Gut Microbial Signatures of Broiler Lines Divergently Selected for Inosine Monophosphate and Intramuscular Fat Content

Consumers are increasingly concerned about the flavor quality of poultry meat, yet the relationship between inosine monophosphate (IMP), intramuscular fat (IMF), and the gut microbiota remains largely unclear. This study aimed to characterize the cecal microbiota associated with IMP/IMF deposition in Daheng broilers selectively bred for high-IMP/IMF levels (High group) and low levels (Control group). A two-stage microbiome analysis strategy was applied. Initially, 16S rRNA gene sequencing was conducted to assess microbial diversity and composition. Significant differences were observed between groups in alpha diversity indices (Chao1 and Faith_PD) and beta diversity (<i>p</i> < 0.05). LEfSe analysis identified 55 differentially abundant taxa (LDA > 3, <i>p</i> < 0.05), primarily within the <i>Phylum bacteroidota</i>. To achieve species-level and functional insights, whole-metagenome shotgun sequencing was performed. Taxonomic profiling of 62,443 microbial species revealed significant beta diversity differences (<i>p</i> < 0.05), with 120 dominant species differentially enriched (LDA > 3, <i>p</i> < 0.05), including 77 species in the High group such as <i>Merdivivens faecigallinarum</i>. Enriched functional genes were mainly involved in methane metabolism, starch and sucrose metabolism, and the nucleoside phosphate metabolic process. A total of 882 metagenome-assembled genomes (MAGs) were reconstructed and integrated with 19,628 publicly available chicken MAGs, resulting in 2609 non-redundant genomes, including 52 novel ones. These findings suggest that cecal microbial composition and function are associated with IMP/IMF levels in broilers, providing candidate bacterial species and functional pathways for further validation through gavage-based intervention and multi-omics analysis.