The Emerging Role of the Microbiota in the ICU

Nora Suzanne Wolff; Floor Hugenholtz; Willem Joost Wiersinga


Crit Care. 2018;22(78) 

In This Article

Abstract and Introduction


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 Further information about the Annual Update in Intensive Care and Emergency Medicine is available from


In recent years, the surge of culture-independent methods to study bacterial populations has led to an increasing body of evidence pointing towards the microbiome as an important player in the pathophysiology of a whole spectrum of diseases that affect the critically ill, including trauma and sepsis.[1–4] Techniques such as 16S rRNA and shotgun metagenomic sequencing have opened up a new area of research, enabling detailed investigations of complex populations of bacteria and their effects on health and disease.[5,6] Some have even called the microbiome a separate organ given its numerous roles in metabolism, development of the immune system and host defense against pathogens.[7]

Microbiota is an overarching term for all the microbes in a population, consisting of bacteria, archaea and eukarya.[8] Most studies that have been performed look at the bacterial microbiota because of its high abundance and high diversity. The collective of microbes in a population is referred to as the microbiota and the genetic content as the microbiome.

The real value of all this novel knowledge for the clinical care of patients on the intensive care unit (ICU) still has to be established. Nonetheless, data are accumulating that underscore the potential importance of the microbiome for intensive care medicine. On any given day, three-fourths of all patients on the ICU are treated with antibiotics, which are known to cause severe collateral damage to the microbiome.[9] Besides antibiotics, there are multiple external modulators of the gut microbiota applied during the clinical care of patients on the ICU, such as gastric acid inhibition, the route of feeding, sedatives and opioids.[3,10] Novel strategies are being designed to intervene on the microbiome to prevent or treat trauma and sepsis. Excitingly, a very recent randomized, placebo-controlled trial among 4556 healthy infants in India showed that the oral administration of Lactobacillus plantarum in combination with fructooligosaccharide in the first week of life could reduce the occurrence of sepsis in the first 60 days of life.[4] Other evidence points towards the use of synbiotics as an adjunctive therapy to prevent postoperative complications, such as surgical site infections and sepsis among adult surgical patients.[11] Most research in this field has focused on the intestinal microbiome; however, current research is also starting to show the importance of the lung microbiome for ICU patients.[1] For example, enrichment of the lung microbiome with gut bacteria seems to play a role in the pathogenesis of acute respiratory distress syndrome (ARDS).[12]

In this chapter, we will discuss the emerging role of the bacterial microbiotas in the gut and the lung in the critically ill. First, we will discuss the techniques available to study the bacterial microbiome, then we will continue into the gut and lung microbiome and end with some key questions for future research in the field of microbiota-targeted therapies on the ICU.