Gut Microbiota and Advances in Microbiome Sequencing-Based Technologies: Opportunities for Potential Biologics Discovery in Meat Animals

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.