Driving gut microbiota enterotypes through host genetics

Population stratification based on interindividual variability in gut microbiota composition revealed the existence of several configurations named enterotypes. Enterotypes are often associated with environmental factors whereas the potential impact of host genetics is debated. To explore the genetic determinism of host-microbiota interactions, we established two divergent pig lines with gut microbiota selected for genera pairs specifying two enterotypes ( Prevotella and Mitsuokella , or Ruminococcus and Treponema ). Per line, relative abundances of directly and indirectly selected genera increased, demonstrating that host genetics influences gut microbiota composition and enterotype prevalence over generations. Metagenomics illustrated different functional potentials between enterotypes and their effects on animal growth. Our work paves the way for a holistic use of host genetics, microbiota diversity and enterotype functionalities in understanding holobiont shaping and adaptation.