Abstract: Objectives Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is associated with significant alterations in gut microbiota (GM) composition, affecting transplant success. This study aimed to correlate these GM changes with post-transplant (post-HSCT) outcomes. Methods A prospective multicentre cohort study was conducted between June 2017 and December 2021 in three Spanish hospitals. Stool samples from allo-HSCT recipients were collected before HSCT, and at 14-, 30-, 60-, and 100-days post-HSCT. Bacterial 16S rRNA gene sequences were characterized and microbial diversity assessed. Results Analysis of 409 samples from 95 patients revealed significant longitudinal GM shifts. Alpha diversity significantly decreased at days 14 ( P < 0.001), 30 ( P < 0.001), and 60 ( P = 0.002) compared to baseline. A distinct shift in dominant taxonomic profiles was observed, notably a significant decrease in Blautia abundance ( P < 0.001). Patients with acute gastrointestinal graft-versus-host disease (GI-GVHD) ( P = 0.009), bacteraemia ( P = 0.014), or death ( P < 0.001) exhibited significantly lower Blautia levels. LEfSe analysis identified 22 differential taxa between deceased and surviving patients; the former showed higher abundance of potential pathogens such as Enterococcus_H ( P = 0.026), Enterococcus_A ( P = 0.019), and Staphylococcus ( P = 0.009). Conclusions Significant variations in the GM?s taxonomic profiles and relative abundances post-HSCT, particularly the decrease in Blautia and the increase in certain pathogens, are associated with poorer clinical outcomes.

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