Gut microbiome dysbiosis is associated with increased mortality following solid organ transplantation

Abstract Organ transplantation is a life-saving treatment for patients with end-stage disease, but survival post-transplantation varies considerably. There is now increasing evidence that the gut microbiome is linked to the survival of hematopoietic cell transplant patients, yet little is known about the role of the gut microbiome in solid organ transplantation. We analyzed 1,370 fecal samples from liver and renal transplant recipients using shotgun metagenomic sequencing to assess microbial taxonomy, metabolic pathways, antibiotic resistance genes and virulence factors. To quantify taxonomic and metabolic dysbiosis, we analyzed 1,183 age-, sex- and BMI-matched subjects from the same population. A subset of patients were also followed longitudinally from pre- to post-transplantation. Our data show that transplant recipients suffer from gut dysbiosis—including lower microbial diversity, increased abundance of unhealthy microbial species, decreased abundance of important metabolic pathways, and increased prevalence and diversity of antibiotic resistant genes and virulence factors—that persist up to 20 years post-transplantation. Finally, we demonstrate that the use of immunosuppressive drugs is significantly associated with the observed dysbiosis and that the extent of dysbiosis is associated with increased post-transplant mortality.