Jul 2026· Archives of Current Research International· 0 citations
TL;DR
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.
Abstract
The rumen microbiome is a diverse and dynamic consortium of bacteria, archaea, protozoa, fungi, and viruses that supports feed degradation, nutrient transformation, animal health, and productive performance in ruminants. Advances in microbial ecology, sequencing technologies, and systems biology have created opportunities to manage this microbial ecosystem to improve the efficiency and sustainability of livestock production. This review examines the composition, functions, and ecological interactions of the rumen microbiome, with emphasis on its contribution to fibre digestion, volatile fatty acid production, microbial protein synthesis, feed conversion efficiency, methane formation, and host physiological functions. Current strategies for microbiome modulation, including dietary modification, probiotics, direct-fed microbials, prebiotics, synbiotics, phytogenic compounds, exogenous enzymes, and rumen microbial transplantation, are evaluated in relation to digestive efficiency and animal performance. Emerging approaches, including metagenomics, metatranscriptomics, metabolomics, precision nutrition, synthetic microbial communities, genome-editing tools, and artificial intelligence-based predictive models, are also considered as developing pathways for targeted microbiome engineering. These approaches may support improved nutrient utilisation, milk and meat production, animal health, and mitigation of greenhouse gas emissions from ruminant systems. However, practical implementation remains constrained by microbial ecosystem complexity, inter-animal variability, limited persistence of introduced microorganisms, economic considerations, and regulatory challenges. 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. A deeper understanding of host-microbiome interactions and microbial functional dynamics remains essential for translating scientific advances into practical approaches that support sustainable livestock production, environmental stewardship, and overall global food security.
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
The pursuit of sustainable and efficient animal production systems has intensified global interest in microbiota-targeted nutritional strategies. This review synthesizes current research on prebiotics and probiotics, selectively utilized microbial substrates and beneficial live microorganisms, respectively, that confer health benefits, across major livestock and aquaculture sectors, including poultry, swine, ruminants, fish, and shrimp. It examines the fundamental role of host-specific gut microbiomes in regulating health and productivity and elucidates how prebiotics, alone or in synergistic formulations with probiotics, modulate these microbial communities. Mechanisms of action involve enhanced nutrient digestibility, improved intestinal morphology and barrier integrity, selective stimulation of beneficial bacteria (e.g., Lactobacillus, Bifidobacterium), suppression of pathogens (e.g., Escherichia coli, Salmonella, Vibrio), and potentiation of innate and humoral immune responses. Consistent evidence demonstrates that microbiota-targeted interventions improve key zootechnical indicators, including weight gain, feed conversion ratio, and carcass quality, while enhancing animal welfare and resilience to environmental and physiological stressors. A pivotal finding is their ability to reduce reliance on antimicrobial agents, addressing antibiotic resistance and aligning with consumer demand for ethical and natural production systems. Furthermore, this review highlights the valorisation of agro-industrial by-products (e.g., fruit pomace, cereal brans) and novel substrates such as Hermetia illucens (black soldier fly) as functional, cost-effective sources that embed animal nutrition within a circular bioeconomy framework. By integrating multidisciplinary findings from terrestrial and aquatic species, this review concludes that microbiota-based functional nutrition is indispensable for advancing next-generation sustainable animal production, uniting productivity, environmental stewardship, and animal welfare while supporting safe, ethical, and climate-resilient food systems worldwide. Probiotic and prebiotic integration in swine, poultry, cattle, and aquaculture systems. Supports animal health, feed efficiency, and sustainable by-product use, aligning with SDG 2 and SDG 12. Repurposing agro-industrial residues as novel prebiotics closes the resource loop, reinforcing the circular economy.
