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Graft-Versus-Host Disease

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors

Abstract

Growing evidence suggests that host-microbiota interactions influence GvHD risk following allogeneic hematopoietic stem cell transplant. However, little is known about the influence of the transplant recipient’s pre-conditioning microbiota nor the influence of the transplant donor’s microbiota. Our study examines associations between acute gastrointestinal GvHD (agGvHD) and 16S rRNA fecal bacterial profiles in a prospective cohort of N=57 recipients before preparative conditioning, as well as N=22 of their paired HLA-matched sibling donors. On average, recipients had lower fecal bacterial diversity (P=0.0002) and different phylogenetic membership (UniFrac P=0.001) than the healthy transplant donors. Recipients with lower phylogenetic diversity had higher overall mortality rates (hazard ratio=0.37, P=0.008), but no statistically significant difference in agGvHD risk. In contrast, high bacterial donor diversity was associated with decreased agGvHD risk (odds ratio=0.12, P=0.038). Further investigation is warranted as to whether selection of hematopoietic stem cell transplant donors with high gut microbiota diversity and/or other specific compositional attributes may reduce agGvHD incidence, and by what mechanisms.

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References

  1. Ferrara JL, Levine JE, Reddy P, Holler E . Graft-versus-host disease. Lancet 2009; 373: 1550–1561.

    Article  CAS  Google Scholar 

  2. Magenau J, Runaas L, Reddy P . Advances in understanding the pathogenesis of graft-versus-host disease. Br J Haematol 2016; 173: 190–205.

    Article  Google Scholar 

  3. Murphy S, Nguyen VH . Role of gut microbiota in graft-versus-host disease. Leuk Lymphoma 2011; 52: 1844–1856.

    Article  CAS  Google Scholar 

  4. Mathewson N, Reddy P . The microbiome and graft versus host disease. Curr Stem Cell Rep 2015; 1: 39–47.

    Article  CAS  Google Scholar 

  5. Zama D, Biagi E, Masetti R, Gasperini P, Prete A, Candela M et al. Gut microbiota and hematopoietic stem cell transplantation: where do we stand? Bone Marrow Transplant 2016; 52: 1–8.

    Google Scholar 

  6. Holler E, Butzhammer P, Schmid K, Hundsrucker C, Koestler J, Peter K et al. 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. Biol Blood Marrow Transplant 2014; 20: 640–645.

    Article  Google Scholar 

  7. Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 2012; 55: 905–914.

    Article  CAS  Google Scholar 

  8. Biagi E, Zama D, Nastasi C, Consolandi C, Fiori J, Rampelli S et al. Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT. Bone Marrow Transplant 2015; 50: 992–998.

    Article  CAS  Google Scholar 

  9. Taur Y, Jenq RR, Perales M-A, Littmann ER, Morjaria S, Ling L et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood 2014; 124: 1174–1182.

    Article  CAS  Google Scholar 

  10. Weber D, Oefner PJ, Hiergeist A, Koestler J, Gessner A, Weber M et al. Low urinary indoxyl sulfate levels early after ASCT reflect a disrupted microbiome and are associated with poor outcome. Blood 2015; 126: 1723–1729.

    Article  CAS  Google Scholar 

  11. Jenq RR, Taur Y, Devlin SM, Ponce DM, Goldberg JD, Ahr KF et al. Intestinal blautia is associated with reduced death from graft-versus-host disease. Biol Blood Marrow Transplant 2015; 21: 1373–1383.

    Article  Google Scholar 

  12. Corrêa-Oliveira R, Fachi JL, Vieira A, Sato FT, Vinolo MAR . Regulation of immune cell function by short-chain fatty acids. Clin Transl Immunol 2016; 5: e73.

    Article  Google Scholar 

  13. Mathewson ND, Jenq R, Mathew AV, Koenigsknecht M, Hanash A, Toubai T et al. Gut microbiome-derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease. Nat Immunol 2016; 17: 505–513.

    Article  CAS  Google Scholar 

  14. Jenq RR, Ubeda C, Taur Y, Menezes CC, Khanin R, Dudakov JA et al. Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation. J Exp Med 2012; 209: 903–911.

    Article  CAS  Google Scholar 

  15. Gerbitz A, Schultz M, Wilke A, Linde H-J, Schölmerich J, Andreesen R et al. Probiotic effects on experimental graft-versus-host disease: let them eat yogurt. Blood 2004; 103: 4365–4367.

    Article  CAS  Google Scholar 

  16. Bilinski J, Robak K, Peric Z, Marchel H, Karakulska- Prystupiuk E, Halaburda K et al. The impact of gut colonization by antibiotic-resistant bacteria on the outcomes of allogeneic hematopoietic stem-cell transplantation: a retrospective, single-center study. Biol Blood Marrow Transplant 2016; 22: 1087–1093.

