Protocol to colonize gnotobiotic mice in early life and assess the impact on early life immune programming.

Understanding how changes in gut microbiota in early life impact immune programming can be difficult to study due to variations in the assembly of the microbiota. In this protocol, we describe how to colonize gnotobiotic/germ-free mice in early life with different microbiota community types (e.g., PAMI and PAMII). We detail several assays to determine whether differential colonization alters immune programming in early life. We also describe how to propagate mouse fecal microbiota transplant material if the donor fecal sample is limited. For complete details on the use and execution of this protocol, please refer to Lynn et al. (2021).1.