Evaluating the ileal and cecal microbiota composition of a 1940 heritage genetic line and a 2016 commercial line of white leghorns fed representative diets from 1940 and 2016

Abstract This study was conducted to identify and evaluate the differences between the microbiome composition of the ileum and ceca of 1940 and 2016 genetic strains of white leghorns fed representative contemporary diets from those times. Ileal and cecal samples were aseptically collected from both genetic lines at 69 weeks of age. The genomic DNA of the ileal and cecal contents were extracted and the V4 region of the 16S rDNA was sequenced on an Illumina Miseq. Microbiota data were filtered and aligned using the QIIME2 2020.2 pipeline. Alpha and beta diversity metrics were generated and the Analysis of Composition of Microbiomes (ANCOM) was utilized to determine significantly different taxa. Data were considered significant at P ≤ 0.05 for main effects and Q ≤ 0.05 for pairwise differences. Alpha diversity of the ileum and ceca were significantly different (P = 0.001; Q = 0.001; however, no differences between genetic lineage were observed (P > 0.05; Q > 0.05). The beta diversity between the ileum and ceca, as well as between the genetic lines (1940 vs. 2016) were significantly different from one another (P = 0.001; Q = 0.001). Using ANCOM, Proteobacteria and Actinobacteriota were significantly different than other phyla (P ? 0.05) with a higher relative abundance of Proteobacteria being observed among treatment groups 2 and 3, while Actinobacteriota had higher relative abundance in treatment groups 1 and 4. Among the significantly different genera in the ileum, Pseudomonas, Rhizobiaceae, Leuconostoc, and Aeriscardovia were different (P ? 0.05) with treatment groups 1 and 4 having a higher relative abundance of Aeriscardovia, while treatment groups 2 and 3 had higher relative abundance in both Pseudomonas and Leuconostoc. In the ceca, Proteobacteria, Firmicutes, Actinobacteriota, and Euryarchaeota were significantly different phyla (P ? 0.05) with Firmicutes having the highest relative abundance across all treatment groups. Among the significantly different genera (Pseudomonas, Leuconostoc, Alloprevotella, and Aeriscardovia), Alloprevotella had the highest relative abundance across all treatment groups 1 and 2, while Leuconostoc and Pseudomonas had the highest relative abundance in treatment group 4. Results from this study suggest that genetic makeup in conjunction with the nutritional composition of laying hens influences the cecal and ileal microbiota of corresponding hens.