    Article  Google Scholar 

  17. Shono Y, Docampo MD, Peled JU, Perobelli SM, Velardi E, Tsai JJ et al. Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci Transl Med 2016; 8: 339ra71–339ra71.

    Article  Google Scholar 

  18. Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G et al. Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection. Genome Med 2016; 8: 49.

    Article  Google Scholar 

  19. Lathrop SK, Bloom SM, Rao SM, Nutsch K, Lio C-W, Santacruz N et al. Peripheral education of the immune system by colonic commensal microbiota. Nature 2011; 478: 250–254.

    Article  CAS  Google Scholar 

  20. Cebula A, Seweryn M, Rempala GA, Pabla SS, McIndoe RA, Denning TL et al. Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota. Nature 2013; 497: 258–262.

    Article  CAS  Google Scholar 

  21. Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 2013; 500: 232–236.

    Article  CAS  Google Scholar 

  22. Round JL, Mazmanian SK . Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci USA 2010; 107: 12204–12209.

    Article  CAS  Google Scholar 

  23. Furusawa Y, Obata Y, Hase K . Commensal microbiota regulates T cell fate decision in the gut. Semin Immunopathol 2015; 37: 17–25.

    Article  Google Scholar 

  24. Khosravi A, Yáñez A, Price JG, Chow A, Merad M, Goodridge HS et al. Gut microbiota promote hematopoiesis to control bacterial infection. Cell Host Microbe 2014; 15: 374–381.

    Article  CAS  Google Scholar 

  25. Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 2014; 20: 159–166.

    Article  CAS  Google Scholar 

  26. Josefsdottir KS, Baldridge MT, Kadmon CS, King KY . Antibiotics impair murine hematopoiesis by depleting intestinal microbiota. Blood 2017; 129: 729–739.

    Article  CAS  Google Scholar 

  27. Rowlings PA, Przepiorka D, Klein JP, Gale RP, Passweg JR, Henslee-Downey PJ et al. IBMTR Severity Index for grading acute graft-versus-host disease: retrospective comparison with Glucksberg grade. Br J Haematol 1997; 97: 855–864.

    Article  CAS  Google Scholar 

  28. McInnes P, Cutting M Manual of Procedures for Human Microbiome Project Core Microbiome Sampling Protocol A: HMP Protocol 7-001. Version 9.0. 2010,National Institutes of Health.

  29. Lemas DJ, Young BE, Baker PR, Tomczik AC, Soderborg TK, Hernandez TL et al. Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome. Am J Clin Nutr 2016; 103: 1291–1300.

    Article  CAS  Google Scholar 

  30. Brumbaugh DE, Arruda J, Robbins K, Ir D, Santorico SA, Robertson CE et al. Mode of delivery determines neonatal pharyngeal bacterial composition and early intestinal colonization. J Pediatr Gastroenterol Nutr 2016; 63: 320–328.

    Article  Google Scholar 

  31. Markle JGM, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science 2013; 339: 1084–1088.

    Article  CAS  Google Scholar 

  32. Nadkarni M, Martin FE, Jacques NA, Hunter N . Determination of bacterial load by real-time PCR using a broad range (universal) probe and primer set. Microbiology 2002; 148: 257–266.

    Article  CAS  Google Scholar 

  33. Frank DN . BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics 2009; 10: 362.

    Article  Google Scholar 

  34. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. QIIME allows analysis of high-throughput community sequencing data. Nat Publ Gr 2010; 7: 335–336.

    CAS  Google Scholar 

  35. Edgar RC . Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26: 2460–2461.

    Article  CAS  Google Scholar 

  36. Westcott SL, Schloss PD . De novo clustering methods outperform reference-based methods for assigning 16 S rRNA gene sequences to operational taxonomic units. PeerJ 2015; 3: e1487.

    Article  Google Scholar 

  37. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R . UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011; 27: 2194–2200.

    Article  CAS  Google Scholar 

  38. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al. Greengenes, a chimera-checked 16 S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72: 5069–5072.

    Article  CAS  Google Scholar 

  39. Wang Q, Garrity GM, Tiedje JM, Cole JR . Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73: 5261–5267.

    Article  CAS  Google Scholar 

  40. Price MN, Dehal PS, Arkin AP . Fasttree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26: 1641–1650.

    Article  CAS  Google Scholar 

  41. Faith DP, Baker AM . Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinform Online 2006; 2: 121–128.

    Google Scholar 

  42. Lozupone C, Knight R . UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005; 71: 8228–8235.

    Article  CAS  Google Scholar 

  43. Anderson MJ, Walsh DCI . PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing? Ecol Monogr 2013; 83: 557–574.

    Article  Google Scholar 

  44. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB et al vegan: Community Ecology Package. 2016.

