Modulation of the gut microbiome and resistome in Taihe Black-Boned Silky Fowls by different dietary selenium forms

Selenium is a widely utilized supplement in poultry production. Its bioavailability and tissue deposition vary with chemical form and may affect the gut microenvironment. Taihe Black-Boned Silky Fowl (TBSF), a Chinese endemic breed with systemic melanin deposition, exhibit enhanced absorption and enrichment of diverse compounds. As a metalloid, selenium may also promote antimicrobial resistance in microbiomes, including those of the gut. However, its impact on the TBSF gut microbiota and resistome remains unknown. We therefore investigated how selenium chemical form influences the cecal microbiome and resistome. Four dietary treatment groups of TBSF (n = 120 birds per group; 60 males and 60 females) were fed for 80 days: CK (selenium-deficient control), YS (sodium selenite), JS (yeast-derived selenium), and DS (selenomethionine), with measured dietary selenium concentrations of 0.05 ± 0.002, 0.33 ± 0.023, 0.35 ± 0.017, and 0.36 ± 0.042 mg/kg, respectively. We performed metagenomic sequencing analysis to assess alterations in microbial composition and resistome profiles in cecum. Results demonstrated that selenium supplementation significantly modulated cecal microbiota structure in both male and female birds(Bray-Curtis distance-based analysis, Wilcoxon rank-sum test, P < 0.05), with pronounced sex-dependent differences. The relative abundances of three prevalent antibiotic resistance genes (ARGs), bcrA, efrA, and fusA, were significantly elevated in selenium-supplemented groups compared with the CK group (Kruskal-Wallis H test, FDR-adjusted P < 0.05). Selenium supplementation reduced mobile genetic element (MGE) type diversity while increasing overall MGE relative abundance. Transposases and recombinases were the two most abundant MGE-associated functional classes. Mantel correlation analysis revealed strong associations between cecal microbiota composition and both ARG and MGE profiles (r ≥ 0.5, P ≤ 0.001). The sexually dimorphic cecal microbiota composition in TBSF may underlie the observed sex-dependent resistome response: sodium selenite exerted the strongest effect on ARG and MGE enrichment in roosters, whereas yeast-derived selenium induced the strongest effect in hens. Further network analysis revealed that sodium selenite exerted the most pronounced influence on resistome-microbiota co-occurrence patterns. These findings underscored the dual-sided nature of selenium supplementation from the perspective of ARGs, indicating that selenium supplementation may alter the composition of the cecal microbiota, thereby modulating the relative abundance and community structure of ARGs and MGEs in the TBSF cecum. Given selenium's essential role and narrow therapeutic index, its chemical form and dosage must be evidence-based and rigorously optimized to minimize potential unintended contributions to antimicrobial resistance. This represents a potential ecological and antimicrobial resistance concern from a One Health perspective that warrants further investigation.