Background: The impact of antibiotics on colonic microbiota is poorly characterized. Methods: Three groups of women (N=10 each) treated for bacterial vaginosis were investigated . Metronidazole 3x400mg/day + ciprofloxacin 2x500mg/day were given for 2 weeks. Group I received antibiotics only, Gr.II received Saccharomyces boulardii(Sb) concomitant to, and Gr.III received Sb subsequent to antibiotic therapy. A 250 mg capsule Sb Perenterol® Biocodex was given 3xdaily for two weeks. Microbiota were investigated using structure functional FISH analysis of Carnoy fixated stool cylinders. Stools were collected at days -90,-60,-30,7,14,28,42,56, and 70 as related to the start of antibiotic therapy. 250 bacterial FISH probes were tested and 82 were selected for longitudinal analysis. Results: Bacteroides, F. prausnitzii and Roseburia (habitual groups) were present in all patients (10-30% of the fecal mass each). The occurrence of other bacteria was occasional. The composition of microbiota prior to antibiotics was stable in repeated investigations of the same patient, despite high interindividual variability. Antibiotic therapy suppressed all bacterial groups, and some of the microbiota previously not detected, emerged in marginal concentrations (C.viridae, Streptococcus, Staphylococcus, Bif. longum ). Bifidobacteriaceae, Enterobacteriacae or C.difficile groups increased in the first two to four weeks after the end of the therapy (p ,0.01) and returned to initial levels with recovery of the habitual bacterial groups. Sb concomitant with antibiotics reduced the antibiotic associated suppression of bacteria. After one week of antibiotic therapy, concentrations of F.prausnitzii dropped in Gr.I, II, and III, respectively, from a median of 13.6±3.7 to 3.1±2.0, 8±4.1, and 3±2.1 x 109bacteria/ml. The decrease in microbial concentrations in Gr. II receiving Sb concomitant to antibiotics was moderate and differed significantly from the decrease in Gr.I and III (p,0.001). The microbiota recovered quicker in groups receiving Sb. The habitual bacteria reached initial values 4 weeks after the end of antibiotics in all groups treated with Sb In Group I, F. prausnitzi was still reduced to 9.8±2.8 x 109bacteria/ml and was significantly lower than prior to antibiotics (p=0.04). The composition of microbiota returned quicker to the individual initial profiles in the groups receiving Sb In regard to the 82 investigated bacterial groups, the median number of mismatches in composition of microbiota prior to and after antibiotic therapy was 8.7; 5.2 (p=0.05) and 2.4 (p,0.001) in Gr.I, II and III, respectively. The difference between preand postantibiotic period was significantly higher in Gr.I, receiving no Sb. Conclusions: S. boulardii prevents/reduces effectively the antibiotic-associated changes in colonic microbiota, when given concomitant/subsequent to antibiotic therapy.