Research in pigs shows gut microbiota is partially heritable

Comprising billions of microorganisms, the gut microbiota progressively matures after birth in humans and other animals. While environmental factors, and especially diet, are known to have a major influence on microbiota development and composition, the role of genetics remains a topic of debate. In a groundbreaking study recently published in Microbiome, INRAE researchers used pigs to experimentally demonstrate that gut microbiota composition is partly heritable. They bred two pig lines, selecting for two types of gut microbiota that differed in the abundance of certain bacterial taxa. They found that the frequency of each microbiota type increased across generations within each pig line. Additionally, the researchers discovered that one microbiota type was consistently associated with piglet growth. These findings underscore that livestock breeding efforts should account for gut microbiota composition to improve the sustainability and resilience of livestock farming systems.

The gut microbiota is an ecosystem containing hundreds of microbial species (e.g., bacteria, archaea, yeasts) 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. However, it remains unclear how much of a role is played by host genetics. In an unprecedented study, INRAE researchers bred two pig lines, each selected for one of the two gut microbiota enterotypes. They then studied how genetic factors influenced gut microbiota formation in 1,000 piglets over three generations.

Pig lines bred to host specific gut microbiota

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 (e.g., same location and feed).

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. In particular, for the PM enterotype, there were more bacterial genes associated with starch degradation, carbohydrate metabolism, and the synthesis of important amino acids. Researchers will continue to use these two lines to study lifetime enterotype stability and to explore enterotype influence on pig production, health, and behaviour.

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.

Reference

Larzul C., Estelle J., Borey M. et al. (2024). Driving enterotypes through host genetics. Microbiome 12, 116 DOI : https://doi.org/10.1186/s40168­’024 -01827-8