The role of host genetics in the development of the infant gut microbiome

The infant gut microbiome is crucial for the maturation of the host immune system, and dysbiosis of the infant gut microbiome has been linked to autoimmunity later in life. The infant gut microbiome, itself, is shaped by a number of factors, including the mode of delivery, breastfeeding, and antibiotics. However, it is unclear if host genetics plays a role in shaping the infant gut microbiome, although studies in adults have reported that a handful of taxa are associated with mutations in genes which are involved in immunity. The aim of our study is to determine if host genetics interacts with the infant gut microbiome. We genotyped 902 infants using an Immunochip, and we tracked changes in their gut microbiomes over the first 3 years of life using shotgun metagenomics. Subsequently, we employed linear mixed-effect models to identify microbiome-genotype associations. We show that microbiome-genotype associations were strongest during the first 18 months of life, and we report that the rates at which a subset of species changed over time varied as a function of host genotype. Our results support a role for host genetics in the development of the infant gut microbiome.