Beef Cattle Metagenomics: Predicting Traits from the inside out

Metagenomic analysis is an emerging field of study within the livestock community and has the possibility to advance our knowledge of phenotypic interactions and create new methods of selecting for traits of interest. This raises the question; can variation in the metagenome of the host account for phenotypic variation and can the phenotype of the host be predicted by a subset of the metagenome? With this in mind, fecal samples were collected from 244 Angus calves at approximately 205 days of age and were sequenced using the Illumina platform to generate paired end reads. Multiple phenotypes were also measured (birth, weaning, yearling, and slaughter weight; hot carcass weight; ribeye area; 12^th rib subcutaneous fat thickness; kidney, heart, and pelvic fat; quality grade; marbling score) on these calves. The sequenced reads were used to quantify the fecal metagenome at different phylogenic classification levels. Associations between host phenotypes and metagenome Phylum, Class, Order, Family, Genus, and Species were analyzed with the QuasiSeq package of R. Some metagenomic species were significantly associated (FDR < 0.05) with growth and/or carcass phenotypes. The degree to which variation in the fecal metagenome could account for variation in host phenotype was evaluated with the GenSel software. The fecal metagenome could account for up to 40 percent of the phenotypic variation in a trait and could be used to predict a g-hat value that was significantly (P < 0.05) associated with phenotypic variation. The results of this study indicate that the fecal metagenome is associated with growth and carcass traits within cattle. Furthermore, variation in the fecal metagenome can account for variation in host phenotype and can be used to predict host phenotype. Thus, it appears that the host fecal metagenome may provide a novel way to account for more variation in livestock traits.