Impact of heritable and non-heritable gut microbiota on microbiability estimation and phenotype prediction of production traits in Duroc pigs

Pig phenotypes are influenced by host genetics and the gut microbiota. However, the impacts of classification methods and the heritability of the gut microbiota on production traits in pigs remain unclear. Here, we evaluated the impacts of the gut microbiota with different classifications and heritabilities on the estimation of microbiability (i.e., the proportion of host phenotypic variance explained by the gut microbiota) and prediction of production traits in Duroc pigs. We identified the most effective microbial classification based on heritability and microbiability; determined the relationship between heritability of the microbiota and host phenotypic values; and investigated the impact of components of the gut microbiota with different heritabilities on microbiability estimation and phenotype prediction. In total, 961 Duroc pigs with both phenotypic and pedigree data were evaluated through bacterial 16S rRNA gene sequencing of the gut microbiotas from faecal samples. Microbiability for all traits was higher when estimated using amplicon sequence variants (ASVs) than when using other microbial classifications. Therefore, the ASV classification was used in subsequent analyses. The microbiability estimates of daily gain (DG) and backfat thickness (BF) (0.21 and 0.15, respectively) were higher than those of other traits, such as body measurement traits (range of 0.00-0.06). In total, 154 of 368 ASVs with high prevalence were significantly heritable in this population. Furthermore, 17 and 27 ASVs exhibited significant heritability and were associated with DG and BF, respectively. Microbiability estimates were high using heritable ASVs in DG (0.08) and using non-heritable ASVs in BF (0.09). Phenotype prediction using a model that included the sum of breeding values and heritable ASV effects had the highest prediction accuracy in DG (i.e., 0.45, compared with 0.20 for a model including breeding values alone). No difference was observed between heritable and non-heritable ASV effects in BF. Our results indicate that the gut microbiota explains a substantial portion of phenotypic variance, and microbial effects can be used to predict DG and BF. Our results indicate that it is important to differentiate between heritable and non-heritable ASVs when evaluating the impact of host genetics and the gut microbiota on host phenotypes in pigs.