Considering the number of samples to analyse, molecular inventories were not possible. Pyrosequencing could have been used. Nevertheless we decided to use PCR-TTGE since it was less expensive and allowed a greater number of samples to be analysed. Indeed, methods such as TTGE and DGGE based on sequence-specific separation of 16S rRNA gene amplicons, are among the best methods for rapid high throughput comparison of bacterial communities or bifidobacterial species over time. In the present study, we explored, on a 76-day period, the quantitative and qualitative changes occurring in total microbiota and also in the Bifidobacterium genus, in 18 adult men after a 5-day amoxicillin-clavulanic acid treatment, using specific real-time PCR and PCR-TTGE combined with cloned sequence analysis. The intraindividual similarity indices of the TTGE profiles were calculated, considering day -12, -6 and 0 as reference period. Mean similarity percentage within reference period was 84.5%64.1%. Only seven subjects Wortmannin presented a 100% similarity between day-12, day-6 and day 0, but twelve subjects presented a 100% similarity between day -6 and day 0 and little variations occurred for the others. At day 5, mean similarity percentages were 55.8%67.6%. The microbiota of three subjects did not respond to AMC treatment, whereas there was a marked change of TTGE profiles for the others. One or two months after the end of AMC treatment, the mean similarity percentages of TTGE profiles were 59.6% and 62.3% respectively, showing that microbiota was still modified. To improve comparisons, two groups were constituted. The first gathered volunteers with Dice’s similarity coefficients at day 64$80% ) and the others. The microbiota of three individuals within the 5 showed marked alterations of TTGE profiles at day 5 and returned to similarity percentages $90% at day 64. The last two microbiota were resistant to AMC. In this group, the microbiota studied in the reference period was very stable. Among the other volunteers microbiota, a Dice similarity coefficient between 0 and 78% was found on day 64. The TTGE profiles from Bifidobacterium species of first or second groups were not specific to one group. To check if this profile variation corresponded only to strain change or to species change, identification of bands were realised. Most fragments co-migrated to the same position as reference strains or clones but a few migrated to different positions and could not be identified in this way. Many cultured collection bifidobacteria and many clones are present in our data bank. Recently, twenty six bands were cloned and sequenced. A previous study on the same 18 volunteers focusing only on bacterial resistance showed that the administration of AMC increased the amoxicillin resistant Escherichia coli and enterococci. From a baseline of less than 1%, more than 30% of resistant E. coli and 6% of resistant enterococci were observed and progressively decreased to baseline at day 12. In the present study, the impact of a 5-day AMC treatment was quantitatively and qualitatively assessed at short- and long-term on total microbiota and on fecal Bifidobacterium species in 18 healthy men. Bifidobacteria were detected in all fecal microbiota from the 18 subjects before exposure to AMC. The counts of total bacteria and total bifidobacteria were significantly altered by AMC at day 5 and returned to baseline at day 8. Numerous publications report modifications of fecal microbiota after AMC treatment but only at genus or phylogenetic group level.