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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.,\n Lactobacillus<\/jats:italic>\n ,\n Bifidobacterium<\/jats:italic>\n ), suppression of pathogens (e.g.,\n Escherichia coli<\/jats:italic>\n ,\n Salmonella<\/jats:italic>\n ,\n Vibrio<\/jats:italic>\n ), 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\n Hermetia illucens<\/jats:italic>\n (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.\n <\/jats:p>\n \n Graphical abstract<\/jats:bold>\n <\/jats:p>\n 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.<\/jats:p>","DOI":"10.1007\/s42770-026-02033-4","type":"journal-article","created":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T03:12:21Z","timestamp":1784862741000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Prebiotics and probiotics in animal nutrition: implications for food safety, sustainability, and circular production systems"],"prefix":"10.1007","volume":"57","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1255-5831","authenticated-orcid":false,"given":"Jo\u00e3o Victor","family":"dos Anjos Almeida","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1774-7592","authenticated-orcid":false,"given":"Julia","family":"Memrava Cabrera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2048-6664","authenticated-orcid":false,"given":"Mauro","family":"de Medeiros Oliveira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8590-804X","authenticated-orcid":false,"given":"Ricardo","family":"Pinheiro de Souza Oliveira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8876-3269","authenticated-orcid":false,"given":"Alessandro","family":"M. 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