Antibiotics and the Intestinal Microbiome: Individual Responses, Resilience of the Ecosystem, and the Susceptibility to Infections

  • Sophie Thiemann
  • Nathiana Smit
  • Till StrowigEmail author
Part of the Current Topics in Microbiology and Immunology book series (CT MICROBIOLOGY, volume 398)


The intestinal microbiota is a diverse ecosystem containing thousands of microbial species, whose metabolic activity affects many aspects of human physiology. Large-scale surveys have demonstrated that an individual’s microbiota composition is shaped by factors such as diet and the use of medications, including antibiotics. Loss of overall diversity and in some cases loss of single groups of bacteria as a consequence of antibiotic treatment in humans has been associated with enhanced susceptibility toward gastrointestinal infections and with enhanced weight gain and obesity in young children. Moreover, the extensive use of antibiotics has led to an increased abundance of antibiotic resistance genes (ARGs) within commensal bacteria that can be transferred to invading pathogens, which complicates the treatment of bacterial infections. In this review, we provide insight into the complex interplay between the microbiota and antibiotics focussing on (i) the effect of antibiotics on the composition of the microbiota, (ii) the impact of antibiotics on gastrointestinal infections, and (iii) finally the role of the microbiota as reservoir for ARGs. We also discuss how targeted manipulation of the microbiota may be used as an innovative therapeutic approach to reduce the incidence of bacterial infections as well as resulting complications.


Horizontal Gene Transfer Clostridium Difficile Infection Intestinal Microbiota Mucus Layer Commensal Bacterium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  1. 1.Helmholtz Centre for Infection ResearchBrunswickGermany

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