Systematic review of human gut resistome studies revealed variable definitions and approaches

Jeffery Ho, Yun Kit Yeoh, Nilakshi Barua, Zigui Chen, Grace Lui, Sunny H Wong, Xiao Yang, Martin Cw Chan, Paul Ks Chan, Peter M Hawkey, Margaret Ip

Research output: Contribution to journalReview articlepeer-review

3 Citations (Scopus)
118 Downloads (Pure)


In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.

Original languageEnglish
Article number1700755
Pages (from-to)1-12
Number of pages12
JournalGut Microbes
Issue number1
Early online date16 Jan 2020
Publication statusE-pub ahead of print - 16 Jan 2020


  • Resistome
  • antibiotic resistance
  • fecal microbiota transplantation
  • gut microbiota
  • meta-genomics

ASJC Scopus subject areas

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


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