Analysis of the gut microbiome in beef cattle and its association with feed intake, growth, and efficiency

Abstract Text: Next-generation sequencing has taken a central role in studies of microbial ecology, especially with regard to culture-independent methods based on molecular phylogenies of the small-subunit ribosomal RNA gene (16S rRNA gene).  The ability to relate trends at the species or genus level to host/environmental parameters using 16S profiling has proven powerful.  Within the rumen and lower gastrointestinal tract (GIT), the diverse microbial ecosystems present are essential for the host to digest plant material and regulate nutrient uptake and utilization. Their examination utilizing next-generation technologies has been instrumental to aid in the understanding of the microbial-associated interactions throughout the gut with intake, growth, and feed efficiency. Using a feed efficiency design in which steers were selected from 2 contemporary groups and were ranked based on their standardized distance from the bivariate mean (ADG and ADFI), four steers with the greatest deviation within each Cartesian quadrant were sampled (n = 16/group; 2 groups) in order to examine the association of the microbiome throughout the gut with ADG, average daily DMI (ADFI), and feed efficiency.  In addition, phylogenetic analyses of the ruminal bacterial community were compared based on varying sequencing technologies, 16S variable region selection, and short read 16S amplicons, near full-length 16S amplicons, and metagenomic sequence.  In all studies, although no differences in bacterial diversity and richness metrics were revealed among the quadrants, finer changes in the relative abundance of microbial populations and operational taxonomic units did reveal differences between feed efficiency groups (P< 0.05), suggesting throughout the GIT, the microbial communities differ at the 16S level in cattle that vary in ADG, ADFI, and feed efficiency.  However, additional phylogenetic analyses on the rumen bacterial community demonstrated that utilizing near full-length 16S reads may be useful in conducting a more thorough study, or for developing a niche-specific database to utilize in analyzing data from shorter read technologies when budgetary constraints preclude use of near-full length 16S sequencing. Partially funded by National Institute of Food and Agriculture Grant 2011-68004-30214 National Program for Genetic Improvement of Feed Efficiency in Beef Cattle.  

Keywords: feed efficiency, microbiome, 16S rRNA