Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand microbiota evolution in these models, we carried out a 6-year experiment in mice colonized with 12 representative taxa. Increased non-synonymous to synonymous mutation rates indicate positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that evolved within a single taxon can stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts trigger rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains are also rapidly altered after dietary shift. This indicates that microbial taxa within a mouse colony adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions. Display omitted •Long-term evolutionary experiment shows the genomic evolution of the microbiota•Microbiota adaptation occurs through long-term positive selection of variants•Host gut environmental changes trigger short-term alterations of microbial transcriptomes•Sub-strains evolve and coexist within an individual taxon Yilmaz et al. report a 6-year experiment in mice stably colonized with 12 representative fully sequenced taxa, showing how strains and sub-strains evolve within the colony over extended periods. Microbiota adaptation is achieved through long-term positive selection of variants, and short-term alterations of transcriptomes and sub-strain frequencies.