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Background  We investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota.    Methodology/Principal Findings  Feces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria,  Bacteroides , bifidobacteria,  Clostridium  cluster  IV  and  XIVa  as well as  C. difficile  with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037) following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the  Bacteroides  while the  Clostridium  cluster  IV  and  XIVa  were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of  Clostridium  cluster  IV  and  XIVa  in response to chemotherapy with cluster  IV  diversity being particularly affected by antibiotics. The occurrence of  C. difficile  in three out of seventeen subjects was accompanied by a decrease in the genera  Bifidobacterium ,  Lactobacillus ,  Veillonella  and  Faecalibacterium prausnitzii .  Enterococcus faecium  increased following chemotherapy.    Conclusions/Significance  Despite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with  C.difficile  and  Enterococcus faecium . Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics.

Changes in Human Fecal Microbiota Due to Chemotherapy Analyzed by TaqMan-PCR, 454 Sequencing and PCR-DGGE Fingerprinting