Beef Cattle Metagenomics: Predicting Growth 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 with microbes and identify new phenotypes and biomarkers. This raises the question; can variation in animal metagenomic population account for phenotypic variation and can phenotype be predicted by a subset of the metagenome? Fecal samples were taken on Angus calves at approximately 205 days of age and were sequenced using Illumina chemistry to generate paired end reads (24 animals with approximately 109 million reads on average, 289 animals with approximately 17.8 million reads on average) to determine if fluctuations in the metagenome were associated with various growth and carcass traits (i.e. 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).  Sequenced reads were first analyzed with the MG-RAST analysis pipeline to obtain counts at different phylogenic classifications. Phylum, Class, Order, Family, Genus, and Species were all analyzed separately utilizing the QuasiSeq package of R. Genus appeared to be the most informative with 36 Genus being significantly (FDR < 0.05) associated with four phenotypes: weaning weight, yearling weight, quality grade, and numeric marbling score. The preliminary results from analysis indicate that there is a subset of the metagenome that is associated with phenotype. Further analysis is needed to determine if this subset can predict phenotype or account for environmental variation.