Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome

Alexander Crits-Christoph, Haley Anne Hallowell, Kalia Koutouvalis, Jotham Suez

Research output: Contribution to journalReview articlepeer-review


A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.

Original languageEnglish (US)
Article number2055944
JournalGut Microbes
Issue number1
StatePublished - 2022


  • Microbiome
  • antibiotic resistance genes (ARG)
  • antibiotics
  • antimicrobial resistance (AMR)
  • fecal microbiome transplantation (FMT)
  • metagenomics
  • probiotics
  • resistome

ASJC Scopus subject areas

  • Gastroenterology
  • Microbiology (medical)
  • Infectious Diseases
  • Microbiology


Dive into the research topics of 'Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome'. Together they form a unique fingerprint.

Cite this