ICU stays result in drastic community changes. (A, B) SourceTracker proportions for ICU patients with samples obtained both at admission and at discharge in fecal (A) and oral (B) communities. The first row shows samples obtained at admission sorted by expected community type. The second shows samples obtained at discharge in patient order with the first row. Sources included samples from the healthy AGP subject subset, skin samples from decomposing bodies, soil samples from around decomposing bodies, fecal samples from healthy children in the Global Gut study, and dust samples from a house forensics study. A lack of color indicates an unknown source. For complete SourceTracker distribution plots, see Fig. S1 to 3 in the supplemental material. (C) Rarefaction curves using phylogenetic diversity of the ICU patient and healthy AGP subject samples. Error bars show standard errors. (D) Unweighted UniFrac distance distributions of within-time-point distances for fecal (P = 1.24e−28; Bonferroni corrected), oral (P = 1.75e−71; Bonferroni corrected), and skin (no significant difference) sites. The letters A and D on the x axis denote admission and discharge, respectively; whiskers are at 1.5 times the interquartile range. For a comparable weighted UniFrac analysis, see Fig. S4 in the supplemental material.
ICU patients differ markedly from healthy AGP subjects. (A, B) Principal-coordinate (PC) plots of unweighted UniFrac distances of both ICU patient and healthy AGP subject samples: A, fecal, skin, and oral samples with the ICU patient samples enlarged to aid in differentiation; B, oral samples in isolation. (C) Stacked taxonomy bar charts for fecal split by time point, showing a random subsample of healthy AGP subject samples. (D) Rank-abundance curves for all three body sites split by time point, showing random subsamples from the healthy AGP subject subset.
Significantly different OTUs assessed by ANCOM for each body site between the healthy AGP subject samples and ICU patient cohort samples. A significance level of 0.05 was used following multiple-hypothesis correction by the Holm-Bonferroni method. Download Table S1, XLSX file, 0.1 MB.
Co-occurrence networks observed in fecal and oral communities suggesting that inflammatory clades co-occur. Blue edges indicate a positive correlation, and red indicates a negative correlation. The size of the edge shows the magnitude of the correlation. Layouts are the Cytoscape default. The labels used are the most informative taxon associated with the each OTU. All observed networks are available in the supplemental Cytoscape file. (A) Fecal samples obtained at admission. (B) Fecal samples obtained at discharge. (C) Oral samples obtained at admission. (D) Oral samples obtained at discharge. Download Figure S6, PDF file, 2.1 MB.