A recent article in Cell Reports demonstrates how polymorphic host genes shape the intestinal microbiota1. Mice that were colonized with a given composition of microbiota (the "input") were allowed to produce G1 offspring, whose resulting microbiomes were sequenced to determine the "output". This multi-faceted study analyzes how host genetics influence the output microbiota in genetically-identical and genetically-diverse mouse models. The publication also offers an excellent analysis of how genetic background and adaptive immune system components such as major histocompatibility complexes (MHCs) play a role in shaping the microbial composition of the host.
Germ-free mouse models played a key role in this study because they could be colonized with a distinct microbiota and subsequently monitored to better understand gene function and development. When choosing a germ-free model for your study, some aspects to consider are the desired study length, breeding performance, genetic background, and availability of controls at other health standards.