pronounced under antibiotic prophylaxis and treatment of neutropenic infections. The shift was particularly prominent in patients that developed subsequently or suffered from active gastrointestinal (GI) graft-versus-host disease (GVHD). The mean proportion of enterococci in post-transplant stool specimens was 21% in patients who did not develop GI GVHD as compared with 46% in those that subsequently developed GI GVHD and 74% at the time of active GVHD. Enterococcal PCR confirmed predominance of Enterococcus faecium or both E. faecium and Enterococcus faecalis in these specimens. As a consequence of the loss of bacterial diversity, mean urinary indoxyl sulfate levels dropped from 42.5 ± 11 μmol/L to 11.8 ± 2.8 μmol/L in all post-transplant samples and to 3.5 ± 3 μmol/L in samples from patients with active GVHD. Our study reveals major microbiome shifts in the course of allogeneic SCT that occur in the period of antibiotic treatment but are more prominent in association with GI GVHD. Our data indicate early microbiome shifts and a loss of diversity of the intestinal microbiome that may affect intestinal inflammation in the setting of allogeneic SCT.
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany. Electronic address: ernst.holler@ukr.de.
Ernst
E
Holler
Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.
Peter
P
Butzhammer
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Karin
K
Schmid
Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.
Christian
C
Hundsrucker
Institute of Microbiology, University Medical Center, Regensburg, Germany.
Josef
J
Koestler
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Katrin
K
Peter
Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.
Wentao
W
Zhu
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Daniela
D
Sporrer
Institute of Immunology, University of Regensburg, Regensburg, Germany.
Thomas
T
Hehlgans
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Marina
M
Kreutz
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Barbara
B
Holler
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Daniel
D
Wolff
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Matthias
M
Edinger
Department of Hematology/Oncology, University Medical Center, Regensburg, Germany.
Reinhard
R
Andreesen
University of Michigan Medical Center, Blood and Marrow Transplantation Program, Ann Arbor, Michigan.
John E
JE
Levine
University of Michigan Medical Center, Blood and Marrow Transplantation Program, Ann Arbor, Michigan.
James L
JL
Ferrara
Institute of Microbiology, University Medical Center, Regensburg, Germany.
Andre
A
Gessner
Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.
Rainer
R
Spang
Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.
Peter J
PJ
Oefner
D000328:Adult; D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D044822:Biodiversity; D013293:Enterococcus faecalis / Q000187:drug effects / Q000235:genetics; D016984:Enterococcus faecium / Q000187:drug effects / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D041981:Gastrointestinal Tract / Q000187:drug effects / Q000276:immunology / Q000382:microbiology*; D006086:Graft vs Host Disease / Q000188:drug therapy / Q000276:immunology / Q000382:microbiology*; D018380:Hematopoietic Stem Cell Transplantation; D006801:Humans; D007200:Indican / Q000652:urine; D008297:Male; D054892:Metagenome; D064307:Microbiota; D008875:Middle Aged; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014184:Transplantation, Homologous
D000900:Anti-Bacterial Agents; D012336:RNA, Ribosomal, 16S; D007200:Indican
Clinical allogeneic transplantation; GVHD; Metagenomics; Microbiome