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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Publications at this Location » Publication #295646

Title: Investigation of bacterial diversity in the feces of cattle fed different diets

item Kim, Min
item KIM, JAEHYOUNG - University Of Nebraska
item Kuehn, Larry
item Bono, James - Jim
item Berry, Elaine
item Kalchayanand, Norasak - Nor
item Freetly, Harvey
item BENSON, A - University Of Nebraska
item Wells, James - Jim

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2013
Publication Date: 2/12/2014
Publication URL:
Citation: Kim, M.S., Kim, J., Kuehn, L.A., Bono, J.L., Berry, E.D., Kalchayanand, N., Freetly, H.C., Benson, A.K., Wells, J. 2014. Investigation of bacterial diversity in the feces of cattle fed different diets. Journal of Animal Science. 92:683-694.

Interpretive Summary: Recent research has indicated that diet may greatly influence the shedding of E. coli O157:H7, however little is known about the influence of diet on other bacteria in the gastrointestinal tract. Fecal samples were collected from 290 feedlot cattle fed finishing diets with high levels of corn or moderate levels of corn and from 136 cattle fed a forage-based diet. Compositions of the bacteria in the feces were determined using modern DNA sequencing methods. Within a dietary group, the compositions of the bacteria were similar across multiple animals. Between the dietary groups, the composition of bacteria was different due to diet. Forage had a greater influence on the differences than did the level of corn in the diet. From this study, it appears that the bovine diet can greatly influence the composition of the bacteria in the gastrointestinal tract and feces. Understanding the influence of indigenous microflora on the colonization and shedding of E. coli O157:H7 will provide a possible avenue for intervention in the preharvest beef production environment not yet exploited.

Technical Abstract: The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dryrolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage-and concentrate-based diets.