Gut microbiota of critically ill patients are dysbiotic but do not differ among those with or without bloodstream infection.

Stool samples all critically ill subjects enrolled in the study were compared with healthy individuals reported from the Human Microbiome Project (HMP). (A) Bar graph representing phylum level composition of critically ill and healthy subjects clustered by Bray-Curtis dissimilarity. Some critically ill subjects’ gut microbiota resembles the gut microbiome composition of healthy individuals, while others are dysbiotic and dominated by Proteobacteria, Firmicutes, or fungi (Ascomycota). (B) Alpha diversity using the Shannon index. Critically ill subjects are colored based on whether they did (BSI+; green) or did not (BSI-; red) have a bloodstream infection. Healthy and critically ill are significantly different (p = 0.003; Wilcoxon rank-sum with Benjamini-Hochberg adjustment for false discovery) but there is no difference between critically ill/BSI + and critically ill/BSI- groups. (C) Dominance by the Berger-Parker dominance index. Healthy and critically ill are significantly different (p = 0.008; Wilcoxon rank-sum with Benjamini-Hochberg adjustment for false discovery), but there is no difference between critically ill/BSI+ and critically ill/BSI- groups. (D) Principal coordinate analysis of stool microbiota based on Bray-Curtis dissimilarity. Critically ill subjects diverge significantly from healthy individuals (PERMANOVA with Benjamini-Hochberg adjustment for false discovery; p = 0.008) but critically ill/BSI+ and critically ill/BSI- do not differ from each other from each other. Panel A includes all stool samples, while panels B-D include just the first collected sample for each subject.