First Insights into Changes in the Gut Microbiota of Landes Geese Infected with Eimeria stigmosa

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.