Therapeutic Potential of the Gut Microbiota in the Management of Sepsis

Matteo Bassetti; Alessandra Bandera; Andrea Gori


Crit Care. 2020;24(105) 

In This Article

Abstract and Introduction


This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2020. Other selected articles can be found online at Further information about the Annual Update in Intensive Care and Emergency Medicine is available from


During the last 20 years, the fields of microbiology and infectious diseases have faced a paradigm shift thanks to the discovery of the complex interactions between the host, its immune system, its microbiome, and various pathogens. In fact, the development of various techniques, such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has let scientists discover the inner structure of human genetic composition. The human microbiome has been defined as the collective genome of millions of bacteria, viruses, and fungi that exists on every human host. It plays an elegant mutualistic relationship with the human host from birth.[1] Specifically, the human gastrointestinal tract contains trillions of bacteria that compose a complex ecosystem known as the intestinal microbiota that has relevant implications in human health and disease, especially in the hospital setting.[2] Resident microbiota can outcompete pathogens for space, metabolites and nutrients, and can inhibit pathogens with the calibration of the host immune response. Perturbation of these mechanisms is a common starting point for infection, with antibiotic therapy representing the most common cause of microbiome dysregulation.[3]

The interaction between sepsis and the microbiome has been defined as an "incompletely understood bi-directional relationship." Some evidence has shown that a diverse and balanced gut microbiota is able to enhance host immunity to both enteric and systemic pathogens and that disturbance of this balance potentially leads to increased susceptibility of sepsis. On the other hand, other studies have shown that the composition of the intestinal microbiota is severely affected by sepsis and its treatment, but the clinical consequences of these disturbances need to be further investigated. In this chapter, we provide an overview of the mechanisms through which gut microbiota can contribute to both susceptibility and outcome of sepsis. We will then describe potential therapeutic effects of interventions on the gut microbiome in the setting of septic and critically ill patients.