Long-reads metagenomics reveals the effects of dulse supplementation on the poultry caecal bacteriome and its associated genetic repertoire

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Introduction Dulse ( Palmaria palmata ) is a macroalgal feed ingredient rich in polysaccharides and bioactive compounds that offers a sustainable strategy to enhance animal health and productivity through modulation of gut microbiota. However, the impact of dulse supplementation on the taxonomic composition and genetic repertoire of the broiler chicken caecal microbiota remains poorly characterised. Methods We applied long-read shotgun metagenomic sequencing on 18 caecal samples collected from 27-day-old male Ross 308 broilers following a 7-day feeding trial with three dietary treatments — a reference diet, a soyabean meal-supplemented diet, and a diet supplemented with 30% dulse — to investigate the effects of dulse inclusion on microbial community composition, genetic diversity, and antimicrobial resistance (AMR) and virulence determinants. Results Across all dietary treatments, the Clostridia class predominated (71%), whereas primary fermenters ( L. phocaeense ), lactic acid bacteria ( L. salivarius ), and hydrogenotrophic cross-feeders ( B. hydrogenotrophica ) were enriched in the reference diet, dulse-supplemented and soyabean meal-supplemented groups, respectively (KW p < 0.05), contributing to potential improvements in caecal function, immune resilience, and nutrient utilisation while reducing pathogen load. The overall resistome profiles were comparable across dietary treatments and were dominated by genes conferring resistance to tetracyclines, lincosamides, and aminoglycosides. In contrast, the virulome displayed diet-associated shifts: Enterobacteriaceae were enriched in the dulse and reference diets relative to the soyabean meal diet, with an expanded functional repertoire of virulence-associated genes, particularly those involved in adhesion, iron acquisition, and secretion systems. Multidrug resistance genes, virulence determinants, and Col / IncF -type plasmid replicons were associated with E. coli reads, highlighting its potential resistance and virulence arsenal within the caecal microbiota. Discussion Our findings suggest that the benefits of dulse extend beyond its nutritional value, residing in its ability to foster ecosystem resilience; by promoting a diverse, niche-stabilised microbiota, dulse minimises the risk of opportunistic pathogen proliferation, supporting its use as a sustainable, functional feed ingredient.

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