Original Article

Subject Category: Microbe-microbe and microbe-host interactions

The ISME Journal (2007) 1, 56–66; doi:10.1038/ismej.2007.3

Long-term ecological impacts of antibiotic administration on the human intestinal microbiota

Cecilia Jernberg1, Sonja Löfmark1, Charlotta Edlund1,2 and Janet K Jansson3

  1. 1Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
  2. 2Medical Products Agency, Uppsala, Sweden
  3. 3Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden

Correspondence: Professor JK Jansson, Department of Microbiology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden. E-mail: janet.jansson@mikrob.slu.se

Received 27 October 2006; Revised 12 February 2007; Accepted 14 February 2007.



Antibiotic administration is known to cause short-term disturbances in the microbiota of the human gastrointestinal tract, but the potential long-term consequences have not been well studied. The aims of this study were to analyse the long-term impact of a 7-day clindamycin treatment on the faecal microbiota and to simultaneously monitor the ecological stability of the microbiota in a control group as a baseline for reference. Faecal samples from four clindamycin-exposed and four control subjects were collected at nine different time points over 2 years. Using a polyphasic approach, we observed highly significant disturbances in the bacterial community that persisted throughout the sampling period. In particular, a sharp decline in the clonal diversity of Bacteroides isolates, as assessed by repetitive sequence-based PCR (rep-PCR) and long-term persistence of highly resistant clones were found as a direct response to the antibiotic exposure. The Bacteroides community never returned to its original composition during the study period as assessed using the molecular fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP). Furthermore, using real-time PCR we found a dramatic and persistent increase in levels of specific resistance genes in DNA extracted from the faeces after clindamycin administration. The temporal variations in the microbiota of the control group were minor compared to the large and persistent shift seen in the exposed group. These results demonstrate that long after the selection pressure from a short antibiotic exposure has been removed, there are still persistent long term impacts on the human intestinal microbiota that remain for up to 2 years post-treatment.


Bacteroides, clindamycin, rep-PCR, faeces, T-RFLP


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