The Human Gut Antibiotic Resistome in the Metagenomic Era: Progress and Perspectives

Abstract

The human gut is populated by a vast number of bacteria, which play a critical role in human health. In recent years, attention has focused on the gut bacteria as a reservoir of antibiotic resistance genes (ARGs). Both culture-dependent and culture-independent methods have been applied to investigate numerous ARGs, collectively called the antibiotic resistome, harbored by gut bacteria. This has led to an increased understanding of the overall profile of the gut antibiotic resistome, although it remains incompletely understood. In this review, we summarize the recent research findings on the human gut antibiotic resistome, with an emphasis on progress achieved using the culture-independent metagenomic strategy. We also describe the features of different available ARG databases used for annotation in metagenomic analysis, discuss the potential problems and limitations in current research, and suggest several directions for future investigation.