Applied Hologenomics: Feasibility and Potential in Aquaculture

Trends Biotechnol. 2018 Mar;36(3):252-264. doi: 10.1016/j.tibtech.2017.12.006. Epub 2018 Jan 31.


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.

Keywords: aquaculture; holo-omic analysis; holobiont; hologenome; sustainable production.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Aquaculture*
  • Epigenomics
  • Feasibility Studies*
  • Fishes / microbiology*
  • Food Industry
  • Gastrointestinal Microbiome / genetics
  • Gastrointestinal Microbiome / immunology
  • Genome, Microbial / genetics
  • Genome, Microbial / immunology
  • Humans
  • Immune System / immunology
  • Immune System / microbiology
  • Metagenomics*
  • Proteomics
  • Transcriptome