Fig. 1: Sample overview and alpha diversity.

a Longitudinal sampling of patients (n = 58 patients). Each line represents one patient. Yellow lines span the days spent in ward, while blue lines span the days spent in ICU. Red points mark hospital discharge dates. Crosses indicate the timepoints where swab samples were obtained for microbiome analyses. b Top 15 most abundant genera in this cohort. Samples with >10,000 reads assigned to microbial taxa at the genus level (n = 101) were stratified according to the sampling moment: upon admission, throughout the ICU stay or at ICU discharge/during treatment in ward. c Effect of the length of ICU stay and SARS-CoV-2 viral load on upper respiratory tract microbiome diversity (n = 89, after removal of samples with missing data). The plot shows the model-predicted Shannon index as a function of the days in ICU, for different levels of SARS-CoV-2 viral load (selected within the range of observed data). Confidence intervals for the predictions are shown in Supplementary Figure 1c. d Association of the length of ICU stay and calprotectin gene expression levels with upper respiratory tract microbiome diversity (n = 89, after removal of samples with missing data). The plot shows the model-predicted Shannon index as a function of the days in ICU, for different levels of calprotectin RNA (subunit S100A8) gene expression, selected within the range of observed data. Confidence intervals for the predictions are shown in Supplementary Figure 1d. Source data are provided as a Source Data file.