Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Evaluation of Bacterial Diversity in the Rumen and Feces of Cattle

  • Todd R. Callaway
  • André-Denis G. Wright
  • Georgia Olympia Brikis
  • Tom S. Edrington
  • David J. Nisbet
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_644-1



The rumen is a pre-gastric, anaerobic fermentation chamber populated by a consortium of bacteria, archaea, protozoa, and fungi, which break down feedstuffs in a truly symbiotic relationship within the host animal. The bacterial population is the best known component and is made up of more than 2,000 bacterial species and strains at populations in excess of 1011 cells/ml. Molecular techniques have increased the numbers of bacterial isolates associated with the rumen and have revealed much of the population remains unknown. Further developments have revolutionized our understanding of the microbial ecology of the rumen and gastrointestinal tract and how interactions occur between members of the consortium and the host animal.


The rumen of cattle is a large anaerobic fermentation chamber that is home to a large, diverse microbial consortium. This microbial population...


Microbial Population Microbial Consortium Foodborne Pathogen Microbial Ecosystem Nutrient Niche 
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  1. Callaway TR, Carr MA, Edrington TS, Anderson RC, Nisbet DJ. Diet, Escherichia coli O157:H7, and cattle: a review after 10 years. Curr Issues Mol Biol. 2009;11:67–80.PubMedGoogle Scholar
  2. Callaway TR, Dowd SE, Edrington TS, Anderson RC, Krueger N, Bauer N, Kononoff PJ, Nisbet DJ. Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing. J Anim Sci. 2010;88:3977–83.PubMedCrossRefGoogle Scholar
  3. Dowd SE, Callaway TR, Sun Y, McKeehan T, Hagevoort RG, Edrington TS. Evaluation of the bacterial diversity in the feces of cattle using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 2008;8:125–32.PubMedCentralPubMedCrossRefGoogle Scholar
  4. Durso LM, Harhay GP, Smith TP, Bono JL, Desantis TZ, Harhay DM, Andersen GL, Keen JE, Laegreid WW, Clawson ML. Animal-to-animal variation in fecal microbial diversity among beef cattle. Appl Environ Microbiol. 2010;76:4858–62.PubMedCentralPubMedCrossRefGoogle Scholar
  5. Durso LM, Harhay GP, Smith TPL, Bono JL, Desantis TZ, Clawson ML. Bacterial community analysis of beef cattle feedlots reveals pen surface is distinct from feces. Foodborne Pathog Dis. 2011;8:647–9.PubMedCrossRefGoogle Scholar
  6. Durso LM, Wells JE, Harhay GP, Rice WC, Kuehn L, Bono JL, Shackelford S, Wheeler T, Smith TPL. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers’ grain with solubles. Lett Appl Microbiol. 2012;55:109–14.PubMedCrossRefGoogle Scholar
  7. Freter R. Control mechanisms of the large-intestinal microflora and its influence on the host. Acta Gastroenterol Latinoam. 1989;19:197–217.PubMedGoogle Scholar
  8. Frey JC, Pell AN, Berthiume R, Lapierre H, Lee S, Ha JK, Mendell JE, Angert ER. Comparative studies of microbial populations in the rumen, duodenum, ileum and faeces of lactating dairy cows. J Appl Microbiol. 2010;108:1982–93.PubMedGoogle Scholar
  9. Hook SE, Steele MA, Northwood KS, Wright ADG, McBride BW. Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows. Microb Ecol. 2011;62:94–105.PubMedCrossRefGoogle Scholar
  10. Hristov AN, Callaway TR, Lee C, Dowd SE. Ruminal bacterial, archaeal, and fungal diversity of dairy cows with normal and reduced ruminal fauna. J Anim Sci. 2012;90:4449–57.PubMedCrossRefGoogle Scholar
  11. Hungate RE. The rumen and its microbes. New York: Academic Press; 1966.Google Scholar
  12. Krause DO, Nagaraja TG, Wright ADG, Callaway TR. Rumen microbiology: leading the way in microbial ecology. J Anim Sci. 2013;91:331–41.PubMedCrossRefGoogle Scholar
  13. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008;6:776–788.PubMedCentralPubMedCrossRefGoogle Scholar
  14. Lyte M. The microbial organ in the gut as a driver of homeostasis and disease. Med Hypotheses. 2010;74:634–8.PubMedCrossRefGoogle Scholar
  15. Russell JB, Hino T. Regulation of lactate production in Streptococcus bovis: a spiraling effect that contributes to rumen acidosis. J Dairy Sci. 1985;68:1712–21.PubMedCrossRefGoogle Scholar
  16. Shanks OC, Kelty CA, Archibeque S, Jenkins M, Newton RJ, McLellan SL, Huse SM, Sogin ML. Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol. 2011;77:2992–3001.PubMedCentralPubMedCrossRefGoogle Scholar
  17. Taschuk R, Griebel PJ. Commensal microbiome effects on mucosal immune system development in the ruminant gastrointestinal tract. Anim Health Res Rev. 2012;13:129–41.PubMedCrossRefGoogle Scholar
  18. Wells JE, Shackelford SD, Berry ED, Kalchayanand N, Bosilevac JM, Wheeler TL. Impact of reducing the level of wet distillers grains fed to cattle prior to harvest on prevalence and levels of Escherichia coli O157:H7 in feces and on hides. J Food Prot. 2011;74:1611–7.PubMedCrossRefGoogle Scholar
  19. Yokoyama MG, Johnson KA. Microbiology of the rumen and intestine. In: Church DC, editor. The ruminant animal: digestive physiology and nutrition. Englewood Cliffs: Waveland Press; 1988.Google Scholar
  20. Zoetendal EG, Collier CT, Koike S, Mackie RI, Gaskins HR. Molecular ecological analysis of the gastrointestinal microbiota: a review. J Nutr. 2004;134:465–72.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Todd R. Callaway
    • 1
  • André-Denis G. Wright
    • 2
  • Georgia Olympia Brikis
    • 3
  • Tom S. Edrington
    • 1
  • David J. Nisbet
    • 1
  1. 1.Food and Feed Safety Research UnitUSDA, Southern Plains Agricultural Research Center, Agricultural Research ServiceCollege StationUSA
  2. 2.Department of Animal ScienceThe University of VermontBurlingtonUSA
  3. 3.Technical University of MunichMunichGermany