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

Authors: WELCH, CHRISTINA - University Of Georgia; LOURENCO, JEFERSON - University Of Georgia; DAVIS, DYLAN - University Of Georgia; KRAUSE, TAYLOR - University Of Georgia; CARMICHAEL, MIA - University Of Georgia; Rothrock, Michael; PRINGLE, DEAN - University Of Georgia; CALLAWAY, TODD - University Of Georgia

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/13/2020
Publication Date: 7/20/2020
Citation: Welch, C.B., Lourenco, J.M., Davis, D.B., Krause, T.R., Carmichael, M.N., Rothrock Jr, M.J., Pringle, D.T., Callaway, T.R. 2020. The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot. Journal of Animal Science. 98(7):skaa230.

Interpretive Summary: With feed costs being the most expensive part of animal production, reducing these costs is critical to increase profit margins of producers. In ruminants, the microbes within the gastrointestinal tract (GIT) play an important role in nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the taxonomic profile of the rumen, cecum, and feces of feedlot steers in order to determine the link between feed efficiency and the GIT microbiota from these 3 locations. Twenty steers were selected from a herd of purebred Angus cattle and divided into two groups according to their residual feed intake (RFI) classification assessed 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 those samples to determine their microbial composition. One-way ANOVA was performed on the microbial traits using RFI classification as factor. Overall, the ruminal microbiome was the most different in terms of taxonomic profile compared to the cecal and fecal as revealed by beta-diversity analysis (P<0.001). Moreover, bacterial richness (Chao1) was greater in the rumen of the high-RFI group (P=0.04). The cecal and fecal microbiomes followed similar patterns regarding bacterial richness and diversity, with Chao1 being greater in the cecum of low-RFI steers (P=0.01), and Shannon diversity index being greater in both the cecum and feces of low-RFI steers (P=0.01 and P=0.003 respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P=0.01) and Bifidobacteriaceae was more abundant in the high-RFI group in the feces (P=0.03). No significant correlations (P'0.07) between any bacterial family and RFI were detected in the rumen; however, Ruminococcaeae, Mogibacteriaceae, Christensenellaceae, and BS11 were found to be negatively correlated with RFI (P<0.05) in the cecum and feces. Succinivibrionaceae was positively correlated with RFI in the cecum (P=0.05), and Bifidobacteriaceae was positively correlated with RFI in the feces (P=0.02). These results indicate that not only the ruminal, but lower gut fermentation can have a significant impact on feed efficiency and nutrient utilization in feedlot steers, so the intestinal microbiome should also be considered in studies involving feed efficiency in ruminants.

Technical Abstract: With feed costs being the most expensive part of animal production, reducing these costs is critical to increase profit margins of producers. In ruminants, the microbes within the gastrointestinal tract (GIT) play an important role in nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the taxonomic profile of the rumen, cecum, and feces of feedlot steers in order to determine the link between feed efficiency and the GIT microbiota from these 3 locations. Twenty steers were selected from a herd of purebred Angus cattle and divided into two groups according to their residual feed intake (RFI) classification assessed 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 those samples to determine their microbial composition. One-way ANOVA was performed on the microbial traits using RFI classification as factor. Overall, the ruminal microbiome was the most different in terms of taxonomic profile compared to the cecal and fecal as revealed by beta-diversity analysis (P<0.001). Moreover, bacterial richness (Chao1) was greater in the rumen of the high-RFI group (P=0.04). The cecal and fecal microbiomes followed similar patterns regarding bacterial richness and diversity, with Chao1 being greater in the cecum of low-RFI steers (P=0.01), and Shannon diversity index being greater in both the cecum and feces of low-RFI steers (P=0.01 and P=0.003 respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P=0.01) and Bifidobacteriaceae was more abundant in the high-RFI group in the feces (P=0.03). No significant correlations (P'0.07) between any bacterial family and RFI were detected in the rumen; however, Ruminococcaeae, Mogibacteriaceae, Christensenellaceae, and BS11 were found to be negatively correlated with RFI (P<0.05) in the cecum and feces. Succinivibrionaceae was positively correlated with RFI in the cecum (P=0.05), and Bifidobacteriaceae was positively correlated with RFI in the feces (P=0.02). These results indicate that not only the ruminal, but lower gut fermentation can have a significant impact on feed efficiency and nutrient utilization in feedlot steers, so the intestinal microbiome should also be considered in studies involving feed efficiency in ruminants.