Applied Hologenomics: Feasibility and Potential in Aquaculture

Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture. Both the host genotype and gut microbiota of an animal play significant roles in shaping key phenotypes of aquacultural relevance, including growth metabolism and immune functions. Traditional approaches to improve production have relied on selecting for direct genotype–phenotype correlations or on directly modulating gut microbiome communities. The hologenome theory argues that the genomes of host organisms and their associated microbial communities are subject to biological interactions and cannot be viewed independently. The gut microbiota can be viewed as a collection of genotypes contributing to holobiont phenotypes linked to the host genotype, and any attempts to modify the gut microbiota can only be successful in the context of the host genotype ‘environment’. A hologenomic approach to aquaculture has potential to improve growth, health, and sustainable production.