The mammalian alimentary tract harbors hundreds of species of commensal microbes that critically influence a multitude of host physiological functions. Unfavorable alterations of the gut microbiota composition are called ‘dysbiosis’, and often correlate with negative health outcomes. Thus, the amelioration of microbiota dysbiosis is a promising route for future therapeutics for several diseases. To explore the role of individual components of the gut microbiota and to understand mechanisms distinguishing homeostatic from pathogenic microbiota-host interactions, we have adopted culture techniques for anaerobes, methods for generation and maintenance of gnotobiotic animals, together with the high-throughput sequencing technique. Combining these methods, we have been aiming to understand the functions, particularly immunological attributes, of the microbiota, and trying to identify responsible bacterial species and factors for shaping the immune system. We have succeeded in isolation of human and mouse gut-associated commensal bacterial strains that specifically affect the development and function of Th17 cells, Treg cells, Th1 cells or CD8 T cells. Our findings would allow for designing bacterial consortia that activate or suppress specific adaptive immune programs, potentially resulting in development of better therapeutics for numerous diseases involving the immune system, including infectious disease, autoimmunity, allergy, and cancer.