Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance

J Infect Dis. 2021 Jun 16;223(12 Suppl 2):S214-S221. doi: 10.1093/infdis/jiab184.


Antimicrobial resistance has become a worldwide medical challenge [1], so impactful that vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have entered the common vernacular. We have attempted to reduce the selective pressure through antimicrobial stewardship, curtail the spread by identifying and isolating carriers and individuals with symptomatic infection, and treat antibiotic-resistant organisms (AROs) by developing novel antimicrobials. Despite these extraordinary measures, the challenge of AROs continues to grow. The gut microbiome, the ecosystem of microbes (ie, the microbiota) and metabolites present upon and within all humans, is an emerging target for both the risk for colonization and defense against infection with AROs. Here, informed from experiences and successes with understanding the role of the microbiome in mediating risk of Clostridioides difficile infection (CDI), we (1) review our understanding of the risk from ARO acquisition; (2) review our current understanding of the gut microbiome's ability to resist colonization with AROs; (3) describe how experimental model systems can test these initial, global insights to arrive at more granular, mechanistic ones; and (4) suggest a path forward to make further progress in the field.

Keywords: antimicrobial resistance; fecal microbiota transplantation; metagenomics; microbial ecology; microbiome; next-generation sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Animals
  • Anti-Bacterial Agents / adverse effects
  • Clostridioides difficile / growth & development
  • Clostridioides difficile / pathogenicity
  • Clostridium Infections / etiology
  • Clostridium Infections / microbiology
  • Disease Models, Animal
  • Drug Resistance, Microbial / drug effects
  • Drug Resistance, Microbial / genetics*
  • Gastrointestinal Microbiome / drug effects
  • Gastrointestinal Microbiome / genetics*
  • Gastrointestinal Microbiome / immunology
  • High-Throughput Nucleotide Sequencing
  • Host-Pathogen Interactions
  • Humans


  • Anti-Bacterial Agents