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Additional file 1: Table S1. Cohort characteristics. 1Two patients had 2 transplants, one patient had 3 transplants. The first patient had a peripheral blood and a cord transplant, another had a bone marrow and a peripheral blood transplant. A single patient had 2 CAR T-cell infusions and an HSCT. 2Matched refers to a full HLA match (10/10; 12/12); 3Mismatched refers to a lesser HLA match. Haplo refers to a half HLA match to the patient. 4Transplant-related mortality is defined as mortality due to a complication other than a relapse following an HSCT. Antimicrobial administration refers to an antimicrobial given at any point during inpatient stay for HSCT.

Additional file 13: Table S4. Univariate Cox model with Viraemia as the dependent variable and dominance as the independent variable. The 95% CI and P values were estimated using the robust sandwich estimator. P value of 30% Relative abundance.

Additional file 7: Figure S6. Bray-Curtis dissimilarity of the last collected sample for each patient in respect to the baseline sample.

Additional file 5: Figure S4. Baseline taxonomic composition and alpha diversity in patients undergoing autologous HSCT. a) Relative abundance family level taxonomic plot and b) alpha diversity of patient baseline samples (n = 6) and unmatched healthy control samples (n = 8). Only taxa with relative abundance of >10% are labelled ***

Additional file 15: Table S6. A logistic regression model with viraemia as the dependent variable. P value of

Additional file 12: Figure S9. Kaplan-Meier plot of probability of viraemia in the first 100 days stratified by the microbiome CSTs.

Additional file 14: Table S5. Univariate Cox model with GvHD as the dependent variable. The 95% CI and P values were estimated using the robust sandwich estimator. P value of

Additional file 6: Figure S5. Baseline alpha diversity of allogeneic samples (n = 53) stratified by diagnosis, age and sex. Mann-Whitney test. ns- non-significant.

Additional file 2: Figure S1. The number of clusters determined by using the gap statistic evaluation and silhouette width quality validation.

Additional file 11: Table S3. Univariate and multivariate Cox models with Viraemia as the dependent variable. The 95% CI and P values were estimated using the robust sandwich estimator. P value of

Additional file 18: Figure S12. Metabolites at baseline in samples from allogeneic HSCT patients on (n = 33) and off (n = 10) total parenteral nutrition. Kruskal-Wallis univariate comparison.

Additional file 9: Table S2. Univariate and multivariate Cox models with Enterococcus domination (>30%) as the dependent variable. The 95% CI and P values were estimated using the robust sandwich estimator. P value of

Additional file 3: Figure S2. sPLS regression of taxa and clinical parameters. a) Correlation circle plot for the first two sPLS dimensions (correlations > 0.3/< − 0.3 are shown). Grey circles indicate correlation radii at 0.5 and 1.0. Bacterial families are displayed as circles and are coloured according to the cluster they are affiliated with (cluster 1: blue; cluster 2: orange; cluster 3: grey). Variables situated perpendicularly to each other are not correlated. b) Loading plots of families with their contributions to component 1 and 2. The bars are coloured according to the cluster they affiliate with.

Additional file 4: Figure S3. Metabolomic profiling of HSCT patients at baseline versus Healthy controls. a) An OPLS-DA coefficients plots of the model comparing healthy controls to baseline HSCT samples with the peaks between 1.07-1.2 and 4.98-5.28 ppm removed. Significant peaks are coloured.

Additional file 17: Figure S11. Metabolite profiles during the first five weeks of transplantation. Week -1 denotes days -7 to -1 relative to transplantation (sample range 19-26/week). The blue line indicates the mean for each week.

Additional file 10: Figure S8. Taxonomic composition of the CSTs a) Taxonomic CST composition of all samples (n = 540) b) Distribution of the top 7 taxa among the CSTs.