A Paired Ileum–Caecum Study of the Goose Gut Microbiome in Response to Fattening Protocol and Postbiotic Supplementation

The gut microbiota plays a central role in poultry health and production performance, yet its response to intensive fattening protocols and postbiotic supplementation in geese remains poorly characterized. This study used 16S rRNA gene amplicon sequencing to profile ileal and caecal microbial communities from geese raised under two fattening protocols, with or without postbiotic supplementation, and assessed the effect of 24 h post-mortem chilling on apparent community composition. Fattening protocol was associated with the largest differences in gut microbial structure, producing significant shifts in beta diversity in both the ileum and the caecum (although protocol, age at slaughter, and duration of postbiotic exposure co-varied between cohorts and cannot be fully disentangled), accompanied by extensive taxon-level differences identified by LEfSe. Postbiotic supplementation did not significantly alter overall community structure under force-feeding conditions but produced a taxon-specific, trend-level shift in the caecum under restricted feeding, suggesting that its effect depends on the continuity of supplementation relative to slaughter. Alpha diversity did not differ significantly in the ileum, but caecal richness differed significantly between the G2 and G5 postbiotic-supplemented groups (Conover–Iman test, adjusted p < 0.05). The warm- and chilled-dissection groups differed in ileal but not caecal community composition (individual-animal variation cannot be separated from the effect of chilling in this comparison, as the two groups consisted of different birds), indicating that dissection timing is an important methodological variable in goose microbiome research. These findings highlight cohort- and protocol-related differences as key correlates of gut microbial composition in geese and provide a framework for optimizing postbiotic supplementation strategies and sampling standardization in waterfowl production.