Host genetics drives differences in caecal microbiota composition and immune traits of laying hens raised in the same environment

Background Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition are two likely drivers of this heterogeneity. Methodology We studied 94 animals belonging to 4 lines of laying hens: a White Leghorn experimental line genetically selected for a high antibody response against the Newcastle Disease Virus (NDV) vaccine (ND3) and its unselected control line (CTR), and 2 commercial lines (White Leghorn (LEG) and Rhode Island Red (RIR)). Animals were reared in the same conditions from hatching to 42 days of age, and animals from different genetic lines were mixed. Animals were vaccinated at 22 days of age and their humoral vaccine response against NDV was assessed by hemagglutination inhibition assay and ELISA from blood samples collected at 15, 19, and 21 days after vaccination. The immune parameters studied were the three immunoglobulins subtypes A, M, and Y and the blood cell composition was assessed by flow cytometry. The composition of the caecal microbiota was assessed at the end of the experiment by analyzing amplified 16S rRNA gene sequences to obtain amplicon sequence variants (ASV). Results The four lines showed significantly different levels of NDV vaccine response at the three measured points, with, logically, a higher response of the genetically selected ND3 line, and intermediate and low responses for the unselected CTR control line and for the two commercial lines, respectively. The ND3 line displayed also a higher proportion of immunoglobulins (IgA, IgM, and IgY). The RIR line showed the most different blood cell composition. The 4 lines showed significantly different microbiota characteristics: composition, abundances at all taxonomic levels, and correlations between genera and vaccine response. Conclusion The tested genetic lines differ for immune parameters and gut microbiota composition and functions. These phenotypic differences can be attributed to genetic differences between lines. Causal relationships between both types of parameters are discussed and will be investigated in further studies.