Metagenomic Analysis Revealed Distinct Cecal Core Functional Taxa in Taihe Black-Boned Silky Fowls Across Selenium Sources

Selenium (Se) is an essential trace element, and host intestinal microecology bidirectionally regulates Se metabolism and bioavailability. How the cecal microbiota of Taihe Black-Boned Silky Fowl (TBSF)—a breed with extensive melanin deposition and distinctive metabolic traits—responds to different Se chemical forms remains unelucidated. Here, metagenomic sequencing characterized the cecal microbiome of TBSF supplemented with sodium selenite (YS), selenomethionine (DS), and Se-enriched yeast (JS) at recommended levels, together with a control group (CK, no Se) (n = 6 per group). All three Se sources modulated community structure with ANOSIM separation increasing from phylum (R = 0.468, p = 0.001) to genus (R = 0.771, p = 0.001) and species (R = 0.818, p = 0.001). The relative abundances of several Lactobacillus and Limosilactobacillus species were significantly higher in the Se-supplemented groups than in the CK group, particularly in the YS group (Kruskal–Wallis test, FDR-adjusted p < 0.05). Genes encoding Se-metabolism enzymes (e.g., iscS, glnA, ASMT, and PSTK) differed among groups, and Se supplementation enriched functions related to translation, ribosome biogenesis and structure, as well as recombination and DNA repair (Kruskal–Wallis test, FDR-adjusted p < 0.05). Se sources enriched distinct classes of antibiotic resistance genes (ARGs): multidrug in the CK group; glycopeptides and fluoroquinolones in the JS group; polypeptide in the YS group; and tetracycline in the DS group (LEfSe, LDA > 2, p < 0.05). Co-occurrence network topology further indicated that these functional profiles are strongly correlated with shifts in the relative abundance of specific bacterial taxa (|r| ≥ 0.8, p < 0.05). Collectively, distinct Se sources differentially shape poultry cecal microbiota composition and function, with host microbes actively mediating Se metabolism and absorption. Whether optimizing Se supplementation strategies, such as co-administering lactic acid bacteria with sodium selenite, could yield synergistic benefits warrants further investigation.