Microbiome and biological blood marker changes in hens at different laying stages in conventional and cage free housings

With the majority of conventional cage (CC) laying facilities transitioning into cage-free (CF) systems in the near future, it is important to characterize biological markers of health in layers housed in commercial housings for sustainable production. The objectives of this study were to compare i) blood markers, that is heterophil:lymphocyte (H:L) ratios and susceptibility to avian pathogenic Escherichia coli (APEC) and ii) lung and ceca microbiome between hens at different maturity stages in commercial CC and CF farms. Laying hens at 3 maturity stages were randomly sampled (N = 20 per maturity and per farm). Blood was tested for H:L ratios and APEC killing ability using microscopy and in vitro assay, respectively. Microbiomes were assessed using 16S rRNA sequencing and QIIME2 analysis. Data show H:L ratios did not differ between maturities in both farms. Avian pathogenic Escherichia coli killing was only different in CC hens, where χ7122 level was higher (P < 0.05) in peak compared with early lay. In both farms, microbiome diversity was consistently different (P < 0.05) in both ceca and lung of early lay compared with peak and late lay. In the ceca and lung, relative abundances of the 3 predominant phyla (Bacteroidetes, Firmicutes, and Proteobacteria) did not significantly change with maturity in both farms. Potential pathogens Campylobacter and Staphylococcus reached greater (P < 0.05) abundances in CC lungs in early lay and in CF lungs in late lay, respectively. Overall, this study showed no differences in the stress marker H:L but identified some differences in resistance to APEC and microbiome composition across maturity stages in CC and CF. The lung and gut microbiomes were highly similar, with both serving as potential reservoirs for Campylobacter and Staphylococcus. Future studies on controllable environments for CF and CC are needed to develop adequate strategies for each housing and maturity stage to reduce pathogens and optimize disease-resistance.