Layers, broiler chickens and their F1 cross develop distinctly different caecal microbial communities when hatched and reared together

Aim To compare the caecal microbiota of layer, broiler, and intermediate F1 layer × broiler cross birds with the hypothesis that significant differences in caecal microbial composition would persist between the three groups when host and environmental interactions were minimized. Methods and Results Caecal contents were characterized using 16S rRNA for males of broiler (n = 12), layer (n = 12) and F1 layer × broiler cross (n = 9) birds that were hatched and reared under the same conditions. The microbial community structure differed significantly between the three groups of birds at phylum, genus and OTU levels, with clear separation of the groups observed. Firmicutes was the phylum most represented across samples; however, the high abundance of Proteobacteria in the layer birds at d28 post‐hatch was unexpected, and driven by a higher abundance of E. coli. Conclusions The microbiota phylotype between broilers, layers and their F1 cross significantly differed in community structure, diversity and relative abundance in the absence of environmental confounding, which is generally difficult to avoid in microbial studies. Significance and Impact of Study The results provide a unique comparison and evidence that there is a strong genetic component driving microbial composition within poultry strains, despite the embryonic development occurring in ovo.