The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot

Abstract

Feed is the greatest cost of animal production so reducing it is critical to increase producer profits. In ruminants, the microbial population within the gastrointestinal tract (GIT) is critical to nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the bacterial taxonomic profile of the rumen, cecum, and feces of feedlot steers at slaughter in order to link feed efficiency and the GIT bacterial populations from these 3 locations. Twenty commercial Angus steers were selected and divided into two groups according to their residual feed intake (RFI) classification determined during the feedlot-finishing period: high-RFI (n=10) and low-RFI (n=10). After the ruminal, cecal, and fecal samples were collected at slaughter, DNA extraction and 16S rRNA gene sequencing were performed on them to determine their bacterial composition. One-way ANOVA was performed on the animal performance data, alpha diversities, and bacterial abundances using RFI classification as the fixed effect. Overall, the ruminal bacterial population was the most different in terms of taxonomic profile compared to the cecal and fecal populations as revealed by beta diversity analysis (P<0.001). Moreover, bacterial richness (Chao1) was greatest (P=0.01) in the rumen of the high-RFI group compared to the low-RFI group. In contrast, bacterial richness and diversity in the intestinal environment showed that Chao1 was greater (P=0.01) in the cecum, and Shannon diversity index was greater in both the cecum and feces of low-RFI compared to high-RFI steers (P=0.01 and P<0.001, respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P=0.01); and fecal Bifidobacteriaceae was more abundant in high-RFI steers (P=0.03). No correlations (P≥0.13) between any ruminal bacterial family and RFI were detected; however, Ruminococcaeae, Mogibacteriaceae, Christensenellaceae, and BS11 were negatively correlated with RFI (P<0.05) in the cecum and feces. Succinivibrionaceae in the cecum was positively correlated with RFI (P=0.05), and fecal Bifidobacteriaceae was positively correlated with RFI (P=0.03). Results collectively indicate that in addition to the ruminal bacteria, the lower gut bacterial population has a significant impact on feed efficiency and nutrient utilization in feedlot steers, therefore the intestinal bacteria should also be considered when examining the basis of ruminant feed efficiency.

Evaluation of the Fecal Bacterial Communities of Angus Steers With Divergent Feed Efficiencies Across the Lifespan From Weaning to Slaughter

“…Other researchers have also shown that microbial diversity measures differed between the rumen and the feces of cattle ( 10 , 18 , 26 ). The present study found bacterial evenness and diversity to be greater in the feces of the most efficient steers which somewhat contradicts the hypothesis proposed by Shabat et al ( 9 ); however, our findings conform the biological theory regarding the intestinal environment outlined by Welch et al ( 11 ). Nutrient availability differs widely throughout the GIT of cattle, and the digesta that reaches the large intestine contains less-digestible nutrients, which are essentially non-digested nutrients that escaped ruminal microbial degradation and small intestinal digestion.…”

“…Shabat et al ( 9 ) hypothesized that ruminal microbial populations with less richness and diversity carried out fewer, but more relevant metabolic pathways, leading to a more limited metabolite pool but with greater biological relevance in the rumen. However, in the intestinal environment, Welch et al ( 11 ) found that bacterial richness and diversity were greater in both the cecal contents and feces of steers with higher feed efficiency. Other researchers have also shown that microbial diversity measures differed between the rumen and the feces of cattle ( 10 , 18 , 26 ).…”

“…Previous studies have found low-RFI (more efficient) steers to have an increase in energy converted in the rumen ( 2 , 59 ), suggesting that host efficiency may be directly related to additional VFA produced by microbial fermentation of the rumen. Welch et al ( 11 ) reported a numerical increase in VFA production in the rumen of efficient steers compared to inefficient steers; however, fecal samples collected post slaughter were reversed, with VFA concentrations being highest in the less efficient steers. The present study observed similar patterns, with the inefficient steers having more total fecal VFA than the efficient steers.…”

“…Many studies have found a direct link between feed efficiency and the microbial population in cattle's GIT ( 8 – 10 ); however, most of these studies targeted on the ruminal microbial population. In contrast, a recent study has shown that certain bacterial families present in the hindgut of cattle can be correlated with feedlot RFI and may be important in driving the host's feed efficiency ( 11 ); however, it is still unknown at what point these bacterial families diverge within the hindgut of steers.…”

Microbiome Clusters Disclose Physiologic Variances in Dairy Cows Challenged by Calving and Lipopolysaccharides

“…Therefore, the present study offers new insights into the response of static and dynamic dairy cow microbiomes to different challenges. It was observed that animals with a dynamic microbiome had low fecal alpha-diversities and positive REI values, consistent with the results of previous studies on steers, where high fecal alpha-diversities correlated with low residual feed intake (RFI) ( 24 ). Animals with a dynamic microbiome, mostly associated with the C-Bifi group, were observed to have higher milk quality (milk LogSCC, protein, and fat), lower body weight, fewer health issues, and lower ketosis risk (low NEFA, BHB, and TG; high glucose and carnitine).…”