  45. Therneau TM A Package for Survival Analysis in S. 2015.

  46. Ramette A . Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 2007; 62: 142–160.

    Article  CAS  Google Scholar 

  47. Whangbo J, Ritz J, Bhatt A . Antibiotic-mediated modification of the intestinal microbiome in allogeneic hematopoietic stem cell transplantation. Bone Marrow Transplant 2016; 52: 183–190Online: 1–8.

    Article  Google Scholar 

  48. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R . Diversity, stability and resilience of the human gut microbiota. Nature 2012; 489: 220–230.

    Article  CAS  Google Scholar 

  49. Donaldson GP, Lee SM, Mazmanian SK . Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 2016; 14: 20–32.

    Article  CAS  Google Scholar 

  50. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M et al. Human gut microbiome viewed across age and geography. Nature 2012; 486: 222–227.

    Article  CAS  Google Scholar 

  51. Weber D, Oefner PJ, Dettmer K, Hiergeist A, Koestler J, Gessner A et al. Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation. Bone Marrow Transplant 2016; 51: 1087–1092.

    Article  CAS  Google Scholar 

  52. Troy EB, Kasper DL . Beneficial effects of Bacteroides fragilis polysaccharides on the immune system. Front Biosci 2010; 15: 25–34.

    Article  CAS  Google Scholar 

  53. López P, González-Rodríguez I, Gueimonde M, Margolles A, Suárez A . Immune response to Bifidobacterium bifidum strains support Treg/Th17 plasticity. PLoS ONE 2011; 6: e24776.

    Article  Google Scholar 

  54. Tawara I, Liu C, Tamaki H, Toubai T, Sun Y, Evers R et al. Influence of donor microbiota on the severity of experimental graft-versus-host-disease. Biol Blood Marrow Transplant 2013; 19: 164–168.

    Article  Google Scholar 

  55. Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009; 139: 485–498.

    Article  CAS  Google Scholar 

  56. Gensollen T, Iyer SS, Kasper DL, Blumberg RS . How colonization by microbiota in early life shapes the immune system. Science 2016; 352: 539–544.

    Article  CAS  Google Scholar 

  57. Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT et al. Host genetic variation impacts microbiome composition across human body sites. Genome Biol 2015; 16: 191.

    Article  Google Scholar 

  58. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R et al. Human genetics shape the gut microbiome. Cell 2014; 159: 789–799.

    Article  CAS  Google Scholar 

  59. Arrieta MC, Stiemsma LT, Amenyogbe N, Brown EM, Finlay B . The intestinal microbiome in early life: health and disease. Front Immunol 2014; 5: 427.

    Article  Google Scholar 

  60. Tamburini S, Shen N, Wu HC, Clemente JC . The microbiome in early life: implications for health outcomes. Nat Med 2016; 22: 713–717.

    Article  CAS  Google Scholar 

  61. Kverka M, Zakostelska Z, Klimesova K, Sokol D, Hudcovic T, Hrncir T et al. Oral administration of Parabacteroides distasonis antigens attenuates experimental murine colitis through modulation of immunity and microbiota composition. Clin Exp Immunol 2011; 163: 250–259.

    Article  CAS  Google Scholar 

  62. Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV et al. Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection. J Infect Dis 2015; 211: 19–27.

    Article  CAS  Google Scholar 

  63. Andermann TM, Rezvani A, Bhatt AS . Microbiota manipulation with prebiotics and probiotics in patients undergoing stem cell transplantation. Curr Hematol Malig Rep 2016; 11: 19–28.

    Article  Google Scholar 

  64. Peled JU, Jenq RR, Holler E, van den Brink MRM . Role of gut flora after bone marrow transplantation. Nat Microbiol 2016; 1: 16036.

    Article  CAS  Google Scholar 

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Acknowledgements

We thank our study participants and clinical staff. We thank Jørgen V Bjørnholt, Merete Eggesbø, and Tore Midtvedt for use of their antibiotic classification scale in our sensitivity analysis and thank Keith Hazleton for consulting on antibiotic classifications. We are grateful for our anonymous peer reviewers for their feedback on our manuscript. This research was generously supported by the Amy Strelzer Manasevit Research Program and Denver Golfers Against Cancer.

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Correspondence to C A Lozupone.

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Liu, C., Frank, D., Horch, M. et al. Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors. Bone Marrow Transplant 52, 1643–1650 (2017). https://doi.org/10.1038/bmt.2017.200

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