Meat Animal Biologics Discovery from the Rumen Microbiome: Application of Genomics

The gastrointestinal tract (GIT) microbiome of food animals harbors a wide range of multifunctional microorganisms. The GIT microbiota can utilize most dietary substrates that the animal consumes, including complex carbohydrates, and subsequently converts these into a wide array of fermentation end products and metabolites that can either be used directly by the host or mediate microbe-host crosstalk. GIT microorganisms, particularly those of food-producing animals, which are readily available during animal harvest, also represent an underexplored resource for biologics discovery. The range of biologically active molecules produced by GIT microorganisms varies tremendously, providing several pathways for discovery and innovation. This review summarizes advances in the discovery of bioactive molecules produced by gut microorganisms with an emphasis on the rumen microbiome. Genomics, high-throughput sequencing technologies, and other omics have revolutionized our understanding of these microbial communities, enabling the discovery of novel enzymes, antimicrobial peptides, and other metabolites with significant applications in animal health and productivity. The strategic use of these biologics can help prevent or control animal diseases, improve the efficiency of feed conversion, and alleviate the pressure on antimicrobial resistance, thus promoting the sustainability of meat production practices.