Age, breed, and gut section shape the active microbiome of commercial laying hens

Gut microbiota strongly influences nutrient absorption, pathogen resistance, gut barrier integrity, and immune function in laying hens. To investigate how host genetics and production stage shape these communities, we profiled the active gut microbiome of two commercial breeds, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks). We extracted RNA from 500 digesta samples and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both breed and age had highly significant effects on community composition. The most dramatic shifts occurred between early development (10 weeks) and the onset of lay (16–24 weeks), with distinct genera rising or declining in each breed and compartment. To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing breed-specific changes in functional profiles associated with the transition into egg production. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.