Probiotics are popular health supplements taken by the general population. The influence of probiotics on the composition of gut microbiota has not been fully evaluated, and the duration of the effects of probiotics administration is still unclear. This study aimed to investigate the changes in the composition and diversity of gut microbiota by the administration of probiotics in healthy individuals. The study was carried out in Korea. 12 healthy volunteers aged between 30 and 42 years were given probiotic capsules containing five billion colony forming units of a mixture Bifidobacterium, Lactobacillus, and Enterococcus for four weeks. Stool samples were collected at the beginning of the study, after four weeks of probiotics, and again two weeks after stopping the probiotics. The overall diversity of faecal microbiota was not significantly altered by the probiotics, but significantly decreased two weeks after stopping them. The composition of faecal microbiota was not significantly changed by the probiotics at the phylum level, but the proportions of Bacteroidetes and Actinobacteria significantly changed 2 weeks after stopping the probiotics. The proportions of Lactobacillus and Enterococcus were significantly increased by the probiotics, but the proportions of Bifidobacterium, Lactobacillus, and Enterococcus decreased two weeks after stopping the probiotics. There was no difference in the levels of calprotectin between the start and end of the study. The authors concluded that the proportion of faecal microbiota at the genus level, but not diversity, is significantly altered by the administration of probiotics in healthy people. This effect does not seem to last long, probably because of homeostasis or dietary influence.