Effect of gut microbiota on production traits, interaction with genetics

Gut microbiota is a key contributor to feed use in monogastric species, in particular via the digestion dietary fibres. Molecular techniques are now available to run large studies and decipher the potential of gut microbiota to improve livestock. Studies on human and mice are more advanced: different factors have been demonstrated to influence the gut microbiota composition and functions, including maternal transmission, environment (diet composition and quantity, humidity and heat), age and physiological status. Studies also evaluated if the host controls its gut microbiota. In pigs, chicken and rabbits, microbiota differences between animals of extreme phenotypes within populations, and between lines divergently selected for specific traits, are reported. Other studies reported that some microbiota abundancies are heritable. Linear mixed models have been used to evaluate its contribution to trait variability, or microbiability, with different data (full vs 16S sequencing of gut or faecal contents) and different variance matrices. They showed significant contribution to production traits, reaching more than 30%. However, confounding effects exist, such as the maternal inheritance of the microbiota and the genetic determinism by the host: many studies show reduction of the genetic additive variance, in addition to reduction of the residual variance with microbiability. Specific datasets, testing a given genetic in different environments or using cross-fostering, are used to better understand the relative contribution of each effect (host genetics and microbiota) to the trait variance, and propose solutions to livestock. This work is part of the European Union’s H2020 Feed-a-Gene Project (grant 633531).