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

M. Kim, J. Kim, L. A. Kuehn, J. L. Bono, E. D. Berry, N. Kalchayanand, H. C. Freetly, Andrew K Benson, J. E. Wells

Research output: Contribution to journalArticle

48 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)683-694
Number of pages12
JournalJournal of animal science
Volume92
Issue number2
DOIs
StatePublished - Feb 14 2014

Fingerprint

cattle feeds
Feces
feces
Diet
Zea mays
diet
Silage
cattle
corn silage
Microbiota
rRNA Genes
Succinivibrio
Coprococcus
Roseburia
ribosomal RNA
Prevotella
Bacteroidetes
haylage
Firmicutes
corn

Keywords

  • 16S ribosomal ribonucleic acid gene
  • Diet
  • Fecal microbiota
  • Feedlot cattle
  • Operational taxonomic units
  • Pyrosequencing

ASJC Scopus subject areas

  • Food Science
  • Animal Science and Zoology
  • Genetics

Cite this

Kim, M., Kim, J., Kuehn, L. A., Bono, J. L., Berry, E. D., Kalchayanand, N., ... Wells, J. E. (2014). Investigation of bacterial diversity in the feces of cattle fed different diets. Journal of animal science, 92(2), 683-694. https://doi.org/10.2527/jas.2013-6841

Investigation of bacterial diversity in the feces of cattle fed different diets. / Kim, M.; Kim, J.; Kuehn, L. A.; Bono, J. L.; Berry, E. D.; Kalchayanand, N.; Freetly, H. C.; Benson, Andrew K; Wells, J. E.

In: Journal of animal science, Vol. 92, No. 2, 14.02.2014, p. 683-694.

Research output: Contribution to journalArticle

Kim, M, Kim, J, Kuehn, LA, Bono, JL, Berry, ED, Kalchayanand, N, Freetly, HC, Benson, AK & Wells, JE 2014, 'Investigation of bacterial diversity in the feces of cattle fed different diets', Journal of animal science, vol. 92, no. 2, pp. 683-694. https://doi.org/10.2527/jas.2013-6841
Kim M, Kim J, Kuehn LA, Bono JL, Berry ED, Kalchayanand N et al. Investigation of bacterial diversity in the feces of cattle fed different diets. Journal of animal science. 2014 Feb 14;92(2):683-694. https://doi.org/10.2527/jas.2013-6841
Kim, M. ; Kim, J. ; Kuehn, L. A. ; Bono, J. L. ; Berry, E. D. ; Kalchayanand, N. ; Freetly, H. C. ; Benson, Andrew K ; Wells, J. E. / Investigation of bacterial diversity in the feces of cattle fed different diets. In: Journal of animal science. 2014 ; Vol. 92, No. 2. pp. 683-694.
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