Rumen bacterial community structure impacts feed efficiency in beef cattle

Abstract

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterized to identify specific bacterial members (operational taxonomic units [OTUs]) associated with feed efficiency traits (ADFI, ADG, and G:F) in beef cattle. The heifer and steer cohorts were fed a forage-based diet and a concentrate-based diet, respectively. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was determined through 16S rRNA gene sequencing of the V4 region. Based on a regression approach that used individual performance measures, animals were classified into divergent feed efficiency groups. Within cohort, an extreme set of 16 animals from these divergent groups was selected as a discovery population to identify differentially abundant OTUs across the rumen bacterial communities. The remaining samples from each cohort were selected to perform forward stepwise regressions using the differentially abundant OTUs as explanatory variables to distinguish predictive OTUs for the feed efficiency traits and to quantify the OTUs collective impact on feed efficiency phenotypes. OTUs belonging to the families Prevotellaceae and Victivallaceae were present across models for heifers, whereas OTUs belonging to the families Prevotellaceae and Lachnospiraceae were present across models for steers. Within the heifer cohort, models explained 19.3%, 25.3%, and 19.8% of the variation for ADFI, ADG, and G:F, respectively. Within the steer cohort, models explained 27.7%, 32.5%, and 26.9% of the variation for ADFI, ADG, and G:F, respectively. Overall, this study suggests a substantial role of the rumen microbiome on feed efficiency responses.

Genetic mechanisms underlying feed utilization and implementation of genomic selection for improved feed efficiency in dairy cattle

“…Studying the rumen microbiome using "-omics" technologies Previous studies have used metagenomic and meta-transcriptomic approaches to quantify microbial content/abundance and microbial gene expression, respectively, and its potential link to feed efficiency in cattle (Shabat et al 2016;Li and Guan 2017;Paz et al 2018). Research investigating the rumen metagenome and its association with feed efficiency has revealed differential bacteria abundances across divergent rumen metabolic efficiencies by classifying specific bacteria using operational taxonomic units (OTU; Paz et al 2018), which measure various microbial species and their abundance. Specific OTU have been characterized in beef cattle across divergent feed efficiency groups and revealed that specific OTU abundance from bacterial families, including Prevotellaceae and Lachnospiraceae, were associated with feed efficiency in beef steers (Paz et al 2018).…”

“…Research investigating the rumen metagenome and its association with feed efficiency has revealed differential bacteria abundances across divergent rumen metabolic efficiencies by classifying specific bacteria using operational taxonomic units (OTU; Paz et al 2018), which measure various microbial species and their abundance. Specific OTU have been characterized in beef cattle across divergent feed efficiency groups and revealed that specific OTU abundance from bacterial families, including Prevotellaceae and Lachnospiraceae, were associated with feed efficiency in beef steers (Paz et al 2018). Feed efficiency and rumen microbiome have been previously associated (Hayes et al 2013;Sasson et al 2017;Paz et al 2018), revealing that models used to explain feed efficiency traits (e.g., DMI, average daily gain, and gain to feed ratio) explained up to 20% of the total variation in feed utilization when including OTU abundance parameters (Paz et al 2018).…”

“…Specific OTU have been characterized in beef cattle across divergent feed efficiency groups and revealed that specific OTU abundance from bacterial families, including Prevotellaceae and Lachnospiraceae, were associated with feed efficiency in beef steers (Paz et al 2018). Feed efficiency and rumen microbiome have been previously associated (Hayes et al 2013;Sasson et al 2017;Paz et al 2018), revealing that models used to explain feed efficiency traits (e.g., DMI, average daily gain, and gain to feed ratio) explained up to 20% of the total variation in feed utilization when including OTU abundance parameters (Paz et al 2018). This evidence suggests that microbial OTU abundance may serve as a predictor of feed efficiency (Paz et al 2018).…”

Microbiomes in ruminant protein production and food security.

“…For example, Ruminococci are cellulolytic, and are known to produce acetate, formate and hydrogen; all important metabolites of ruminal metabolism [37]. Rather than large changes in bacterial populations, these finer shifts in organisms have also been identified in other research [38,39]. Organisms, including Succinivibrio spp., Eubacterium spp., and Robinsoniella spp.…”

Influence of the artificial sodium saccharin sweetener Sucram®on the microbial community composition in the rumen content and attached to the rumen epithelium in dairy cattle: A pilot study

“…GI tract microbial communities of ruminants perform important roles in host metabolism (i.e. cellulose degradation) [12] and are largely distinct from those found in monogastric species. Rumen microbial fermentation provides key metabolic products for the host animal such as short chain fatty acids (SCFA) and vitamins via the breakdown of cellulose, hemicellulose, pectin and other ingested feed [13, 14].…”