Though a number of Eimeria species have been described in geese, the host responses to these parasites at the molecular level have yet to be explored. In the present study, fresh fecal samples were collected for single-oocyst isolation. The recovered oocysts were identified based on molecular analysis using PCR and sequencing. Subsequently, we examined the transcriptional response of the Landes goose cecum following infection with the isolated Eimeria strain. Molecular analysis showed that the isolated Eimeria strain was Eimeria stigmosa, which was named the E. stigmosa SX-01 strain. Transcriptomic profiling identified 3806 differentially expressed genes (DEGs), including 2238 genes with increased expression and 1568 genes with decreased expression. The results obtained from the quantitative reverse transcription PCR (qRT-PCR) analysis confirmed that the RNA sequencing (RNA-seq) data were reliable. According to pathway enrichment analysis for the obtained DEGs, 24 pathways were significantly affected following infection with the E. stigmosa SX-01 strain, such as cytokine–cytokine receptor interaction, intestinal immune network for IgA production, cell adhesion molecules, gap junction, arachidonic acid metabolism, alpha-Linolenic acid metabolism, retinol metabolism, and PPAR signaling pathway. These transcriptional alterations were observed in E. stigmosa-infected geese without obvious clinical signs, indicating that E. stigmosa infection may trigger a strong subclinical host response related to metabolism, immune and inflammatory responses, and intercellular junctional complex-associated processes. Collectively, these findings have implications for better understanding the E. stigmosa–goose interactions at the molecular level and provide a foundation for future functional and comparative studies to dissect the pathogenic mechanisms and molecular markers associated with disease resistance, which are expected to inform the design of effective control strategies.

While multiple Eimeria species have been identified in geese, their effects on the host gut microbiota have not yet been investigated. In the present study, 16S ribosomal RNA gene sequencing was used to characterize the microbial changes in the jejunal and cecal segments of Landes geese following Eimeria stigmosa infection. At 2.5 days post-infection (dpi), the jejunum of infected geese was dominated by Bacillota, Pseudomonadota and Bacteroidota, whereas controls were dominated by Bacillota and Actinomycetota. At 4.5 dpi, the jejunum of infected geese showed increased Bacillota compared to controls. In the cecum, both groups shared similar phylum-level dominance of Bacillota and Bacteroidota. At 2.5 and 4.5 dpi, the jejunal microbiota of infected geese was primarily dominated by the genus Ligilactobacillus. α-diversity analysis revealed a significant reduction in the Shannon and Pielou’s evenness indices only in the jejunum of infected geese at 4.5 dpi. Beta-diversity analysis showed significant differences between the infected and control groups at 2.5 dpi based on weighted UniFrac distances. LEfSe analysis revealed that the genus Pseudomonas were significantly enriched in the jejunum of infected geese at 2.5 dpi, while the genera Massiliomicrobiota and Shuttleworthia were significantly enriched in the cecum of infected geese at 4.5 dpi. These findings revealed time- and site-specific shifts in the gut microbiota of geese following E. stigmosa infection, having implications for better understanding of the complex interactions of E. stigmosa, host and the microbiome.