Romboutsia is a dominant genus in the goose intestine. Recent studies have suggested that Romboutsia lituseburensis might regulate serum immunoglobulin levels in female geese, although the underlying mechanisms remain unclear. In this study, we administered Romboutsia lituseburensis (R. lituseburensis) orally to female geese, leading to successful colonization of the ileum. Subsequent analysis showed that the levels of IgM, IgA, and IgG in the serum significantly decreased after colonization (P <
0.01). 16S rRNA sequencing revealed that R. lituseburensis significantly altered the microbial composition and increased the relative abundance of Jeotgalicoccus (P <
0.01), Turicibacter, and Bacillus (P <
0.05) in the ileum. Transcriptome sequencing further identified 263 differentially expressed genes (DEGs) in the ileum (146 upregulated, 117 downregulated) and 725 DEGs in the spleen (300 upregulated, 425 downregulated). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these DEGs were enriched in 17 pathways in the ileum and 21 pathways in the spleen. Notably, the "Intestinal immune network for IgA production" pathway was significantly enriched in the spleen (P <
0.05). Further, Short Time-series Expression Miner (STEM) analysis grouped the DEGs in these 2 tissues into 49 clusters, with clusters 27 and 29 showing the highest significance and similar expression patterns. Pathway analysis confirmed that the "Intestinal immune network for IgA production" pathway was enriched in both clusters. Furthermore, a protein-protein interaction (PPI) network of these 2 clusters, along with correlation analysis between microbiota abundance and gene expression, highlighted KEL, SERPING1, CALR, and OSTN as key hub genes. Overall, R. lituseburensis significantly increased the abundance of Jeotgalicoccus, Turicibacter, and Bacillus in the ileum. Concurrently, it might downregulate the "Intestinal immune network for IgA production" pathway in the spleen (CCR9, TNFRSF13B, AICDA) via KEL, SERPING1, CALR, and OSTN, thereby contributing to the reduction of serum immunoglobulin levels. These findings offer new insights into how R. lituseburensis influences immune function in female geese and provide a theoretical basis for further research into its other physiological roles in geese.