Genetic control of fecal microbiota composition of growing pigs in three contrasted environments

Fecal samples for 1600 pigs were collected in a temperate farm, in a tropical farm, and during an acute heat stress (i.e., 3 weeks at 30°C at 23 weeks of age) in the temperate farm, in a genetically connected design between all environments. The V3-V4 regions of the 16SRNA were sequenced and 1688 OTU were obtained. All animals were genotyped for 60K SNP. Linear mixed models were used to evaluate the variance components of the animal additive genetic effect in each environment, and association studies were run to detect variants involved in the genomic control of fecal microbiota in all environmental conditions. A total of 1685 OTU had heritabilities estimated. More than 1573 had heritabilities different from zero, with a mean of 0.34 +/-0.17 in the temperate environment, 0.32 +/-0.15 during the acute heat stress, and 0.24 +/-0.16 in the tropical environment. The heritability distributions for the OTU were similar in the three environments, with slightly more values below 0.10 in the tropical farm. About 10% of the OTU had heritability close to zero in one environment and higher than 0.2 in another environment, suggesting an influence of the environment on the genetic control of some OTU. Some association signals were identified for these OTU:  most differed between the three environments, suggesting different genomic control of the fecal microbiota composition of growing pigs in temperate, acute heat stress and tropical chronic stress conditions. This study is part of the Feed-a-Gene Project, funded from the European Union’s H2020 Programme under grant agreement no 633531.