Dysbiosis of the gut microbiome in critically ill patients, coupled with impaired innate immuneresponses, may lower the barrier to acquiring infectious pathogens in the hospital setting. BraedonMcdonald microbejared SnyderInstitute UCalgaryMed
. Dimensionality reduction and visualization of the differences in plasma inflammatory mediators between patients with and without microbiota Enterobacteriaceae enrichment was performed using NMDS of mediator concentrations using the Vegan package v.2.6 in R. Figures showing logFC of individual mediators between ICU patients with or without Enterobacteriaceae enrichment were calculated on absolute concentration using the limma package v.3.48.3 and plotted with ggplot2 .
Connectivity between microbiota, cellular immune landscape and inflammatory mediators was determined using Chord diagram analysis. A Spearman correlation coefficient was calculated for pairings of all microbial taxa , immune cell subset counts and inflammatory mediatory concentrations and significant values were visualized using the circlize package v.0.4.15 in R.
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