Digestive tract microbiota of beef cattle that differed in feed efficiency

Authors: Freetly, Harvey; Dickey, Aaron; Lindholm-Perry, Amanda; Thallman, Richard - Mark; Keele, John; Foote, Andrew; Wells, James - Jim

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2020
Publication Date: 2/1/2020
Citation: Freetly, H.C., Dickey, A., Lindholm-Perry, A.K., Thallman, R.M., Keele, J.W., Foote, A.P., Wells, J.E. 2020. Digestive tract microbiota of beef cattle that differed in feed efficiency. Journal of Animal Science. 98(2):1-16. https://doi.org/10.1093/jas/skaa008.
DOI: https://doi.org/10.1093/jas/skaa008

Interpretive Summary: Bacteria are found down the length of the digestive tract. In many cases, bacteria modify consumed nutrient before the animal has an opportunity to use them. This is particularly the case in ruminant animals whom have an anatomic feature that results in fermentation of their feed before it reaches their true stomach. We proposed that differences in feed utilization may be associated with differences in the bacterial communities in the digestive tract. We found the make up of the bacterial communities changed in different regions of the digestive tract. We found that cattle that differed in converting feed to weight gain tended to have different bacteria in the small intestine. This study suggests that intestinal differences in microbiota of ruminants may be associated with animal performance.

Technical Abstract: We hypothesized cattle that differed in BW gain had different digestive tract microbiota. Two experiments were conducted. In both experiments steers received a diet that consisted of 8.0% chopped alfalfa hay, 20% wet distillers grain with solubles, 67.75% dry-rolled corn, and 4.25% vitamin/mineral mix (including monensin) on a dry matter basis. Steers had ad libitum access to feed and water. In Exp. 1, 144 steers (age = 310 ± 1.5 d; BW = 503 ± 37.2 kg) were individually fed for 105 d. Ruminal digesta samples were collected from 8 steers with the greatest (1.96 ± 0.02 kg/d) and 8 steers with the least ADG (1.57 ± 0.02 kg/d) that were within ± 0.32 SD of the mean (10.1 ± 0.05 kg/d) dry matter. In Exp. 2, 66 steers (age = 396 ± 1 d; BW = 456 ± 5 kg) were individually fed for 84 d. Rumen, duodenum, jejunum, ileum, cecum, and colon digesta samples were collected from 8 steers with the greatest (2.39 ± 0.06 kg/d) and 8 steers with the least ADG (1.85 ± 0.06 kg/d) that were within ± 0.55 SD of the mean dry matter intake (11.9 ± 0.1 kg/d). In both studies, DNA was isolated and the V1 to V3 regions of the 16S rRNA gene were sequenced. Operational taxonomic units were classified using 0.03 dissimilarity and identified using the Greengenes 16S rRNA Gene Database. In Exp.1, there were no differences in the Chao1, Shannon, Simpson, and InvSimpson diversity indexes or the PERMANOVA (P = 0.57). The hierarchical test returned 6 clades as being differentially abundant between steer classifications (P < 0.05). In Exp. 2, Chao1, Shannon, Simpson, and InvSimpson diversity indexes and PERMANOVA between steer classified as less or greater ADG did not differ (P > 0.05) for the rumen, duodenum, ileum, cecum, and colon. In the jejunum, there tended to be a difference in the Chao1 (P = 0.09) and Simpson diversity (P = 0.09) indexes between steer classifications, but there was no difference in the Shannon (P = 0.14) and InvSimpson (P = 0.14) diversity indexes. Classification groups for the jejunum differed (P = 0.006) in the PERMANOVA. The hierarchical dependence false discovery rate procedure returned 11 clades as being differentially abundant between steer classifications in the jejunum (P < 0.05). The majority of the OTU were in the Families Corynebacteriaceae and Coriobacteriaceae. This study suggests that intestinal differences in microbiota of ruminants may be associated with animal performance.