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Background <p>The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.</p> Results <p>We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA <i>p</i> &gt; 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. <i>Bacteroides fragilis</i> emerged as a dominant associate, correlating positively with a diverse range of metabolites (<i>n</i> = 271). Functional gene analysis suggested a link between <i>Mediterraneibacter</i> spp. and soyasaponin deglycosylation, while <i>Ruminococcaceae</i> UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.</p> Conclusion <p>Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.</p>

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Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月4日

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  • Gladys Maria Pangga,
  • Anne Richmond,
  • Callie Hughes,
  • Androniki Psifidi,
  • Dong Xia,
  • Damer Blake,
  • Umer Zeeshan Ijaz,
  • Ozan Gundogdu

摘要

Background

The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.

Results

We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p > 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.

Conclusion

Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.