Diet-Dependent Shifts in the Bacterial Population of the Rumen Revealed with Real-Time PCR

K. Tajima, Rustam Aminov, T. Nagamine, H. Matsui, M. Nakamura, Y. Benno

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A set of PCR primers was designed and validated for specific detection and quantification of Prevotella ruminicola, Prevotella albensis, Prevotella bryantii, Fibrobacter succinogenes, Selenomonas ruminantium-Mitsuokella multiacida, Streptococcus bovis, Ruminococcus flavefaciens, Ruminobacter amylophilus, Eubacterium ruminantium, Treponema bryantii, Succinivibrio dextrinosolvens, and Anaerovibrio lipolytica. By using these primers and the real-time PCR technique, the corresponding species in the rumens of cows for which the diet was switched from hay to grain were quantitatively monitored. The dynamics of two fibrolytic bacteria, F. succinogenes and R. flavefaciens, were in agreement with those of earlier, culture-based experiments. The quantity of F. succinogenes DNA, predominant in animals on the hay diet, fell 20-fold on the third day of the switch to a grain diet and further declined on day 28, with a 57-fold reduction in DNA. The R. flavefaciens DNA concentration on day 3 declined to approximately 10% of its initial value in animals on the hay diet and remained at this level on day 28. During the transition period (day 3), the quantities of two ruminal prevotella DNAs increased considerably: that of P. ruminicola increased 7-fold and that of P. bryantii increased 263-fold. On day 28, the quantity of P. ruminicola DNA decreased 3-fold, while P. bryantii DNA was still elevated 10-fold in comparison with the level found in animals on the initial hay diet. The DNA specific for another xylanolytic bacterium, E. ruminantium, dropped 14-fold during the diet switch and was maintained at this level on day 28. The concentration of a rumen spirochete, T. bryantii, decreased less profoundly and stabilized with a sevenfold decline by day 28. The variations in A. lipolytica DNA were not statistically significant. After an initial slight increase in S. dextrino-solvens DNA on day 3, this DNA was not detected at the end of the experiment. S. bovis DNA displayed a 67-fold increase during the transition period on day 3. However, on day 28, it actually declined in comparison with the level in animals on the hay ration. The amount of S. ruminantium-M. multiacida DNA also increased eightfold following the diet switch, but stabilized with only a twofold increase on day 28. The real-time PCR technique also uncovered differential amplification of rumen bacterial templates with the set of universal bacterial primers. This observation may explain why some predominant rumen bacteria have not been detected in PCR-generated 16S ribosomal DNA libraries.
Original languageEnglish
Issue number6
Pages (from-to)2766-2774
Number of pages9
Publication statusPublished - 2001
Externally publishedYes


  • Animal Feed
  • Animals
  • Bacteria
  • Cattle
  • DNA Primers
  • DNA, Ribosomal
  • Diet
  • Ecosystem
  • Female
  • Molecular Sequence Data
  • Phylogeny
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S
  • Rhinitis, Allergic, Seasonal
  • Rumen
  • Sequence Analysis, DNA
  • primer DNA
  • ribosome DNA
  • RNA 16S
  • animal
  • animal disease
  • animal food
  • article
  • bacterium
  • cattle
  • classification
  • diet
  • DNA sequence
  • ecosystem
  • female
  • genetics
  • hay fever
  • isolation and purification
  • methodology
  • microbiology
  • molecular genetics
  • phylogeny
  • polymerase chain reaction
  • ruminant stomach
  • RUMEN (Ruminants)
  • Microbiology
  • animal diets microbial effects
  • bacterial populations analysis, diet-dependent shifts
  • Artiodactyla Mammalia Vertebrata Chordata Animalia (Animals, Artiodactyls, Chordates, Mammals, Nonhuman Vertebrates, Nonhuman Mammals, Vertebrates) - Bovidae [85715] cows
  • Mammalia Vertebrata Chordata Animalia (Animals, Artiodactyls, Chordates, Mammals, Nonhuman Vertebrates, Nonhuman Mammals, Vertebrates) - Artiodactyla [85705] ruminants
  • Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteria [05000] bacteria
  • DNA analysis
  • ribosomal DNA libraries applications
  • 07502, Ecology: environmental biology - General and methods
  • 07508, Ecology: environmental biology - Animal
  • 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines
  • 13202, Nutrition - General studies, nutritional status and methods
  • 14004, Digestive system - Physiology and biochemistry
  • 29500, Microorganisms - General
  • 31000, Physiology and biochemistry of bacteria
  • Environmental Sciences
  • Ingestion and Assimilation
  • rumen digestive system microbial analysis
  • real-time polymerase chain reaction technique analytical method, applications
  • Digestive System
  • Ecology
  • Nutrition

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