BackgroundThe aim of the present study was to determine differences in the intestinal microbiota and metabolites of broiler breeders with different egg laying rate; and its possible relationships between intestinal microbiota and intestinal metabolites were also explored.MethodsA total of 200 AA+ parent broiler breeders (41-week-old) were separated into two groups according to their different egg laying rate: average reproductive group (AR: 77.26%±0.88%) and high reproductive group (HR: 86.67%±0.75%), with 10 replicates and 10 birds each 42-days study.ResultsFeed conversion ratio (FCR), ovary cell apoptosis rate (ApoCR) and abdominal fat pad weight percentage were lower (p < 0.05), while the hatchability of qualified egg rate (HQR) was higher (p < 0.05) in HR group than that in AR group. At phylum level, Firmicutes and Proteobacteria were the dominant bacteria in small intestines, while Bacteroidetes was dominant bacteria in cecum. At genus level, Lactobacillus was dominant in small intestines while Bacteroides were dominant in cecum. In HR Phascolarctobacterium were lower (p < 0.05) in ileum. A positive correlation was observed between Actinobacteria in the small intestines and ApoCR (r = 0.34 & p < 0.05). A positive correlation was observed between FCR and Spirochaetes in cecum (r = 0.54 & p < 0.05). The metabolomics analysis on ileal digesta content revealed a higher concentration of Octadecanoic acid, 9,12-Octadecadienoic acid, 11-trans-Octadecenoic acid, d-Ribose and Inositol in HR broiler breeders. Moreover, inositol was enriched in "Phosphatidylinositol signaling system", "Inositol phosphate metabolism", "Ascorbate and aldarate metabolism", "Galactose metabolism", "ABC transporters", and Octadecanoic acid was enriched in "Fatty acid biosynthesis", "Biosynthesis of unsaturated fatty acids".ConclusionsOur results suggest that glycerol, inositol modulate energy partitioning in fat metabolism to influence reproductive performances. Microbiota, such as Actinobacteria (phylum), Spirochaetes (phylum), and Phascolarctobacterium (genus) may have negative relationship with broiler breeders’ reproductive performances.