The gut microbiota is a diverse ecosystem. While bacteria are present in the greatest numbers, other microorganisms such as fungi and protists are also present, influencing many physiological functions. Analyses of the gut microbiome in livestock species have increased recently with improvements in technology and decreased cost. However, little is known about host genetic control over gut microbial communities. A recent study examined this relationship using healthy Duroc pigs. Using genome-wide association studies, researchers identified a gene regulatory network comprising 3,561 genes and 738,913 connections. Within this complex and polygenic network, five main regulators stood out. The proteins were associated with immune cell development, cell signaling in immune cells, and the vaccine response and a large number of predicted targets were genes associated with microbiota in pigs, mice, and humans. Host genetic variants associated with microbial functions were also identified. Together, these results identify key regulators, target genes, and mechanisms linked with microbiome modulation in pigs. And highlight the value identifying markers and candidate genes to improve host performance and microbial traits.