Fig. 2: Longitudinal analysis of bacterial composition showed a progressive loss of obligate anaerobes in oral and lung communities as well as enrichment for recognized respiratory pathogens in all three compartments.

Top Panels (A, B): Relative abundance barplots for oral, lung, and gut samples with the classification of bacterial genera by oxygen requirement into obligate anaerobes (anaerobes), aerobes, facultative anaerobes, microaerophiles, genera of variable oxygen requirement and unclassifiable. Comparisons of centered-log ratio (CLR) transformed relative abundances for the three main categories of bacteria (obligate anaerobes, aerobes, and facultative anaerobes) by follow-up interval (baseline, middle and late). Data in boxplots (B) are represented as individual values of untransformed relative abundances, with their median as the line inside the box, interquartile range (25th–75th percentile) as the box itself, whiskers extend to 1.5 times the interquartile range, and individual dots beyond whiskers signify outlier observations. Comparisons between intervals were done by non-parametric Wilcoxon tests, with p-values adjusted for multiple comparisons by the Bonferroni method. Bottom Panels (C, D): Relative abundance barplots for oral, lung and gut samples with the classification of bacterial genera by plausible pathogenicity into oral commensals, recognized respiratory pathogens, and “other” category. Comparisons of CLR-transformed relative abundances for these categories of bacteria by follow-up interval (baseline, middle, and late) in boxplots (D), with p-values adjusted for multiple comparisons. Source data are provided as a Source Data file. Displayed data include 583 oral, 543 lung, and 343 gut samples from ICU patients. All statistical tests were two-sided.