HUMAN MICROBIOME Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota 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 Received: 16 February 2018 /Accepted: 6 July 2018 # Springer Science+Business Media, LLC, part of Springer Nature 2018 Abstract 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. Keywords Gut microbiota . Genome . Mobile genetic elements . Horizontal gene transfer . Antibiotics . Antimicrobial resistance Introduction Antimicrobial resistance (AMR) among clinically relevant bac- terial species has drawn the attention of scientists, health workers, policymakers, and pharmaceuticals entrepreneurs be- cause of its notorious role in complicating the infectious disease management, surgery, and organ transplantation [1–3]. In addi- tion, the antibiotics that are used to treat infections are not specific to the pathogens, and their administration could equal- ly affect the commensal microbiota living in the same ecosys- tem [4]. Therefore, given their selective advantage, genes encoding AMR are not only restricted to the pathogens, but are also widespread among environmental and human com- mensal bacteria [5, 6]. Several in silico metagenomics studies have revealed a plethora of commensals, symbionts, and op- portunistic pathogens inhabiting in the human gastrointestinal Satyabrata Bag and Tarini Shankar Ghosh contributed equally to this work. * Bhabatosh Das bhabatosh@thsti.res.in 1 Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad—Gurgaon Expressway, PO Box #04, Faridabad, Haryana 121001, India 2 Division of Infectious Diseases, Department of Medicine, All India Institute of Medical Sciences, New Delhi, India 3 Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India Microbial Ecology https://doi.org/10.1007/s00248-018-1228-7