Metabolomics is a high-throughput technology that is widely used across disciplines to identify and quantify metabolites in biological samples; however, its use has been limited in meat and animal science. The use of metabolomics, especially in these fields, is often curtailed by challenges with data processing and analysis. Improvements in data analysis platforms have broadened metabolomics applications and offer promise for determining metabolic pathways that directly influence animal health and livestock production. This review will present an overview of metabolomics concepts and current applications of metabolomics techniques in meat and animal science. Furthermore, we present evidence of the need to incorporate metabolomics in a systems biology context for the improvement of livestock production with an emphasis on animal health and production efficiency.

The gastrointestinal (GIT) microbiome of food animals represents a promising source of biologically active compounds with applications in animal health, nutrition, and sustainable production. Recent advances in 16S rRNA gene sequencing have transformed microbiome research, enabling detailed taxonomic profiling of microbial communities across diverse animal hosts. This review explores the potential of GIT microbiome-derived biologics—including short-chain fatty acids, antimicrobial peptides, and probiotics—as alternatives to traditional feed additives and antibiotics, as well as the potential impact on meat quality. While short-read sequencing remains foundational, long-read platforms such as PacBio, Oxford Nanopore, and LoopSeq offer enhanced taxonomic resolution and support the identification of functionally critical microbial strains. Practical considerations for sequencing method selection, database compatibility, and bioinformatics challenges are discussed, emphasizing the importance of curated, system-specific reference datasets. Ultimately, multi-omics approaches are necessary to characterize microbial activity and host-microbial interactions to unlock the microbiome’s functional potential. These strategies pave the way for precision microbiome engineering and novel biologics tailored to specific species and production systems. The review concludes with recommendations to standardize methodologies, invest in functional validation, and align microbiome research with the evolving needs of sustainable meat animal agriculture.

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.