Our objective was to document how intake of Lactobacillus plantarum 299v affects the concentrations of fecal organic acids during and after metronidazole treatment in 19 patients with recurrent Clostridium difficile-associated diarrhea. Fecal samples were analyzed by gas-liquid chromatography. After intake of metronidazole a significant decrease in total short-chain fatty acids was seen in the placebo group (from 77.1 to 45.5 mu mol/g; P=0.028) but not in the Lactobacillus group (79.8-60.4 mu mol/g). In addition, a statistically significant difference between treatment groups was noted for butyrate (5.6-1.2 mu mol/g in the placebo group vs. 7.6-5.6 mu mol/g in the Lactobacillus group; P=0.047). At the end of the study and after cessation of placebo or Lactobacillus, the total short-chain fatty acids rose to the same levels as before antibiotic treatment in the placebo group. Both treatment groups showed a significant decrease in concentrations of succinate at the end of the study in comparison to the time when metronidazole intake was stopped (6.3-1.5 mu mol/g in the placebo group versus 9.3-0.9 mu mol/g in the Lactobacillus group; P=0.028). The present study of fecal samples from a clinical trial is the first to demonstrate that administration of Lactobacillus plantarum 299v reduces the negative effects of an antibiotic on colonic fermentation. The intake of this probiotic strain may thereby provide an additional benefit for patients with recurrent Clostridium difficile-associated diarrhea.