The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field

Abstract

The field of infectious disease is undergoing a paradigm shift as the intestinal microbiome is becoming understood. The aim of this review is to inform infectious disease physicians of the potential relevance of the intestinal microbiome to their practice. We searched Medline using both index and text words relating to infectious diseases, microbiome, and probiotics. Relevant articles published up through 2017 were reviewed within Rayyan. The review illustrates pathophysiologic concepts linking the microbiome and infectious diseases; specifically, the intestinal microbiome's relevance to early immune development, the microbiome and enteric infections, the microbiome's relevance in compromised hosts, and antimicrobial resistance. Within each subject, there are specific examples of diseases and at-risk patient populations where a role for the microbiome has been strongly established. This provides an overview of the significance of the intestinal microbiome to microbiology, pediatric and adult infectious diseases with an underpinning of concepts useful for the practicing clinician.

Keywords: immunology; infectious diseases; intestinal microbiome; microbiology.

Figure 1.

A schematic overview of the infectious diseases in which there is a proven therapeutic role for microbiome manipulation through either probiotics or fecal microbiota transplantation (left panel) and an overview of the subjects for which there is a strong correlation between microbiome composition and risk of infectious disease (right panel). AAD, antibiotic-associated diarrhea; ICU, intensive care unit; NEC, necrotizing enterocolitis; P. falciparum, Plasmodium falciparum; SDD, selective digestive tract decontamination; VAP, ventilator-associated pneumonia.