Understanding the impact of antibiotic perturbation on the human microbiome
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REVIEW
Open Access
Understanding the impact of antibiotic perturbation on the human microbiome D. J. Schwartz1,2*† , A. E. Langdon2,3† and G. Dantas2,3,4,5*
Abstract The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome’s ecological balance, commonly by antibiotics, can cause and exacerbate diseases. To predict and successfully rescue such perturbations, first, we must understand the underlying taxonomic and functional dynamics of the microbiome as it changes throughout infancy, childhood, and adulthood. We offer an overview of the healthy gut bacterial architecture over these life stages and comment on vulnerability to short and long courses of antibiotics. Second, the resilience of the microbiome after antibiotic perturbation depends on key characteristics, such as the nature, timing, duration, and spectrum of a course of antibiotics, as well as microbiome modulatory factors such as age, travel, underlying illness, antibiotic resistance pattern, and diet. In this review, we discuss acute and chronic antibiotic perturbations to the microbiome and resistome in the context of microbiome stability and dynamics. We specifically discuss key taxonomic and resistance gene changes that accompany antibiotic treatment of neonates, children, and adults. Restoration of a healthy gut microbial ecosystem after routine antibiotics will require rationally managed exposure to specific antibiotics and microbes. To that end, we review the use of fecal microbiota transplantation and probiotics to direct recolonization of the gut ecosystem. We conclude with our perspectives on how best to assess, predict, and aid recovery of the microbiome after antibiotic perturbation. Keywords: Gut microbiome, Resistome, Antibiotics, Perturbation, Resilience, Dynamics, Recolonization
Introduction The human gut microbiome consists of bacteria, viruses, and fungi ideally living symbiotically with their human host, though this review will focus exclusively on bacterial residents within the gut microbiome [1]. Individual species and collective bacterial functions within the gut microbiome confer many benefits throughout life including metabolizing dietary * Correspondence: [email protected]; [email protected] † D. J. Schwartz and A. E. Langdon contributed equally to this work. 1 Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 2 The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA Full list of author information is available at the end of the article
contributions, educating the immune system, defending against pathogens, and contributing to overall health and optimal growth [2–6]. The gut microbiome is affected by and influences pathologies including inflammatory bowel disease (IBD), alle
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