Extended Data Fig. 2: Inter-bacterial dynamics in the fecal microbiota of ICU patients.

(a) Multi-Omics Factor Analysis (MOFA) was used to calculate the explained variance of microbiota composition between healthy volunteers and ICU patients on day 1 of admission, showing top 10 taxonomic factors (families) and their relative contributions to explained variance (factor weight). (b) Spearman correlation between the relative abundance of Enterobacteriaceae and taxonomic richness (Chao1) in ICU patients across all sampling timepoints. Dots show individual patient samples, regression line and 95% confidence interval (shaded area) shown. (c) Spearman correlation network of the most abundant bacterial families in healthy volunteers and ICU patients on day 1 of admission (upper quartile, 25%). (d, e) Spearman correlation between Enterobacteriaceae relative abundance and the relative abundance of Lachnospiraceae (D) and Ruminococcaceae (E) in ICU patients across all sampling timepoints. Dots show patient samples, regression line and 95% confidence interval (shaded area) shown. (f) Penalized ridge regression of the 15 most abundant bacterial families in ICU patients and their importance towards the progressive change in Enterobacteriaceae relative abundance from day 1 to 3 of admission (∆Enterobacteriaceae). (g) Relative abundance of Enterobacteriaceae on days 1, 3, and 7 of ICU admission in patients with (N = 18) or without (N = 26) progressive enrichment of Enterobacteriaceae in their fecal microbiota. (h) Progressive change in total bacterial density, and (i) Enterobacteriaceae absolute abundance in rectal swab samples from day 1 to 3 of admission (shown as log fold change) in patients with (N = 17, one patient had insufficient remaining sample for qPCR) or without (N = 26) progressive enrichment of Enterobacteriaceae in their fecal microbiota. Dots are individual patients, central line is median, box shows IQR, whiskers show range, statistical analysis by 2-sided Mann–Whitney test. P values as shown.