The emerging role of the microbiota in the ICU

Abstract

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2018. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2018 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901 .

Fig. 1

Overview of techniques to detect bacterial microbiota. To detect which bacterial species there are in a sample, there are three options: 1) use quantitative polymerase chain reaction (qPCR) to detect total bacterial 16S rRNA gene and/or in combination with a specific qPCR for a bacterial group or species; 2) use 16S rRNA gene for amplicon multiplex sequencing to get information on the taxonomic distribution in a sample; 3) use total DNA of a sample for shot-gun sequencing of the metagenomics content to get information on taxonomic distribution and functions, examples of which are indicated in the box, to show that you have functional information within a taxonomic group, in this case butyrate kinase and glycoside hydrolase. The dollar sign below the different techniques is an indicator of the price: depending on the sample type and information depth, prices are variable, but, roughly, a one-dollar sign is around 5–10 dollars per sample; the two-dollar sign is 50–150 dollars per sample, and the three-dollar sign is 300–1000 dollars per sample

Fig. 2

Intestinal microbiota in health and critical illness. The microbiota in a healthy individual is a diverse ecosystem with beneficial and commensal bacteria and low abundances of opportunistic pathogens, which are not harmful in small numbers. As a result of certain therapies, such as antibiotics, the microbial composition can be disrupted. The intestinal microbiota of critically ill patients is less diverse and contains more opportunistic pathogens and less beneficial and commensal bacteria

Fig. 3

The gut and lung microbiota in critical illness. A healthy gut microbiome plays a protective role in host defense against local and pulmonary pathogen invasion. In the critically ill, there is often dysbiosis in the lung and intestinal microbiotas, which can contribute to diseases like pneumonia and acute respiratory distress syndrome (ARDS)