Background: Gut microbiota diversity and abundance are critical in maintaining human health, and subject to significantly reduce in seniors. Gut microbiota are reported to be stable across the long adulthood in general, but lack of careful examination, especially for the midlife people.Results: To characterize the gut microbiota in midlife, we investigated the faecal microbiota between two groups of healthy people, young, 20-39 years old, n=15; and midlife, 40-60 years old, n=15. Metabolic responses of the microbiota were studied through in vitro batch fermentation model. Despite no difference was observed in the diversity indies between the two age groups, a wide range taxonomic changes were found in the faecal microbiota. Furthermore, substantial Bifidobacterium reduction was also found in both faecal and fermented samples. The level of SCFAs in both faecal and starch fermented samples is similar in both groups. However, when fermentation was performed with inulin as the sole carbon source, the acetate concentration and inulin degradation rate decreased while the gas production increased in midlife group, suggesting a deficiency of saccharolytic potential in midlife, especially for non-digestible carbohydrate. Conclusions: Our data demonstrate that gut microbiota begin to change as early as in midlife. The reduction in Bifidobacterium dominates the change of the microbiota composition in midlife resulting in attenuated saccharolytic capability of inulin, leading to insufficient acetate production which might be associated with healthy problems in this transition period from young to elderly.