Intestinal microbiota-host crosstalk reveals mechanisms regulating residual feed intake in egg-type ducks

As an important economic trait in ducks, residual feed intake (RFI) may be influenced by the intestinal microbiota. However, the mechanisms underlying microbiota-host crosstalk remain unclear. We analyzed the total egg number (TEN), total egg weight (TEW), total feed intake (TFI), feed conversion ratio (FCR), and RFI of 1,370 ducks over a 32-day period. Within the high-TEW ducks, 60 low RFI ducks and 60 high RFI ducks were selected to form the LH group (LH) and HH group (HH), respectively. The TFI, FCR, and RFI were significantly lower in the LH than in the HH (P < 0.001). Based on 16S rRNA sequencing, the duodenal microbiota in the LH showed a significantly higher evenness index compared to the HH (P < 0.05). Using linear discriminant analysis effect size (LEfSe), differential bacterial genera were identified in the duodenum and jejunum between groups (LDA > 3.5, P < 0.05). Functional prediction results indicated that, compared to the HH, the duodenal microbiota of the LH appeared to be more active in metabolism. Further analysis revealed four genera (Paenibacillus, Kocuria, Corynebacterium, and Bacillus) that showed significant differences in both the duodenum and jejunum (LDA > 3.5, P < 0.05). Their abundances in the LH were significantly higher than those in the HH (P < 0.05). Subsequently, 419 and 384 differentially expressed genes (DEGs) were identified in the duodenum and jejunum using DESeq2, respectively (|Log2FC)|≥ 1, P < 0.05). Functional enrichment analysis showed that 22 and 16 pathways were significantly enriched in the duodenum and jejunum (P < 0.05). Among them, five metabolism-related pathways, such as steroid biosynthesis, were co-enriched in both intestinal segments. We constructed a protein–protein interaction (PPI) network of DEGs from the five pathways and utilized the MCODE plugin to extract the top-ranking subnetwork. The expression levels of genes in this subnetwork (HMGCS1, MSMO1, ACAT2, LSS, FDFT1, SQLE, IDI1, CYP51A1) were significantly correlated with the abundance of key genera. Paenibacillus, Kocuria, Corynebacterium, and Bacillus were identified as key microbiota influencing feed efficiency in ducks. Their abundances were closely associated with the expression of HMGCS1, MSMO1, ACAT2, LSS, FDFT1, SQLE, IDI1, and CYP51A1. The specific mechanisms require further validation in future studies. These findings provide a preliminary investigation into the intestinal microbiota-host crosstalk affecting feed efficiency and offer novel perspectives for reducing RFI in egg-type ducks.