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

Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, 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 of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii,​​ Megamonas funiformis, ​​Phocaeicola ​​coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas ​testosteroni,​ ​Aeromonas ​caviae,​ ​Acinetobacter ​johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium ​​anatis​ and ​​Megamonas ​​hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.