Lactobacillus johnsonii La1 (La1) is a probiotic strain capable of stimulating the immune system of the host and interfering with gastrointestinal pathogens. This study evaluates how the ingestion of different amounts of La1 influences the main bacterial populations of the fecal microbiota. Eight asymptomatic volunteers participated in the study. After a basal period, they ingested daily 100 mL of a product containing 108 CFU mL−1 of La1 during the first week, 200 mL during the second week and 500 mL during the third week. Fecal samples were obtained at the end of each period and subsequently during 7 weeks. Lactobacilli were determined by culture on MRS agar and La1 colonies were confirmed by ERIC-PCR. The main populations of fecal bacteria were identified by FISH and flow cytometry. At baseline, 37.7% of the total fluorescent bacteria were Eubacterium rectale, 18.3%Fusobacterium prausnitzii, 13.2%Bacteroides, 8.6%Atopobium, 2.30%, Clostridium histolyticum, 2.05%Bifidobacterium and 0.95%Lactobacillus. Fecal excretion of La1 increased during the intake period and decreased during the post-ingestion period, so that no La1 was observed in the stools of the volunteers seven weeks after the intake product has been finished. La1 intake increased the populations of C. histolyticum (p= 0.049), Lactobacillus (p= 0.056) and Bifidobacterium (p= 0.067), and decreased those of F. prausnitzii (p= 0.005) while it did not affect Bacteroides, E. rectale and Atopobium populations. These bacterial populations returned to their baseline levels during the post-ingestion period. The regular intake of a La1-containing product beneficially affects the homeostasis of the human fecal microbiota, probably contributing to the health-promoting effects of this probiotic.