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.

In the plant-plant pathosystem of rice ( Oryza sativa) and the parasitic plant Striga hermonthica, cell walls from either plant are important defensive and offensive structures. Here, we reveal the cell wall dynamics in both Striga and rice using simultaneous RNA sequencing. We used weighted gene co-expression network analysis to home in on cell wall modification processes occurring in interactions with a resistant rice cultivar (Nipponbare) compared with a susceptible one (IAC 165). Likewise, we compared the cell wall dynamics in Striga infecting resistant and susceptible rice. Our study revealed an intense battlement at the Striga-rice cell walls involving both parasite (offense) and host (defense) factors, the outcome of which makes the difference between successful or failed parasitism. Striga activates genes encoding cell wall-degrading enzymes to gain access to the host, expansins to allow for cell elongation, and pectin methyl esterase inhibitors for rigidity during infection. In the susceptible host, immune response processes are not induced, and Striga-derived cell wall-degrading enzymes easily breach the host cell wall, resulting in successful parasitism. In contrast, the resistant host invokes immune responses modulated by phytohormones to fortify the cell wall through polysaccharides and lignin deposition. Through these processes, the cell wall of the resistant host successfully obstructs parasite entry. We discuss the implications of these findings in the context of practical agriculture in which cell wall modification can be used to manage parasitic plants. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Sudden death syndrome (SDS) is a major disease that affects soybean ( Glycine max) production, primarily caused by the soilborne fungus Fusarium virguliforme in North America. Understanding the interactions among soybeans, F. virguliforme, and microorganisms in the soil near the vicinity of roots can provide microbial candidates for SDS management. The objective of this study was to elucidate the role of rhizosphere microbial composition and activity, both in the presence and absence of F. virguliforme, across two commercial soybean cultivars with differing susceptibility to SDS. Bacterial and fungal community dynamics were assessed using full-length 16S rRNA and internal transcribed spacer 1 (ITS1) sequencing, respectively. Microbial activity was further evaluated with an optimized metatranscriptome workflow. Our analysis revealed that SDS-tolerant soybeans recruit microbes with growth-promoting and biocontrol potential, such as members of the genera Bacillus, Pseudomonas, Trichoderma, Mortierella, and Talaromyces, when exposed to F. virguliforme. This distinct microbial recruitment strategy in response to F. virguliforme could provide the ability for soybeans to survive under pathogen stress. In contrast, pathogen inoculation reduced the abundance and activity of the nitrogen-fixing Bradyrhizobium spp. These findings suggest that selective recruitment of beneficial microbes likely contributes to SDS tolerance, whereas pathogen pressure compromises symbiotic nitrogen fixation. The results highlight candidate taxa and interactions for developing synthetic microbial communities to support SDS management. The information generated from this study will be useful for assembling a combined synthetic microbial community and testing. [ ] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .