Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota

  • Satyabrata Bag
  • Tarini Shankar Ghosh
  • Sayantan Banerjee
  • Ojasvi Mehta
  • Jyoti Verma
  • Mayanka Dayal
  • Anbumani Desigamani
  • Pawan Kumar
  • Bipasa Saha
  • Saurabh Kedia
  • Vineet Ahuja
  • Thandavarayan Ramamurthy
  • Bhabatosh Das
Human Microbiome


Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.


Gut microbiota Genome Mobile genetic elements Horizontal gene transfer Antibiotics Antimicrobial resistance 



BD acknowledges the Japan Society for the Promotion of Science (JSPS) for the support during writing the article.

Author Contribution

BD conceived the idea and designed the experiments. Identification and collection of samples were done by BD, VA, SBe, and SBg. Experiments were performed by BD, SBg, TSG, OM, JV, MD, AD, PK, BS, and SK. Data analysis was done by BD, TSG, SBg, and TR. BD wrote the manuscript. All authors have read and approved the manuscript.

Funding Information

The work was funded by the Department of Biotechnology, Govt. of India (Grant No. BT/MB/THSTI/HMC-SFC/2011). Funding agency has no role in study designing, sample collection, analysis and interpretation of data, and writing the manuscript.

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Satyabrata Bag
    • 1
  • Tarini Shankar Ghosh
    • 1
  • Sayantan Banerjee
    • 2
  • Ojasvi Mehta
    • 1
  • Jyoti Verma
    • 1
  • Mayanka Dayal
    • 1
  • Anbumani Desigamani
    • 1
  • Pawan Kumar
    • 1
  • Bipasa Saha
    • 1
  • Saurabh Kedia
    • 3
  • Vineet Ahuja
    • 3
  • Thandavarayan Ramamurthy
    • 1
  • Bhabatosh Das
    • 1
  1. 1.Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology InstituteNCR Biotech Science ClusterFaridabadIndia
  2. 2.Division of Infectious Diseases, Department of MedicineAll India Institute of Medical SciencesNew DelhiIndia
  3. 3.Department of GastroenterologyAll India Institute of Medical SciencesNew DelhiIndia

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