The animal microbiome as a partner in sustainable food production

Prebiotics, probiotics, and synbiotics are gaining attention as tools to improve feed efficiency, support animal welfare, and reduce antibiotic dependence
The animal microbiome as a partner in sustainable food production
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Springer International Publishing
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Prebiotics and probiotics in animal nutrition: implications for food safety, sustainability, and circular production systems - Brazilian Journal of Microbiology

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. Graphical abstract 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.

Modern animal production faces a complex challenge: producing more food while reducing environmental impacts, limiting antibiotic use, and responding to growing expectations around animal welfare. In this context, the gut microbiome has become an important area of research, offering new ways to support animal health through nutrition rather than pharmaceutical interventions.

A recent, open access review published in the Brazilian Journal of Microbiology brings together findings from livestock and aquaculture research to examine how prebiotics and probiotics influence animal performance and health. The review covers poultry, swine, cattle, fish, and shrimp production, highlighting how microbiota-targeted strategies are being investigated across very different production systems.

The evidence synthesized by the authors shows that these interventions can help shape gut microbial communities, improve nutrient utilization, strengthen intestinal barrier function, and support immune responses. Across the studies surveyed, researchers have reported improvements in indicators such as weight gain, feed conversion, and resilience to physiological and environmental stressors. The review also discusses their role in reducing the prevalence of pathogens including Salmonella, Escherichia coli, and Vibrio species.

Circular bioeconomy
One aspect that makes this field particularly interesting is its connection with broader sustainability goals. The authors describe how agro-industrial by-products, including fruit and cereal processing residues, can be repurposed as sources of functional ingredients. They also discuss emerging substrates such as the black soldier fly (Hermetia illucens), illustrating how animal nutrition research is increasingly intersecting with circular bioeconomy approaches.

The review also revisits a topic that continues to receive attention worldwide: reducing dependence on antimicrobials in food production. According to the authors, prebiotics and probiotics offer opportunities to support animal health while contributing to efforts aimed at addressing antimicrobial resistance. Rather than presenting these tools as universal solutions, the paper examines the biological mechanisms that may explain their benefits and the conditions under which they are most effective. 

Importantly, the authors note that this work is a narrative review rather than a systematic review or meta-analysis. Given the diversity of animal species, production systems, interventions, and outcome measures covered, the article provides an integrative overview of the field rather than a quantitative assessment of effectiveness. Even so, the review offers a valuable perspective on how microbiome-centered nutrition is becoming part of the conversation around the future of sustainable animal production. 

Author's note: I used Microsoft Copilot to assist in creating this post.

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