Major factors altering microbiota homeostasis after allogeneic haematopoietic stem cell transplantation (allo-HSCT) include conditional chemotherapy and/or irradiation, antibiotic therapy, graft-versus-host disease (GVHD), mucositis and infection (for example, with Clostridium difficile). Patients experience neutropenia after a conditioning regimen, and this often requires treatment with antibiotics. These factors contribute to microbiota dysbiosis, which is represented by decreased bacterial diversity, lower numbers of anaerobic commensal bacteria and expansions of pathobionts.