Feather Microbiome of White Leghorn Laying Hens in Conventional and Floor Pen Housing Styles

Poultry feathers are largely seen as a byproduct of poultry production, particularly because they are not seen as a human food source, with little attention directed towards the microbial populations present. Since poultry production employs various housing styles, this allows unique microbial populations to arise from the varying composition of these environments. Conventional cages are the primary method used in industry with a shift towards aviary-style floor pen systems becoming more prominent; however, it has yet to be seen how the feather microbiome is affected by the change in environment. The main objective was to determine the feather microbiome of White Leghorn layer hens housed in either conventional cages or aviary-style floor pens and across the breast, dorsal, and wing feather tracts. Genomic DNA was extracted and amplified with the use of custom, dual-indexed primers and sequenced with Illumina MiSeq. Sequences were analyzed with QIIME2-2023.7, with alpha and beta diversity being assessed with Kruskal-Wallis and ANOSIM, respectively. Interactions throughout the linear mixed effect model were determined with ADONIS. Taxonomic differences were analyzed with ANCOM-BC. The results indicated that the microbial populations of the conventional and floor pen housing styles significantly differed over time in terms of taxonomic abundance. There were also differences between the various feather tracts; however, they were not as pronounced as those observed between housing styles. Members of the Empedobacter, Staphylococcus, and Aerococcus genera demonstrated the most enrichment of abundance in the floor pen housing style whereas members of the Faecalibacterium, Deinococcus, and Bifidobacterium genera were more prevalent in the conventional cages. Compared to the breast feathers, both the wing and dorsal regions revealed a depletion of the Oscillibacter and Desulfovibrio genera. These results indicate that housing style has the potential to alter the feather microbiome. In addition, it has been shown that different feather tracts harbor different microorganisms, regardless of housing style. Therefore, housing style does impact the feather microbiome with the feather tract microbial communities differing.