Erik Thiele Orberg, MD, PhD, on Recovery of the Intestinal Microbiome in Patients at Day +100 after Allogeneic Stem Cell Transplantation Is Defined by Microbial Metabolite Profiles and Linked to Long-Term Outcomes

Hello, my name is Erik Orberg from the University Hospital, Regensburg. The human microbiome is a predictor of outcomes in allogeneic stem cell transplantation. A high diversity is associated with better overall survival, and previous studies have shown that the pre-engraftment period is correlated with these clinical outcomes. However, microbial diversity is dynamic during, but also after sentinel stem cell transplantation, and may shape long-term outcomes. And so we asked whether the post-engraftment microbiome is important, and indeed, others had shown that dysbiosis after allogeneic stem cell transplantation is associated with higher rates of chronic graft-versus-host disease. However, whether and to what extent microbiome recovers remains unclear. And so our hypothesis was that recovery is characterized by a restoration of diversity and that this correlates with clinical outcomes. Our aim was to characterize microbiome recovery during the post-transplant period at day 100. Therefore, in a prospective longitudinal cohort of patients receiving allogeneic stem cell transplantation at the Technical University of Munich University Hospital, we performed longitudinal stool sampling beginning at day 100 up until day 100 after allogeneic stem cell transplantation. We confirmed that diversity is decreased during the pre-engraftment period, but can improve by the post-transplant period and however did remain below baseline values. So at this point, it was a point to define recovery in our patient cohort, and we defined it as those patients that were able to reach at least 25% of their baseline by the post-transplant period, therefore allocating patients into the recovery versus non-recovery group. Based on this, patients in the recovery group had a significantly higher alpha diversity at late time points compared to non-recovery patients. However, recovery versus non-recovery was unable to differentiate between patients with better or worse overall survival. At a three year follow-up, we considered whether this may have to do with community composition or functional capacity, and decided to look at microbiota-derived metabolites. These are small molecules produced by microbial metabolism, which may deliver a functional readout. Earlier this year, we reported on a prospective to centric longitudinal study where we discovered immunomodulatory metabolites associated with clinical outcomes and building on this established an immunomodulatory metabolite risk index. In short, to our surprise, there was no difference in metabolite levels between recovery and non-recovery patients when looking at classes such as branch chain fatty acids, short-chain fatty acids, and bile acids. Yeah, this suggested that recovery of microbial diversity was not linked to restoration of metabolite profiles. Therefore, we performed longitudinal profiling in our entire cohort, learning that in patients that recovered, only two thirds of patients did so with a microbiome composition that was similar to baseline. Based on these findings, we speculated that a different community composition may be associated with different functional capacity, for example, to produce metabolites. So in a subset of patients, we use metagenomic sequencing to interrogate metabolite biosynthesis pathways. Patients that receive a similar microbiome sustained abundance of these synthesis pathways, while those that had a dissimilar microbiome lost the expression. We speculate that a functional readout of the human microbiome via metagenomic sequencing or mass spectrometry may be a better and more robust biomarker for association with outcomes in this cohort of patients. Therefore, we explored our IMR and applied it to late time points, and by doing so, observed a strong correlation with three-year overall survival in low-risk IMR patients. In conclusion, we show that recovery of microbial diversity does not necessarily correlate with the restoration of metabolite profiles. Metabolites, however, hold promise in that they may provide a more robust biomarker for association of prognosis in patients undergoing stem cell transplantation. Furthermore, they may hold potential as microbiome-based therapies to treat or prevent complications after allogeneic stem cell transplantation.