Probiotics, including bacteria and yeast, are live microorganisms that have demonstrated beneficial effects on human health. Recently, probiotic bacteria are constantly being studied and their applications are also being considered in promising adjuvant treatments for various intestinal diseases. Clinical trials and in vivo experiments have extended our current understanding of the important roles that probiotics play in human gut microbiomeassociated diseases. It has been documented through many clinical trials that probiotics could shape the intestinal microbiota leading to potential control of multiple bowel diseases and promotion of overall wellness. In this review, we focused on the relationship between probiotics and the human gut microbiota and its roles in gut microbiome-associated diseases. Here, we also discuss future directions and research areas that need further elucidation in order to better understand the roles of probiotics in the treatment of intestinal diseases.