Employing pigs to decipher the host genetic effect on gut microbiome: advantages, challenges, and perspectives

ABSTRACT

The gut microbiota is a complex and diverse ecosystem comprised of trillions of microbes and plays an essential role in host’s immunity, metabolism, and even behaviors. Environmental and host factors drive the huge variations in the gut microbiome among individuals. Here, we summarize accumulated evidences about host genetic effect on the gut microbial compositions with emphases on the correlation between host genetic kinship and the similarity of microbial compositions, heritability estimates of microbial taxa, and identification of genomic variants associated with the gut microbiome in pigs as well as in humans. A proportion of bacterial taxa have been reported to be heritable, and numerous variants associated with the diversity of the gut microbiota or specific taxa have been identified in both humans and pigs. LCT and ABO gene have been replicated in multiple studies, and its mechanism have been elucidated clearly. We also discuss the main advantages and challenges using pigs as experimental animals in exploring host genetic effect on the gut microbial composition and provided our insights on the perspectives in this area.

KEYWORDS:

• Gut microbiome
• host genetics
• heritability estimates
• genome-wide association study
• pigs

Acknowledgments

We are grateful to Hui Yang, Jinyan Wu and the colleagues in the State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, and Professor Michel Georges and Dr. Carole Charlier in the Unit of Animal Genomics, GIGA-Institute and Faculty of Veterinary Medicine, University of Liege for working together on the host genetic effects on pig gut microbiome.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by The National Natural Science Foundation of China (32272831, 31790410, 31772579) and National pig industry technology system (CARS-35).