João Victor dos Anjos Almeida, Julia Memrava Cabrera, Mauro de Medeiros Oliveira et al.· Brazilian Journal of Microbi...· 1 citation
Aquaculture is central to global food security, but intensification of production has increased disease risk and environmental pressure. The gut microbiome of aquatic organisms is now recognized as a key mediator of host physiology, nutrition, immunity, and pathogen resistance, making it a promising alternative to antimicrobial-based disease control. This review summarizes current knowledge on the composition, assembly, and functional roles of the gut microbiome in fish and crustaceans of aquacultural importance. Major bacterial phyla include Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Actinobacteria, and Verrucomicrobia. Community structure is shaped by environment, diet, host age, genetics, stress, and stochastic processes, with differences between marine and freshwater systems. The microbiome contributes to immune defense through short-chain fatty acid production, Toll-like receptor signaling, cytokine regulation, mucosal immunoglobulin responses, antimicrobial peptide and bacteriocin production, and competitive exclusion of pathogens. It also supports productivity by improving nutrient assimilation, vitamin and enzyme synthesis, and feed conversion. Probiotics, prebiotics, and synbiotics are discussed as strategies for targeted microbiome modulation, although unstable colonization and the lack of standardized protocols remain major challenges. Overall, targeted microbiome manipulation offers a promising route toward sustainable, antimicrobial-reduced aquaculture.
Liudmila E. Khmelevtsova, E.V. Prazdnova, Maria Mazanko et al.· Microorganisms· 0 citations
The rumen microbiome plays a crucial role in controlling animal health, feed efficiency, and production sustainability. Given that certain components of the rumen microbiome are heritable, it represents a promising additional target for genetic selection. The study was based on 192 cows (180 in a genome-wide association study), housed in the same commercial free-stall barn and fed the same TMR. Rumen fluid samples were collected by rumenocentesis and analysed for microbiome composition (bacterial and archaeal fractions) using Illumina sequencing of the V3-V4 region of the 16S rRNA gene. Association analysis of bacteria abundance, production traits and animal genotypes was performed using various statistical models. Several bacterial phyla and genera were found to be associated with milk production and health parameters, with the strongest correlations observed for rumen pH, milk fat percentage, and milk urea concentration. Moreover, through a microbiome genome-wide association study (microbiome-GWAS), we demonstrated that the abundance of several microbial taxa is potentially influenced by host genetic variation, showing moderate to high heritability estimates. Overall, these results (based on a limited sample size) suggest that variation in host genetics and rumen microbiome composition is associated with variability in production traits, supporting the thesis on the potential of microbiome-informed breeding strategies. This study provides an initial foundation for integrating host genomics with rumen microbiome, aiming to improve the performance of dairy cattle.
D. Motyka, I. Jasielczuk, J. Pokorska et al.· Scientific Reports· 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
The gut microbiota plays an important role in nutrient utilization, intestinal homeostasis, immune regulation, and production performance in poultry. Its composition and functional activity are shaped by complex interactions among host species, developmental stage, intestinal segment, diet, genetic background, and rearing environment. This review summarizes current knowledge of the poultry gut microbiota, with particular emphasis on its roles in nutrition, metabolism, and production performance. We first examine microbial composition and spatial distribution across major poultry species, including broiler chickens, laying hens, ducks, geese, and turkeys, and discuss the factors contributing to interspecies and interstudy variation. We then evaluate how dietary components, including fiber, protein, amino acids, and lipids, modulate microbial communities and metabolic pathways. Particular attention is given to microbial fermentation, short-chain fatty acid production, microbial nitrogen metabolism, bile acid transformation, and host-microbiota signaling, which collectively influence nutrient utilization, intestinal barrier function, immune homeostasis, and metabolic regulation. The potential of microbiota-targeted strategies, including probiotics, prebiotics, synbiotics, dietary fiber manipulation, reduced-protein diets, and emerging microbial interventions, to improve feed efficiency, growth performance, carcass characteristics, meat quality, and resilience to environmental stress is also discussed. In addition, the implications of gut microbiota regulation for nitrogen utilization, ammonia emissions, animal welfare, and antibiotic-free production are considered. Despite substantial progress, the translation of microbiome research into practical applications remains limited by inconsistent experimental designs, methodological heterogeneity, insufficient functional validation, and a lack of causal evidence. Integrating multi-omics approaches with controlled intervention studies and standardized experimental frameworks will be essential for defining causal microbiota-host interactions and developing precision microbiota-based strategies. Overall, a functional understanding of the diet-microbiota-host axis may provide new opportunities to improve poultry productivity, health, and sustainability.
