Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks

Abdominal fat deposition is an important economic trait in poultry, as excessive accumulation reduces feed efficiency and carcass yield. The gut microbiota is known to influence host energy metabolism and fat storage, suggesting its potential involvement in fat deposition. This study examined the relationship between intestinal microbiota and abdominal fat deposition in an F₂ population derived from Cherry Valley Ducks (♂) × Runzhou Crested White Ducks (♀) at 42 days of age. Based on abdominal fat rate, ducks with values of 0-0.75% and 1.5-2.25% were defined as the low (LF) and high (HF) abdominal fat groups, respectively. A combined multi-omics approach was used, including 16S rRNA gene sequencing, metagenomics, and whole transcriptomics, to compare high and low abdominal fat rate groups. 16S rRNA gene sequencing results showed that the cecum had the highest microbial diversity among all intestinal segments (duodenum, jejunum, ileum, and rectum) and was significantly enriched in carbohydrate metabolism pathways, highlighting its key role in nutrient utilization and growth. Therefore, the cecum was selected for further analysis. Metagenomic analysis of the cecum contents revealed significantly different intestinal microbial β diversity between the high and low abdominal fat rate groups (<i>p</i> < 0.05). The low abdominal fat rate group was enriched in beneficial microorganisms such as <i>Paenibacillus</i>, <i>Butyrivibrio</i>, <i>Coprococcus</i>, Ruminococcaceae, Veillonellaceae (Clostridiales), and Firmicutes. Conversely, the high abdominal fat rate group was characterized by an increased abundance of Bacteroidetes, including both beneficial and potentially pathogenic taxa such as <i>Alistipes</i> and Eggerthellales. The integrated analysis of metagenomic and whole transcriptome sequencing showed that Firmicutes and Bacteroidetes were not only related to energy metabolism, lipid metabolism, and amino acid metabolism, but also to the expression of <i>FGF2</i>, <i>FKBP5</i>, <i>PNPLA2</i>, <i>PLIN3</i>, <i>FGFR2</i>, <i>DGAT2</i>, and <i>ACER2</i>. In addition, Firmicutes and Bacteroidetes were also associated with 7 lncRNAs: XR_003493494.1, XR_003492471.1, XR_001190174.3, TCONS_00005095, XR_001190238.3, TCONS_00005095, and XR_003492841.1. In conclusion, this study highlights that the cecal microbiota is closely associated with abdominal fat deposition in ducks, elucidating its potential influence on host metabolism and gene expression. These findings enhance our understanding of the gut microbiota's relationship with obesity and offer new strategies to modulate gut-microbe interactions to reduce abdominal fat accumulation in poultry.