Infant stool cultured in a continuous flow bioreactor

The human gut microbiota is inoculated at birth and undergoes a process of assembly throughout the first few years of life. Studies in mice and humans have revealed associations between the early-life gut microbiome and susceptibility to immune and metabolic diseases later in life. However, biological complexities continue to challenge efforts to define microbial composition and function, highlighting a need for experimental platforms that support reproducible, longitudinal analysis to advance a comprehensive understanding of the infant gut microbiota. Here we deployed a continuous single-stage chemostat culture model of the human distal gut to study the infant gut microbiota integrating both culture-independent and culture-dependent methodologies. The chemostat cultures recapitulated multiple aspects of the fecal microbial ecosystem and enabled the investigation of relationships between bacterial strains and metabolic function, as well as a resource for the isolation of a diverse library of infant bacterial strains. This study characterizes the longitudinal dynamics of infant gut bacterial communities cultured in an advanced model of the human gut and describes a framework and resources for the study of the infant gut microbiota.