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Abstract Background The human gut microbiota is inoculated at birth and undergoes a process of assembly and diversification during the first few years of life. Studies in mice and humans have revealed associations between the early-life gut microbiome and future susceptibility to immune and metabolic diseases. To resolve microbe and host contributing factors to early-life development and to disease states requires experimental platforms that support reproducible, longitudinal, and high-content analyses. Results Here, we deployed a continuous single-stage chemostat culture model of the human distal gut to study gut microbiota from 18- to 24-month-old children integrating both culture-dependent and -independent methods. Chemostat cultures recapitulated multiple aspects of the fecal microbial ecosystem enabling investigation of relationships between bacterial strains and metabolic function, as well as a resource from which we isolated and curated a diverse library of early life bacterial strains. Conclusions We report the reproducible, longitudinal dynamics of early-life bacterial communities cultured in an advanced model of the human gut providing an experimental approach and a characterized bacterial resource to support future investigations of the human gut microbiota in early childhood.