The composition of the human gut microbiome is highly variable and this variation 30 has been repeatedly tied to variation in human health. However, the sources of microbial 31 variation remain unclear, especially early in life. It is particularly important to understand 32 sources of early life variation in the microbiome because the state of the microbiome in 33 childhood can influence lifelong health. Here we compared the gut microbiomes of children 34 adopted in infancy to those of genetically unrelated children in the same household and 35 genetically related children raised in other households. We observed that shared home 36 environment was the strongest predictor of overall microbiome similarity. Among those 37 microbial taxa whose variation was significantly explained by our models, the abundance of a 38 given taxon was more frequently explained by host genetic similarity (relatedness), while the 39 presence of a given taxon was more dependent upon shared home environment. This suggests 40 that although the home environment may act as a species source pool for the gut microbiome in 41 childhood, host genetic factors likely drive variation in microbial abundance once a species 42 colonizes the gut.