SRP495415 PRJNA1088414 Microbiome changes during stem cell transplantation Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is one of the most efficient therapeutic options available to cure many haematological malignancies. However, severe complications derived from this procedure, including graft-versus-host disease (GVHD) and infections, can limit its success and negatively impact on survival. Previous studies have shown that alterations in bacterial communities inhabiting our gut (the microbiome) are associated with the development of allo-HSCT derived complications. However, most studies relied on single techniques that can only analyse a unique aspect of the microbiome (e.g. taxonomic composition), which hinders our ability to understand how microbiome alterations drive allo-HSCT associated diseases. Here, we have applied multiple omic techniques (16S rRNA and shotgun sequencing, targeted and un-targeted metabolomics) in combination with machine learning approaches to define the most significant microbiome changes following allo-HSCT at multiple modalities (bacterial taxa, encoded functions and derived metabolites).