The gut microbiota is an ecosystem containing hundreds of microbial species that gradually matures after birth in humans and other animals. While each individual has a unique gut microbiota composition, several population-scale studies revealed distinct microbial ecotypes referred to as enterotypes and characterised by a similarity in bacterial makeup. In young animals, gut microbiota composition is thought to be primarily shaped by environmental factors, notably diet and breeding conditions. 

First, the researchers confirmed that the 60-day-old piglets could be discriminated based on their gut microbiota type in two enterotypes. Each enterotype is characterised by a relative overabundance of two bacterial genera. These genera were Prevotella and Mitsuokella for the PM enterotype and Ruminococcus and Treponema for the RT enterotype. To establish the two experimental lines, faecal microbiota analysis was performed to select future reproducers. Individuals with the PM or RT enterotype were chosen. Piglets in the two lines were reared under the exact same conditions

The researchers found that, in the PM line, the frequency of the target enterotype rose from 53% in the initial population to 87% after three generations; for the RT line, this increase was from 47% to 70%. Enterotype-related differences in growth rate were observed, with piglets in the PM line growing faster over their first 70 days of life. Further analyses revealed that the two enterotypes comprised bacteria with different metabolic potential.

These findings indicate that, in animals, host genetics can have a major influence on gut microbiota formation, meaning that the latter is not solely determined by the environment. They also underscore that gut microbiota composition should be exploited during livestock breeding to improve the sustainability and resilience of livestock farming systems.