Fig. 1

Monitoring gut, oral, and nasal microbiota and the host immune system in allogeneic hematopoietic stem cell transplantation (HSCT). A Twenty-nine children were monitored before, at the time of and immediately post allogeneic HSCT, as well as at late follow-up time points. Patients’ baseline characteristics, clinical outcomes, as well as immune cell counts, and inflammation and infection markers over time were monitored. Patient characteristics are described in detail in Table S1 (Additional File 1). Host immune system parameters were related to longitudinal dynamics of the gut, oral, and nasal microbiota that was assessed at the denoted time points. B Bacterial alpha diversity before, at the time of, and after HSCT at each body site, displayed on a log10 transformed y-axis for visualization purposes. Asterisks indicate significant differences in median inverse Simpson index between time points. * P < 0.05. C Tree-based sparse linear discriminant (LDA) analyses by time point in relation to HSCT. For fecal samples, positive LDA scores were observed for samples collected immediately post HSCT. For both oral and nasal samples, positive LDA scores were observed for samples from before HSCT and from late follow-up time points