This review proposes an Africa-specific approach that develops locally grounded, scalable, and resource-sensitive precision nutrition strategies, strengthening antimicrobial stewardship, animal health, food safety, climate resilience, sustainable livestock production, and broader One Health objectives.
Abstract
Livestock production in Africa occurs across highly heterogeneous agroecological and management environments, ranging from extensive pastoral and mixed crop–livestock systems to intensive enterprises. These systems are characterized by seasonal and spatial variation in feed resources, reliance on locally available forage and agricultural by-products, climatic stress, endemic diseases, and the use of indigenous and locally adapted breeds. Such conditions create distinctive microbiome–host interactions that remain poorly represented in global livestock omics research. Although the gut microbiome is central to nutrient utilization, immune function, metabolic homeostasis, and resilience, the functional mechanisms linking microbial communities, diet, host physiology, and productivity in African livestock remain insufficiently characterized. African systems are particularly underrepresented in integrated microbiome–metabolomics datasets, longitudinal studies, and artificial intelligence (AI)-enabled predictive models, limiting the development of context-specific precision nutrition strategies. This review examines the integration of metabolomics and AI with microbiome and host data to advance precision livestock nutrition within an African and One Health context. It identifies both substantial constraints and strategic opportunities. Limited research infrastructure, high-quality regional datasets, computational capacity, and specialized expertise remain major barriers. Conversely, Africa’s diversity of livestock breeds, feed resources, agroecological conditions, and naturally occurring resilience phenotypes provides an important opportunity to identify microbiome–metabolite signatures associated with feed efficiency, disease resilience, climate adaptation, and product quality. Emerging metabolomics and computational capacity, particularly in South Africa, could support regional research networks and continental data infrastructures. Furthermore, the review proposes an Africa-specific approach that develops locally grounded, scalable, and resource-sensitive precision nutrition strategies, strengthening antimicrobial stewardship, animal health, food safety, climate resilience, sustainable livestock production, and broader One Health objectives.
Metagenomics, the study of genetic material directly extracted from environmental samples, has revolutionised microbial research by enabling culture-independent investigation of microbial diversity, community structure, and potential. It has become a potent tool in livestock production systems for addressing major challenges related to animal health, productivity, environmental sustainability, antimicrobial resistance, and greenhouse gas emissions. Metagenomic approaches have provided critical insights into ruminal microbial ecology, host–microbiome interactions, feed efficiency, milk production, heat stress resilience, metabolic disorders, and methane emissions, in addition to facilitating the identification of microbial biomarkers and functional pathways associated with economically important traits. Furthermore, metagenomics has improved One Health surveillance through characterization of resistomes, mobile genetic elements, zoonotic pathogens, and microbial reservoirs of antimicrobial resistance. Applications also extend to uterine and faecal microbiome research, viral detection, novel enzyme discovery, therapeutic development, and biodegradation. The use of metagenomics in precision nutrition, microbiome-informed breeding, disease monitoring, and sustainable livestock management has been greatly increased by recent developments in high-throughput sequencing, bioinformatics, and multi-omics integration. This review highlights the revolutionary potential of metagenomics in livestock production systems by examining its methodological advancements, historical background, and diverse applications.
Dibyasha Kar, Ritik Kumar Singh, Deepti Sinha et al.· Journal of Pure and Applied...· 0 citations
Background: Livestock production is indispensable for global food security, yet it faces constant pressure to maintain a sustainable balance between environmental, economic, and ethical demands. Objective: This study explores the past, present, and future of the livestock industry through genomic technologies. Methods/Approach: Tools such as Next-Generation Sequencing (NGS), Whole-Genome Sequencing (WGS), Genome-Wide Association Studies (GWAS), and Genomic Selection (GS) have accelerated precise genetic improvement of traits like feed efficiency, productivity, and disease resistance. Key Tools: CRISPR-Cas9 gene-editing further fosters livestock with improved genetic potential. Impact: Genomic-based breeding strategies reduce environmental impacts through lower methane-emitting ruminants and rumen microbiome utilization, while enhancing animal welfare via selection for stress resilience and innate disease resistance, reducing veterinary intervention. Conclusion: Overall, genomic approaches provide a powerful pathway for healthier, more productive, and sustainable livestock, supporting global food security amid climate and resource challenges.
Muhammad Younus· Zeugma Biological Science· 0 citations
This review systematically summarizes the core mechanisms by which probiotics modulate meat quality, feed efficiency and small intestinal and cecal health in pigs and broilers via the gut–muscle axis, nutrient metabolic axis, and immune regulatory axis and elucidates the heritable effects of host genetics on shaping the gut microbiome.
The review highlights the need to integrate multi-omics datasets, computational modelling, and precision livestock technologies to develop robust, scalable, and economically viable microbiome management strategies for sustainable livestock production, environmental stewardship, and overall global food security.
Shalu Singh, Yashesh Singh, Jagjiwan Ram et al.· Archives of Current Research...· 0 citations
Simple Summary Dairy farming faces growing challenges as farmers must produce more milk while reducing disease, lowering the use of antibiotics, and limiting environmental impacts. This review examines current and emerging ways to improve the natural communities of helpful microorganisms that live inside dairy cows to support better health and productivity. It compares different approaches, including beneficial feed supplements, the transfer of healthy gut microorganisms, advanced gene-based methods, and data-guided farm management, to assess how close they are to routine use on farms. The evidence shows that beneficial feed supplements are already improving milk production, supporting animal health, reducing disease, and lowering the need for antibiotics. Other promising methods have shown encouraging results but still require further research before they can be safely applied on a large scale. Overall, the review concludes that future progress will depend on choosing the most suitable approach for each individual animal rather than using the same solution for every herd. These advances could help create healthier dairy cows, more sustainable farming systems, safer food production, and a cleaner environment.
M. Ashfaq, M. Tharwat, Sohail Ahmed et al.· Veterinary Sciences· 0 citations
Abstract The microbiome is fundamental to plant performance in agroecosystems, influencing primary productivity and climate resilience. Microbiome modulation refers to the targeted manipulation (or steering) and optimization of microbiota features, including taxonomic structure, diversity, composition, assembly dynamics, stability, functional capacity, interactions, and network architecture. Here, we review the current state-of-the-art knowledge and strategies used for microbiome modulation, encompassing biological interventions such as bacteria, fungi, protists, nematodes, and phages, as well metabolites, compounds, and nutrients derived from plants. We further discuss emerging tools and strategies for next-generation microbiome modulation, including function-oriented, multitrophic defined microbial communities assembled based on ecological traits and interactions across multiple trophic levels to enable their establishment and function within the phytobiome; temperate phages; microbiome transplantation and breeding; and functional synbiotics, defined as combinations of beneficial microorganisms and compounds that improve microbiome health and function. In addition, we highlight key knowledge gaps and research priorities for advancing precision microbiome modulation. Addressing current challenges will require integrated frameworks combining experimental validation in planta and reductionist approaches with in silico modeling and multiomics analyses to better predict, design, and sustain beneficial plant-microbiome outcomes. Overall, microbiome modulation represents a paradigm shift in advancing sustainable and climate-resilient agri-food systems.
Malek Marian, Ioannis A. Stringlis, E. Rolli et al.· Sustainable Microbiology· 0 citations
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